From a8e8a11f1a1028d8f4c03e9c0b1b5c2de724fb2b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 9 Mar 2026 09:35:20 +0100 Subject: [PATCH 001/200] build: split conda environment file into denpendency groups --- environment.base.yml | 83 +++++++++++++++++++++++++++++++++++++++ environment.dev.yml | 35 +++++++++++++++++ environment.fourc.yml | 14 +++++++ environment.tutorials.yml | 10 +++++ 4 files changed, 142 insertions(+) create mode 100644 environment.base.yml create mode 100644 environment.dev.yml create mode 100644 environment.fourc.yml create mode 100644 environment.tutorials.yml diff --git a/environment.base.yml b/environment.base.yml new file mode 100644 index 000000000..0e346d624 --- /dev/null +++ b/environment.base.yml @@ -0,0 +1,83 @@ +--- +name: queens +channels: + - conda-forge + # We want to have a reproducible setup, so we don't want default channels, + # which may be different for different users. All required channels should + # be listed explicitly here. + - nodefaults +dependencies: + - python + # to ensure that performance optimized backends are used, + # the following packages are installed from conda + # for example BLAS libraries like Intel MKL for numpy + - cython + - numba + - numpy + - pandas + - scikit-learn + - scipy + + # Dask packages + - dask + - distributed # dask.distributed + - dask-jobqueue + - bokeh # for dask dashboard + - fabric # for ssh connection + + # Others + - xarray # Special array format + - pyDOE # design of experiments + - SALib # for sensitivity analysis + - vtk # vtk format handler + - pyvista + - autograd # wrapper around numpy for automated differentiation + - chaospy # polynomial chaos + - pyyaml # to load yaml files + - jinja2 + + # Machine learning libraries + - arviz # Bayesian visualization + - gpflow # LV and variational GPs + - optax # google jax based optimizer + - tensorflow + - tensorflow-probability + - jax + - pymc + - stable-baselines3 + + # making fancy plots + - matplotlib + - seaborn + - plotly + + # testing framework + - pytest + - py + - pytest-codestyle + - pytest-cov + - pytest-mock + - pytest-xdist + - mock + - py + + # Terminal utils + - tqdm # a smart progress meter for loops + - tomli # TOML parser + + # Other Python stuff + - pathos # multiprocessing with more complex python objects + - black>=24.4.2 # formatter for code created by QUEENS + + + + # These packages need to be installed via pip + - pip + - pip: + # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run + - gnuplotlib # for gnuplot based terminal ascii plots + - diversipy # sampling from space filling subsets # has no notable dependencies + # Chopin et al. sequential Monte-Carlo, filtering/smoothing package + # - particles # currently causes problem by requiring numpy<2 + - git+https://github.com/nchopin/particles.git + - scikit-activeml>=0.4.1 diff --git a/environment.dev.yml b/environment.dev.yml new file mode 100644 index 000000000..64cc8994f --- /dev/null +++ b/environment.dev.yml @@ -0,0 +1,35 @@ +--- +channels: + - conda-forge + # We want to have a reproducible setup, so we don't want default channels, + # which may be different for different users. All required channels should + # be listed explicitly here. + - nodefaults +dependencies: + # Development + - pylint>=2.16 + - isort>=5.0 + - pre-commit + - pre-commit-hooks>=4.4.0 + - sphinx + - nbsphinx + - pydata-sphinx-theme + - pandoc + - commitizen>=3.12.0 + - docformatter>=1.5.1 + - yamllint>=1.19.0 + - ruff + - nbstripout + - myst-parser + - testbook + - ipykernel + - mypy + + + # These packages need to be installed via pip + - pip + - pip: + # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run + - liccheck + - pylint-exit + - licenseheaders diff --git a/environment.fourc.yml b/environment.fourc.yml new file mode 100644 index 000000000..a2db09a6d --- /dev/null +++ b/environment.fourc.yml @@ -0,0 +1,14 @@ +--- +channels: + - conda-forge + # We want to have a reproducible setup, so we don't want default channels, + # which may be different for different users. All required channels should + # be listed explicitly here. + - nodefaults +dependencies: + # These packages need to be installed via pip + - pip + - pip: + # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run + # 4C + - fourcipp diff --git a/environment.tutorials.yml b/environment.tutorials.yml new file mode 100644 index 000000000..0f823a802 --- /dev/null +++ b/environment.tutorials.yml @@ -0,0 +1,10 @@ +--- +channels: + - conda-forge + # We want to have a reproducible setup, so we don't want default channels, + # which may be different for different users. All required channels should + # be listed explicitly here. + - nodefaults +dependencies: + # Tutorials + - scikit-fem From cd36ad152f9d77f9385ecedcca745986e78b3796 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 18 Mar 2026 18:17:56 +0100 Subject: [PATCH 002/200] build: add tf-keras dependency explicitly and limit setuptools version for gpflow --- environment.base.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/environment.base.yml b/environment.base.yml index 0e346d624..96c6e1188 100644 --- a/environment.base.yml +++ b/environment.base.yml @@ -11,6 +11,7 @@ dependencies: # to ensure that performance optimized backends are used, # the following packages are installed from conda # for example BLAS libraries like Intel MKL for numpy + - setuptools<82 #restriction due to gpflow needing pkg_resources - cython - numba - numpy @@ -42,6 +43,7 @@ dependencies: - optax # google jax based optimizer - tensorflow - tensorflow-probability + - tf-keras - jax - pymc - stable-baselines3 From 1ec8567922f1b4b5a493efd26fb63a55309b2ea7 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 18 Mar 2026 18:18:23 +0100 Subject: [PATCH 003/200] fix: np.linalg imports --- src/queens/models/surrogates/utils/kernel_jitted.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/queens/models/surrogates/utils/kernel_jitted.py b/src/queens/models/surrogates/utils/kernel_jitted.py index 666fa4dbb..ce2247fc6 100644 --- a/src/queens/models/surrogates/utils/kernel_jitted.py +++ b/src/queens/models/surrogates/utils/kernel_jitted.py @@ -19,7 +19,6 @@ import numpy as np from numba import jit, njit, prange from numba.core.errors import NumbaDeprecationWarning, NumbaPendingDeprecationWarning -from numpy.linalg.linalg import cholesky warnings.simplefilter("ignore", category=NumbaDeprecationWarning) warnings.simplefilter("ignore", category=NumbaPendingDeprecationWarning) @@ -74,7 +73,7 @@ def squared_exponential(x_train_mat, hyper_param_lst): partial_sigma_0_sq[i, j] = np.exp(-(delta**2) / (2.0 * l_scale_sq)) # calculate first the cholesky decomposition - cholesky_k_mat = cholesky(k_mat) + cholesky_k_mat = np.linalg.cholesky(k_mat) partial_sigma_n = np.eye(k_mat.shape[0]) @@ -374,7 +373,7 @@ def matern_3_2(x_train_mat, hyper_param_lst): ) # calculate first the cholesky decomposition - cholesky_k_mat = cholesky(k_mat) + cholesky_k_mat = np.linalg.cholesky(k_mat) partial_sigma_n = np.eye(k_mat.shape[0]) From b8bea847a99900f15b2d1bc6675b075ecdd21147 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 14:28:34 +0200 Subject: [PATCH 004/200] build: change to conda driven dependency management --- .../create_python_environment/action.yml | 8 +- .github/workflows/build_documentation.yml | 7 +- .github/workflows/tests_local.yml | 9 +- .gitlab/.gitlab-ci.yml | 11 +- .pre-commit-config.yaml | 2 + CONTRIBUTING.md | 10 +- README.md | 31 +- composed.conda-lock.yml | 17300 ++++++++++++++++ dev-requirements.in | 26 - dev-requirements.txt | 380 - doc/README.md | 4 +- doc/source/faqs/requirements.md | 12 +- environment.yml | 30 - pyproject.toml | 16 +- requirements.in | 69 - requirements.txt | 570 - src/queens/utils/remote_build.py | 9 +- src/queens/utils/remote_operations.py | 31 +- src/queens_interfaces/fourc/README.md | 4 +- .../fourc/fourc_requirements.txt | 1 - .../fourc/random_material_preprocessor.py | 3 +- tutorial-requirements.in | 7 - tutorial-requirements.txt | 107 - 23 files changed, 17398 insertions(+), 1249 deletions(-) create mode 100644 composed.conda-lock.yml delete mode 100644 dev-requirements.in delete mode 100644 dev-requirements.txt delete mode 100644 environment.yml delete mode 100644 requirements.in delete mode 100644 requirements.txt delete mode 100644 src/queens_interfaces/fourc/fourc_requirements.txt delete mode 100644 tutorial-requirements.in delete mode 100644 tutorial-requirements.txt diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml index 475362c66..d72cb645a 100644 --- a/.github/actions/create_python_environment/action.yml +++ b/.github/actions/create_python_environment/action.yml @@ -10,16 +10,16 @@ runs: using: composite steps: - uses: conda-incubator/setup-miniconda@v3 - - name: Create environment and install QUEENS + - name: Create conda-lock environment and install QUEENS id: environment shell: bash -l {0} env: PYTHON_PACKAGE_MANAGER: conda run: | - $PYTHON_PACKAGE_MANAGER env create -f environment.yml + $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y + conda-lock install -n queens composed.conda-lock.yml $PYTHON_PACKAGE_MANAGER activate queens - pip install torch==2.5.1 --index-url https://download.pytorch.org/whl/cpu - pip install -e .[safe_develop,fourc] + pip install --no-deps -e . $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml $PYTHON_PACKAGE_MANAGER list echo "ppm=$PYTHON_PACKAGE_MANAGER" >> $GITHUB_OUTPUT diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 021482be7..f401c8b81 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -37,13 +37,12 @@ jobs: - name: Create Python environment id: environment uses: ./.github/actions/create_python_environment - - name: Add tutorial dependencies + - name: Register Jupyter kernel env: PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}} run: | - $PYTHON_PACKAGE_MANAGER activate queens - pip install -e .[tutorial] - python -m ipykernel install --user --name queens --display-name "Python (queens)" + $PYTHON_PACKAGE_MANAGER activate queens + python -m ipykernel install --user --name queens --display-name "Python (queens)" - name: Install xvfb run: | apt-get update diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index a72dd4ad8..67f335ead 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -71,7 +71,8 @@ jobs: # echo "::endgroup::" echo "::group::Check compatibility with licenses of dependencies..." - liccheck -r requirements.txt + pip freeze --exclude-editable > python_requirements_for_liccheck.txt + liccheck -r python_requirements_for_liccheck.txt echo "::endgroup::" echo "::group::Create an rc file for the license header check..." @@ -90,12 +91,6 @@ jobs: $PYTHON_PACKAGE_MANAGER activate queens pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Add tutorial dependencies - env: - PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}} - run: | - $PYTHON_PACKAGE_MANAGER activate queens - pip install -e .[tutorial] - name: Run pytest for tutorials run: | $PYTHON_PACKAGE_MANAGER activate queens diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index 7c73eae49..c921f8648 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -46,7 +46,7 @@ workflow: before_script: - $PYTHON_PACKAGE_MANAGER activate queens-$CI_PIPELINE_ID # This ensures that the correct queens source is used - - pip install -e .[develop] + - pip install --no-deps -e . - echo Queens source for testing is $(pip list | grep -o '/.*') #--------------------------------------------------------------------------------------------------- # Jobs of stage: build @@ -56,9 +56,10 @@ workflow: before_script: - 'echo "Using python environment manager: `$PYTHON_PACKAGE_MANAGER --version`"' script: - - $PYTHON_PACKAGE_MANAGER env create -f environment.yml -n queens-$CI_PIPELINE_ID + - $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y + - conda-lock install -n queens-$CI_PIPELINE_ID composed.conda-lock.yml - $PYTHON_PACKAGE_MANAGER activate queens-$CI_PIPELINE_ID - - pip install -e .[develop] + - pip install --no-deps -e . - $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml artifacts: name: "conda_env-$CI_PIPELINE_ID.yml" @@ -89,11 +90,11 @@ imcs-build_conda_env: - ENV_PREFIX=queens-$CI_PIPELINE_ID - $PYTHON_PACKAGE_MANAGER create -y --prefix ./$ENV_PREFIX python=3.11 cloudpickle fabric - $PYTHON_PACKAGE_MANAGER activate ./$ENV_PREFIX - - pip install -e . --no-dependencies + - pip install --no-deps -e . - python src/queens/utils/remote_build.py --host=$REMOTE_ADDRESS --user=queens --remote-python=$REMOTE_PYTHON --remote-queens-repository=/home/queens/builds/queens-$CI_PIPELINE_ID --package-manager - $PYTHON_PACKAGE_MANAGER + $PYTHON_PACKAGE_MANAGER --use-conda-lock thought-build_conda_env: extends: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 44d4d0ff7..818b7eb79 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,6 +25,7 @@ repos: entry: check-added-large-files language: python types: [text] + exclude: '^composed\.conda-lock\.yml$' - id: check-license-header name: check for correct license header entry: licenseheaders @@ -70,6 +71,7 @@ repos: - -f=colored language: python types: ["yaml"] + exclude: '^composed\.conda-lock\.yml$' - id: pylint name: pylint entry: pylint diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 2c70452dc..daccb5e72 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -45,14 +45,12 @@ have to solve them yourself. ### :fishing_pole_and_fish: Pull requests #### 1. Install QUEENS in developer mode -Install QUEENS as described in the [README.md](README.md) and run: +Install QUEENS as described in the [README.md](README.md). The development environment is covered by +the standard `mamba env ...` workflow in the README, so no additional dependency installation step is +required. To expose your local checkout inside that environment, run: ``` -pip install -e .[develop] -``` -or to do a safe develop install use: -``` -pip install -e .[safe_develop] +pip install --no-deps -e . ``` diff --git a/README.md b/README.md index 789777edb..0ebdfef49 100644 --- a/README.md +++ b/README.md @@ -57,16 +57,39 @@ QUEENS (**Q**uantification of **U**ncertain **E**ffects in **En**gineering **S** Clone the QUEENS repository to your local machine. Navigate to its base directory, then: ```bash -conda env create +mamba env create -n queens -f environment.base.yml conda activate queens -pip install -e . +pip install --no-deps -e . ``` -**Note**: This installs QUEENS without any fixed dependency versions. In most cases this is no problem and gives you more freedom to install additional packages within your environment. Should there be a problem you can play it safe with fixed versions via +This installs the core QUEENS environment. The local checkout is then exposed in that environment +via `pip install --no-deps -e .`, which does not install any additional Python dependencies. + +Optional feature sets can be added afterwards when needed: ```bash -pip install -e .[safe] +mamba env update -n queens -f environment.dev.yml +mamba env update -n queens -f environment.tutorials.yml +mamba env update -n queens -f environment.fourc.yml ``` +These optional environment files are only needed if you want the corresponding features: + +* `environment.dev.yml` for development tools such as linting, type checks, and documentation builds +* `environment.tutorials.yml` for the tutorial notebooks and examples +* `environment.fourc.yml` for workflows that integrate QUEENS with [4C](https://github.com/4C-multiphysics/4C) + +If you only want to use the core QUEENS functionality, you can skip those optional environment updates. + +For development or if you encounter any problems, we recommend the reproducible `conda-lock` setup because it matches the CI pipeline environment: +```bash +conda-lock install -n queens composed.conda-lock.yml +conda activate queens +pip install --no-deps -e . +``` + +This is the safest option for contributors and debugging because it installs the exact dependency set +used in CI. The tradeoff is that `composed.conda-lock.yml` includes all optional dependency groups as well. + ## :crown: Workflow example diff --git a/composed.conda-lock.yml b/composed.conda-lock.yml new file mode 100644 index 000000000..38e236e6f --- /dev/null +++ b/composed.conda-lock.yml @@ -0,0 +1,17300 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV composed.conda-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile composed.conda-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f environment.base.yml -f environment.dev.yml -f environment.tutorials.yml -f environment.fourc.yml --lockfile composed.conda-lock.yml +version: 1 +metadata: + content_hash: + osx-arm64: f8a8f3d8f619e3992ab90687739b623886774458833c2b4456c20e142f0a7885 + linux-64: 9d02391e0c3322a6f4c9feafda362afd4f748ae85b955c1646c10f45b0ae05d4 + channels: + - url: conda-forge + used_env_vars: [] + platforms: + - linux-64 + - osx-arm64 + sources: + 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+- name: toml + version: 0.10.2 + manager: pip + platform: osx-arm64 + dependencies: {} + url: https://files.pythonhosted.org/packages/44/6f/7120676b6d73228c96e17f1f794d8ab046fc910d781c8d151120c3f1569e/toml-0.10.2-py2.py3-none-any.whl + hash: + sha256: 806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b + category: main + optional: false diff --git a/dev-requirements.in b/dev-requirements.in deleted file mode 100644 index 014cafade..000000000 --- a/dev-requirements.in +++ /dev/null @@ -1,26 +0,0 @@ -# This file contains all the requirements for QUEENS (production runs). - -# Do not fix the version of a package if not strictly necessary. We use pip-tools in order to create a requirements.txt file where the version of the different packages are fixed to the latest stable version w.r.t. QUEENS. From time to time pip-tools is used to upgrade to the newer available versions. - -# Development -pylint>=2.16 -pylint-exit -isort>=5.0 -pre-commit -pre-commit-hooks>=4.4.0 -liccheck -licenseheaders -sphinx -nbsphinx -pydata-sphinx-theme -pandoc -pip-tools -commitizen>=3.12.0 -docformatter>=1.5.1 -yamllint>=1.19.0 -ruff -nbstripout -myst-parser -testbook -ipykernel -mypy diff --git a/dev-requirements.txt b/dev-requirements.txt deleted file mode 100644 index e95ba2c2c..000000000 --- a/dev-requirements.txt +++ /dev/null @@ -1,380 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --constraint=requirements.txt --output-file=dev-requirements.txt dev-requirements.in -# -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==1.0.0 - # via sphinx -argcomplete==3.5.1 - # via commitizen -astroid==3.3.5 - # via pylint -asttokens==3.0.0 - # via stack-data -attrs==24.2.0 - # via - # jsonschema - # referencing -babel==2.16.0 - # via - # pydata-sphinx-theme - # sphinx -beautifulsoup4==4.12.3 - # via - # nbconvert - # pydata-sphinx-theme -bleach==6.1.0 - # via nbconvert -build==1.2.2.post1 - # via pip-tools -certifi==2024.8.30 - # via - # -c requirements.txt - # requests -cfgv==3.4.0 - # via pre-commit -charset-normalizer==3.4.0 - # via - # -c requirements.txt - # commitizen - # docformatter - # requests -click==8.1.7 - # via - # -c requirements.txt - # pip-tools -colorama==0.4.6 - # via commitizen -comm==0.2.3 - # via ipykernel -commitizen==3.30.0 - # via -r dev-requirements.in -debugpy==1.8.16 - # via ipykernel -decli==0.6.2 - # via commitizen -decorator==5.1.1 - # via - # -c requirements.txt - # ipython -defusedxml==0.7.1 - # via nbconvert -dill==0.3.9 - # via - # -c requirements.txt - # pylint -distlib==0.3.9 - # via virtualenv -docformatter==1.7.5 - # via -r dev-requirements.in -docutils==0.21.2 - # via - # myst-parser - # nbsphinx - # pydata-sphinx-theme - # sphinx -executing==2.2.0 - # via stack-data -fastjsonschema==2.20.0 - # via nbformat -filelock==3.16.1 - # via - # -c requirements.txt - # virtualenv -identify==2.6.1 - # via pre-commit -idna==3.10 - # via - # -c requirements.txt - # requests -imagesize==1.4.1 - # via sphinx -ipykernel==6.30.1 - # via -r dev-requirements.in -ipython==8.18.0 - # via ipykernel -isort==5.13.2 - # via - # -r dev-requirements.in - # pylint -jedi==0.19.2 - # via ipython -jinja2==3.1.4 - # via - # -c requirements.txt - # commitizen - # myst-parser - # nbconvert - # nbsphinx - # sphinx -jsonschema==4.23.0 - # via nbformat -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-client==8.6.3 - # via - # ipykernel - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # nbclient - # nbconvert - # nbformat -jupyterlab-pygments==0.3.0 - # via nbconvert -liccheck==0.9.2 - # via -r dev-requirements.in -licenseheaders==0.8.8 - # via -r dev-requirements.in -markdown-it-py==3.0.0 - # via - # -c requirements.txt - # mdit-py-plugins - # myst-parser -markupsafe==3.0.2 - # via - # -c requirements.txt - # jinja2 - # nbconvert -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via pylint -mdit-py-plugins==0.4.2 - # via myst-parser -mdurl==0.1.2 - # via - # -c requirements.txt - # markdown-it-py -mistune==3.0.2 - # via nbconvert -mypy==1.18.2 - # via -r dev-requirements.in -mypy-extensions==1.0.0 - # via - # -c requirements.txt - # mypy -myst-parser==4.0.0 - # via -r dev-requirements.in -nbclient==0.10.0 - # via - # nbconvert - # testbook -nbconvert==7.16.4 - # via nbsphinx -nbformat==5.10.4 - # via - # nbclient - # nbconvert - # nbsphinx - # nbstripout - # testbook -nbsphinx==0.9.5 - # via -r dev-requirements.in -nbstripout==0.8.1 - # via -r dev-requirements.in -nest-asyncio==1.6.0 - # via ipykernel -nodeenv==1.9.1 - # via pre-commit -packaging==24.1 - # via - # -c requirements.txt - # build - # commitizen - # ipykernel - # nbconvert - # sphinx -pandoc==2.4 - # via -r dev-requirements.in -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.4 - # via jedi -pathspec==0.12.1 - # via - # -c requirements.txt - # mypy - # yamllint -pexpect==4.9.0 - # via ipython -pip-tools==7.4.1 - # via -r dev-requirements.in -platformdirs==4.3.6 - # via - # -c requirements.txt - # jupyter-core - # pylint - # virtualenv -plumbum==1.9.0 - # via pandoc -ply==3.11 - # via pandoc -pre-commit==4.0.1 - # via -r dev-requirements.in -pre-commit-hooks==5.0.0 - # via -r dev-requirements.in -prompt-toolkit==3.0.36 - # via - # ipython - # questionary -psutil==6.1.0 - # via - # -c requirements.txt - # ipykernel -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.3 - # via stack-data -pydata-sphinx-theme==0.16.0 - # via -r dev-requirements.in -pygments==2.18.0 - # via - # -c requirements.txt - # accessible-pygments - # ipython - # nbconvert - # pydata-sphinx-theme - # sphinx -pylint==3.3.1 - # via -r dev-requirements.in -pylint-exit==1.2.0 - # via -r dev-requirements.in -pyproject-hooks==1.2.0 - # via - # build - # pip-tools -python-dateutil==2.9.0.post0 - # via - # -c requirements.txt - # jupyter-client -pyyaml==6.0.2 - # via - # -c requirements.txt - # commitizen - # myst-parser - # pre-commit - # yamllint -pyzmq==26.2.0 - # via - # ipykernel - # jupyter-client -questionary==2.0.1 - # via commitizen -referencing==0.35.1 - # via - # jsonschema - # jsonschema-specifications -regex==2024.11.6 - # via licenseheaders -requests==2.32.3 - # via - # -c requirements.txt - # sphinx -rpds-py==0.20.0 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.6 - # via pre-commit-hooks -ruamel-yaml-clib==0.2.12 - # via ruamel-yaml -ruff==0.9.2 - # via -r dev-requirements.in -semantic-version==2.10.0 - # via liccheck -six==1.16.0 - # via - # -c requirements.txt - # bleach - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -soupsieve==2.6 - # via beautifulsoup4 -sphinx==8.1.3 - # via - # -r dev-requirements.in - # myst-parser - # nbsphinx - # pydata-sphinx-theme -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -stack-data==0.6.3 - # via ipython -termcolor==2.5.0 - # via - # -c requirements.txt - # commitizen -testbook==0.4.2 - # via -r dev-requirements.in -tinycss2==1.4.0 - # via nbconvert -toml==0.10.2 - # via liccheck -tomlkit==0.13.2 - # via - # commitizen - # pylint -tornado==6.4.1 - # via - # -c requirements.txt - # ipykernel - # jupyter-client -traitlets==5.14.3 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # nbsphinx -typing-extensions==4.12.2 - # via - # -c requirements.txt - # mypy - # pydata-sphinx-theme -untokenize==0.1.1 - # via docformatter -urllib3==2.2.3 - # via - # -c requirements.txt - # requests -virtualenv==20.27.1 - # via pre-commit -wcwidth==0.2.13 - # via prompt-toolkit -webencodings==0.5.1 - # via - # bleach - # tinycss2 -wheel==0.44.0 - # via - # -c requirements.txt - # pip-tools -yamllint==1.35.1 - # via -r dev-requirements.in - -# The following packages are considered to be unsafe in a requirements file: -# pip -# setuptools diff --git a/doc/README.md b/doc/README.md index 56089b1ac..4f14d1137 100644 --- a/doc/README.md +++ b/doc/README.md @@ -7,10 +7,10 @@ We believe that documentation is essential and therefore welcome any improvement ## :woman_teacher: Build the documentation To build the documentation, you first need to set up a QUEENS environment as described in the [README.md](../README.md). -In this Python environment, you also need to install packages for QUEENS development and tutorials and register the environment as a Jupyter kernel: +Make sure to install the packages for QUEENS development and tutorial. +Next, register the environment as a Jupyter kernel with: ```bash -pip install -e .[safe_develop,tutorial] python -m ipykernel install --user --name queens --display-name "Python (queens)" ``` diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index 4d7be5161..0c601ee0e 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -4,4 +4,14 @@ Currently, QUEENS is only tested on UNIX systems. Besides Python, QUEENS requires [rsync](https://rsync.samba.org/) in order to copy simulation files. -The Python dependencies for QUEENS can be found in the `requirements.txt` file. There are a lot of them and we are working on reducing them, or at least making them optional. +The Python dependencies for QUEENS are managed through the conda environment files in the repository +root: + +- `environment.base.yml` +- `environment.dev.yml` +- `environment.tutorials.yml` +- `environment.fourc.yml` + +For reproducible installs, QUEENS also provides the composed lock file `composed.conda-lock.yml`. + +For more information see the [README.md](README.md). diff --git a/environment.yml b/environment.yml deleted file mode 100644 index e3d344481..000000000 --- a/environment.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: queens -channels: - - conda-forge -# We want to have a reproducible setup, so we don't want default channels, -# which may be different for different users. All required channels should -# be listed explicitly here. - - nodefaults -dependencies: - - python==3.11 -# to ensure that performance optimized backends are used, -# the following packages are installed from conda -# for example BLAS libraries like Intel MKL for numpy - - cython==3.0.11 - - numba==0.60.0 - - numpy==1.26.4 - - pandas==2.2.3 - - scikit-learn==1.5.2 - - scipy==1.14.1 - - libopenblas==0.3.28 -# required for jupyter notebook integration into the sphinx documentation - - pandoc -# required because newer versions have deprecated the pkg_resources module, which is needed for -# liccheck==0.9.2, gpflow==2.9.2 - - setuptools<82 -# Only install pip-tools via pip itself since -# all other pip dependencies should be managed -# via pip-tools in the requirements.in files - - pip - - pip: - - pip-tools diff --git a/pyproject.toml b/pyproject.toml index a45d6f3ed..33515a21e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" [project] name = "queens" authors = [{ name = "QUEENS developers" }] -dynamic = ["version", "dependencies", "optional-dependencies"] +dynamic = ["version"] description = "A general purpose framework for Uncertainty Quantification, Physics-Informed Machine Learning, Bayesian Optimization, Inverse Problems and Simulation Analytics" readme = "README.md" requires-python = ">=3.10" @@ -22,20 +22,6 @@ keywords = [ [tool.setuptools.dynamic] version = { attr = "queens.__VERSION__" } -dependencies = { file = ["requirements.in"] } -optional-dependencies = { safe = { file = [ - "requirements.txt", -] }, develop = { file = [ - "dev-requirements.txt", # We fix the development packages, other linters might fail -] }, safe_develop = { file = [ - "requirements.txt", - "dev-requirements.txt", -] }, fourc = { file = [ - "src/queens_interfaces/fourc/fourc_requirements.txt", -] }, tutorial = { file = [ - "requirements.txt", - "tutorial-requirements.txt", -] } } # cli utils [project.scripts] diff --git a/requirements.in b/requirements.in deleted file mode 100644 index deb3ca439..000000000 --- a/requirements.in +++ /dev/null @@ -1,69 +0,0 @@ -# This file contains all the requirements for QUEENS (production runs). - -# Do not fix the version of a package if not strictly necessary. We use pip-tools in order to create a requirements.txt file where the version of the different packages are fixed to the latest stable version w.r.t. QUEENS. From time to time pip-tools is used to upgrade to the newer available versions. - -# dependencies from environment.yml (i.e., they are handled by conda) -cython==3.0.11 -numba==0.60.0 -numpy==1.26.4 -pandas==2.2.3 -scikit-learn==1.5.2 -scipy==1.14.1 - -# Dask packages -dask -distributed # dask.distributed -dask-jobqueue -bokeh>3 # for dask dashboard -fabric # for ssh connection - -# Others -xarray # Special array format -pyDOE # design of experiments -SALib # for sensitivity analysis -diversipy # sampling from space filling subsets -vtk>=9.2.0 # vtk format handler -pyvista -autograd # wrapper around numpy for automated differentiation -particles # Chopin et al. sequential Monte-Carlo, filtering/smoothing package -chaospy # polynomial chaos -pyyaml # to load yaml files -jinja2 - -# Machine learning libraries -arviz # Bayesian visualization -gpflow # LV and variational GPs -optax # google jax based optimizer -tensorflow -tensorflow-probability -jax -scikit-activeml>=0.4.1 -pymc -stable-baselines3 - -# making fancy plots -matplotlib -seaborn -plotly - -# testing framework -pytest -py -pytest-codestyle -pytest-cov -pytest-mock -pytest-xdist -mock -py - -# Terminal utils -tqdm # a smart progress meter for loops -gnuplotlib # for gnuplot based terminal ascii plots -tomli # TOML parser - -# Other Python stuff -pathos # multiprocessing with more complex python objects -black>=24.4.2 # formatter for code created by QUEENS's create_script_from_input_file() method - -# needed for dev-requirements, check if still needed -importlib-metadata<7 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 05a75c0b3..000000000 --- a/requirements.txt +++ /dev/null @@ -1,570 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --output-file=requirements.txt requirements.in -# -absl-py==2.1.0 - # via - # chex - # keras - # optax - # tensorboard - # tensorflow - # tensorflow-probability -arviz==0.20.0 - # via - # -r requirements.in - # pymc -astunparse==1.6.3 - # via tensorflow -autograd==1.7.0 - # via -r requirements.in -bcrypt==4.2.0 - # via paramiko -black==24.10.0 - # via -r requirements.in -bokeh==3.6.1 - # via -r requirements.in -cachetools==5.5.0 - # via pymc -certifi==2024.8.30 - # via requests -cffi==1.17.1 - # via - # cryptography - # pynacl -chaospy==4.3.17 - # via -r requirements.in -charset-normalizer==3.4.0 - # via requests -check-shapes==1.1.1 - # via gpflow -chex==0.1.87 - # via optax -click==8.1.7 - # via - # black - # dask - # distributed -cloudpickle==3.1.0 - # via - # dask - # distributed - # gymnasium - # pymc - # stable-baselines3 - # tensorflow-probability -cons==0.4.6 - # via - # etuples - # minikanren - # pytensor -contourpy==1.3.0 - # via - # bokeh - # matplotlib -coverage[toml]==7.6.4 - # via pytest-cov -cryptography==43.0.3 - # via paramiko -cycler==0.12.1 - # via matplotlib -cython==3.0.11 - # via -r requirements.in -dask==2024.10.0 - # via - # -r requirements.in - # dask-jobqueue - # distributed -dask-jobqueue==0.9.0 - # via -r requirements.in -decorator==5.1.1 - # via - # fabric - # tensorflow-probability -deprecated==1.2.14 - # via - # fabric - # gpflow -dill==0.3.9 - # via - # multiprocess - # pathos -distributed==2024.10.0 - # via - # -r requirements.in - # dask-jobqueue -diversipy==0.9 - # via -r requirements.in -dm-tree==0.1.8 - # via tensorflow-probability -dropstackframe==0.1.1 - # via check-shapes -etils[epy]==1.10.0 - # via optax -etuples==0.3.9 - # via - # minikanren - # pytensor -execnet==2.1.1 - # via pytest-xdist -fabric==3.2.2 - # via -r requirements.in -farama-notifications==0.0.4 - # via gymnasium -filelock==3.16.1 - # via - # pytensor - # torch - # triton -flatbuffers==24.3.25 - # via tensorflow -fonttools==4.54.1 - # via matplotlib -fsspec==2024.10.0 - # via - # dask - # torch -gast==0.6.0 - # via - # tensorflow - # tensorflow-probability -gnuplotlib==0.42 - # via -r requirements.in -google-pasta==0.2.0 - # via tensorflow -gpflow==2.9.2 - # via -r requirements.in -grpcio==1.67.1 - # via - # tensorboard - # tensorflow -gymnasium==1.0.0 - # via stable-baselines3 -h5netcdf==1.4.0 - # via arviz -h5py==3.12.1 - # via - # h5netcdf - # keras - # tensorflow -idna==3.10 - # via requests -importlib-metadata==6.11.0 - # via - # -r requirements.in - # chaospy - # dask - # numpoly -iniconfig==2.0.0 - # via pytest -invoke==2.2.0 - # via fabric -iteration-utilities==0.13.0 - # via scikit-activeml -jax==0.4.35 - # via - # -r requirements.in - # chex - # optax -jaxlib==0.4.35 - # via - # chex - # jax - # optax -jinja2==3.1.4 - # via - # -r requirements.in - # bokeh - # distributed - # torch -joblib==1.4.2 - # via - # particles - # scikit-activeml - # scikit-learn -keras==3.6.0 - # via tensorflow -kiwisolver==1.4.7 - # via matplotlib -lark==1.2.2 - # via check-shapes -libclang==18.1.1 - # via tensorflow -llvmlite==0.43.0 - # via numba -locket==1.0.0 - # via - # distributed - # partd -logical-unification==0.4.6 - # via - # cons - # minikanren - # pytensor -makefun==1.15.6 - # via scikit-activeml -markdown==3.7 - # via tensorboard -markdown-it-py==3.0.0 - # via rich -markupsafe==3.0.2 - # via - # jinja2 - # werkzeug -matplotlib==3.9.2 - # via - # -r requirements.in - # arviz - # pyvista - # salib - # scikit-activeml - # seaborn - # stable-baselines3 - # vtk -mdurl==0.1.2 - # via markdown-it-py -minikanren==1.0.3 - # via pytensor -ml-dtypes==0.4.1 - # via - # jax - # jaxlib - # keras - # tensorflow -mock==5.1.0 - # via -r requirements.in -mpmath==1.3.0 - # via sympy -msgpack==1.1.0 - # via distributed -multipledispatch==1.0.0 - # via - # etuples - # gpflow - # logical-unification - # minikanren -multiprocess==0.70.17 - # via - # pathos - # salib -mypy-extensions==1.0.0 - # via black -namex==0.0.8 - # via keras -networkx==3.4.2 - # via torch -numba==0.60.0 - # via - # -r requirements.in - # particles -numpoly==1.2.14 - # via chaospy -numpy==1.26.4 - # via - # -r requirements.in - # arviz - # autograd - # bokeh - # chaospy - # chex - # contourpy - # diversipy - # gnuplotlib - # gpflow - # gymnasium - # h5py - # jax - # jaxlib - # keras - # matplotlib - # ml-dtypes - # numba - # numpoly - # numpysane - # optax - # pandas - # particles - # pydoe - # pymc - # pytensor - # pyvista - # salib - # scikit-activeml - # scikit-learn - # scipy - # seaborn - # stable-baselines3 - # tensorboard - # tensorflow - # tensorflow-probability - # xarray - # xarray-einstats -numpysane==0.40 - # via gnuplotlib -opt-einsum==3.4.0 - # via - # jax - # tensorflow -optax==0.2.3 - # via -r requirements.in -optree==0.13.0 - # via keras -packaging==24.1 - # via - # arviz - # black - # bokeh - # dask - # distributed - # gpflow - # h5netcdf - # keras - # matplotlib - # plotly - # pooch - # pytest - # tensorboard - # tensorflow - # xarray -pandas==2.2.3 - # via - # -r requirements.in - # arviz - # bokeh - # pymc - # salib - # seaborn - # stable-baselines3 - # xarray -paramiko==3.5.0 - # via fabric -partd==1.4.2 - # via dask -particles==0.4 - # via -r requirements.in -pathos==0.3.3 - # via -r requirements.in -pathspec==0.12.1 - # via black -pillow==11.0.0 - # via - # bokeh - # matplotlib - # pyvista -platformdirs==4.3.6 - # via - # black - # pooch -plotly==5.24.1 - # via -r requirements.in -pluggy==1.5.0 - # via pytest -pooch==1.8.2 - # via pyvista -pox==0.3.5 - # via pathos -ppft==1.7.6.9 - # via pathos -protobuf==5.28.3 - # via - # tensorboard - # tensorflow -psutil==6.1.0 - # via distributed -py==1.11.0 - # via -r requirements.in -pycodestyle==2.12.1 - # via pytest-codestyle -pycparser==2.22 - # via cffi -pydoe==0.3.8 - # via -r requirements.in -pygments==2.18.0 - # via rich -pymc==5.17.0 - # via -r requirements.in -pynacl==1.5.0 - # via paramiko -pyparsing==3.2.0 - # via matplotlib -pytensor==2.25.5 - # via pymc -pytest==8.3.3 - # via - # -r requirements.in - # pytest-codestyle - # pytest-cov - # pytest-mock - # pytest-xdist -pytest-codestyle==2.0.1 - # via -r requirements.in -pytest-cov==5.0.0 - # via -r requirements.in -pytest-mock==3.14.0 - # via -r requirements.in -pytest-xdist==3.6.1 - # via -r requirements.in -python-dateutil==2.9.0.post0 - # via - # matplotlib - # pandas -pytz==2024.2 - # via pandas -pyvista==0.44.1 - # via -r requirements.in -pyyaml==6.0.2 - # via - # -r requirements.in - # bokeh - # dask - # distributed -requests==2.32.3 - # via - # pooch - # tensorflow -rich==13.9.3 - # via - # keras - # pymc -salib==1.5.1 - # via -r requirements.in -scikit-activeml==0.5.2 - # via -r requirements.in -scikit-learn==1.5.2 - # via - # -r requirements.in - # particles - # scikit-activeml -scipy==1.14.1 - # via - # -r requirements.in - # arviz - # chaospy - # diversipy - # gpflow - # jax - # jaxlib - # particles - # pydoe - # pymc - # pytensor - # salib - # scikit-activeml - # scikit-learn - # xarray-einstats -scooby==0.10.0 - # via pyvista -seaborn==0.13.2 - # via -r requirements.in -six==1.16.0 - # via - # astunparse - # google-pasta - # python-dateutil - # tensorboard - # tensorflow - # tensorflow-probability -sortedcontainers==2.4.0 - # via distributed -stable-baselines3==2.4.1 - # via -r requirements.in -sympy==1.13.1 - # via torch -tabulate==0.9.0 - # via gpflow -tblib==3.0.0 - # via distributed -tenacity==9.0.0 - # via plotly -tensorboard==2.18.0 - # via tensorflow -tensorboard-data-server==0.7.2 - # via tensorboard -tensorflow==2.18.0 - # via - # -r requirements.in - # gpflow - # tensorflow-probability - # tf-keras -tensorflow-io-gcs-filesystem==0.37.1 - # via tensorflow -tensorflow-probability[tf]==0.24.0 - # via - # -r requirements.in - # gpflow -termcolor==2.5.0 - # via tensorflow -tf-keras==2.18.0 - # via tensorflow-probability -threadpoolctl==3.5.0 - # via - # pymc - # scikit-learn -tomli==2.0.2 - # via -r requirements.in -toolz==1.0.0 - # via - # chex - # dask - # distributed - # logical-unification - # minikanren - # partd -torch==2.5.1 - # via stable-baselines3 -tornado==6.4.1 - # via - # bokeh - # distributed -tqdm==4.66.6 - # via -r requirements.in -triton==3.1.0 - # via torch -typing-extensions==4.12.2 - # via - # arviz - # chex - # etils - # gpflow - # gymnasium - # optree - # pymc - # pyvista - # tensorflow - # torch -tzdata==2024.2 - # via pandas -urllib3==2.2.3 - # via - # distributed - # requests -vtk==9.3.1 - # via - # -r requirements.in - # pyvista -werkzeug==3.0.6 - # via tensorboard -wheel==0.44.0 - # via astunparse -wrapt==1.16.0 - # via - # deprecated - # tensorflow -xarray==2024.10.0 - # via - # -r requirements.in - # arviz - # xarray-einstats -xarray-einstats==0.8.0 - # via arviz -xyzservices==2024.9.0 - # via bokeh -zict==3.0.0 - # via distributed -zipp==3.20.2 - # via importlib-metadata - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/src/queens/utils/remote_build.py b/src/queens/utils/remote_build.py index 526e9a2b6..a8bd84e1b 100644 --- a/src/queens/utils/remote_build.py +++ b/src/queens/utils/remote_build.py @@ -57,6 +57,11 @@ choices=SUPPORTED_PACKAGE_MANAGERS, help="package manager used for the creation of the remote environment", ) + parser.add_argument( + "--use-conda-lock", + action="store_true", + help="install the remote environment from composed.conda-lock.yml", + ) args = parser.parse_args(sys.argv[1:]) @@ -69,4 +74,6 @@ ) remote_connection.open() remote_connection.sync_remote_repository() - remote_connection.build_remote_environment(package_manager=args.package_manager) + remote_connection.build_remote_environment( + package_manager=args.package_manager, use_conda_lock=args.use_conda_lock + ) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 5ccf3f8cf..3ea40e1d2 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -335,12 +335,15 @@ def copy_from_remote( def build_remote_environment( self, package_manager: str = DEFAULT_PACKAGE_MANAGER, + use_conda_lock: bool = False, ) -> None: """Build remote QUEENS environment. Args: package_manager: Package manager used for the creation of the environment ("mamba" or "conda") + use_conda_lock: Install the environment from composed.conda-lock.yml instead of the + layered environment files """ if package_manager not in SUPPORTED_PACKAGE_MANAGERS: raise ValueError( @@ -379,13 +382,27 @@ def package_manager_exists_remote(package_manager_name: str) -> bool: _logger.info("Build remote QUEENS environment...") start_time = time.time() environment_name = Path(self.remote_python).parents[1].name - command_string = ( - f"cd {self.remote_queens_repository}; " - f"{package_manager} remove --name {environment_name} --all -y;" - f"{package_manager} env create -f environment.yml --name {environment_name}; " - f"{package_manager} activate {environment_name};" - f"pip install -e ." - ) + if use_conda_lock: + command_string = ( + f"cd {self.remote_queens_repository}; " + f"{package_manager} install -n base -c conda-forge conda-lock -y;" + f"{package_manager} remove --name {environment_name} --all -y;" + f"conda-lock install -n {environment_name} composed.conda-lock.yml; " + f"{package_manager} activate {environment_name};" + f"pip install --no-deps -e ." + ) + else: + command_string = ( + f"cd {self.remote_queens_repository}; " + f"{package_manager} remove --name {environment_name} --all -y;" + f"{package_manager} env create -f environment.base.yml --name {environment_name}; " + f"{package_manager} env update -f environment.dev.yml --name {environment_name}; " + f"{package_manager} env update -f environment.tutorials.yml" + f"--name {environment_name}; " + f"{package_manager} env update -f environment.fourc.yml --name {environment_name}; " + f"{package_manager} activate {environment_name};" + f"pip install --no-deps -e ." + ) result = self.run(command_string, in_stream=False) _logger.debug(result.stdout) diff --git a/src/queens_interfaces/fourc/README.md b/src/queens_interfaces/fourc/README.md index 734f7d751..9e11cef8c 100644 --- a/src/queens_interfaces/fourc/README.md +++ b/src/queens_interfaces/fourc/README.md @@ -5,6 +5,6 @@ This package contains drivers and utilities realted to the for multiphysics code ## Material random field interface In order to create random material field in combintation with 4C, we require the package [fourcipp](https://github.com/4C-multiphysics/fourcipp). Therefore install QUEENS via (in the QUEENS main directory): ``` -pip install -e .[dev,fourc] +mamba env update -n queens -f environment.fourc.yml ``` -(You can omit the `dev` if you don't require the additional development packages). +For this you need a QUEENS environment, for instructions on how to set it up see the [README.md](../README.md). diff --git a/src/queens_interfaces/fourc/fourc_requirements.txt b/src/queens_interfaces/fourc/fourc_requirements.txt deleted file mode 100644 index ea6e568bc..000000000 --- a/src/queens_interfaces/fourc/fourc_requirements.txt +++ /dev/null @@ -1 +0,0 @@ -fourcipp diff --git a/src/queens_interfaces/fourc/random_material_preprocessor.py b/src/queens_interfaces/fourc/random_material_preprocessor.py index adc91f7d1..9a7b54e2a 100644 --- a/src/queens_interfaces/fourc/random_material_preprocessor.py +++ b/src/queens_interfaces/fourc/random_material_preprocessor.py @@ -13,6 +13,7 @@ # see . # """4C random material fields preprocessor.""" + from pathlib import Path import numpy as np @@ -22,7 +23,7 @@ except ImportError as exc: raise ImportError( "The required packages to construct random fields in QUEENS for 4C are not installed." - " Please install them via \n pip install -e .[fourc]" + " Please install them via \n mamba env update -n -f environment.fourc.yml" ) from exc diff --git a/tutorial-requirements.in b/tutorial-requirements.in deleted file mode 100644 index 91de3b7a9..000000000 --- a/tutorial-requirements.in +++ /dev/null @@ -1,7 +0,0 @@ -# This file contains all the requirements for QUEENS Tutorials. - -# Do not fix the version of a package if not strictly necessary. We use pip-tools in order to create a requirements.txt file where the version of the different packages are fixed to the latest stable version w.r.t. QUEENS. From time to time pip-tools is used to upgrade to the newer available versions. - -# Tutorials -scikit-fem -pyvista diff --git a/tutorial-requirements.txt b/tutorial-requirements.txt deleted file mode 100644 index 8b88b0933..000000000 --- a/tutorial-requirements.txt +++ /dev/null @@ -1,107 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --constraint=requirements.txt --output-file=tutorial-requirements.txt tutorial-requirements.in -# -certifi==2024.8.30 - # via - # -c requirements.txt - # requests -charset-normalizer==3.4.0 - # via - # -c requirements.txt - # requests -contourpy==1.3.0 - # via - # -c requirements.txt - # matplotlib -cycler==0.12.1 - # via - # -c requirements.txt - # matplotlib -fonttools==4.54.1 - # via - # -c requirements.txt - # matplotlib -idna==3.10 - # via - # -c requirements.txt - # requests -kiwisolver==1.4.7 - # via - # -c requirements.txt - # matplotlib -matplotlib==3.9.2 - # via - # -c requirements.txt - # pyvista - # vtk -numpy==1.26.4 - # via - # -c requirements.txt - # contourpy - # matplotlib - # pyvista - # scikit-fem - # scipy -packaging==24.1 - # via - # -c requirements.txt - # matplotlib - # pooch -pillow==11.0.0 - # via - # -c requirements.txt - # matplotlib - # pyvista -platformdirs==4.3.6 - # via - # -c requirements.txt - # pooch -pooch==1.8.2 - # via - # -c requirements.txt - # pyvista -pyparsing==3.2.0 - # via - # -c requirements.txt - # matplotlib -python-dateutil==2.9.0.post0 - # via - # -c requirements.txt - # matplotlib -pyvista==0.44.1 - # via - # -c requirements.txt - # -r tutorial-requirements.in -requests==2.32.3 - # via - # -c requirements.txt - # pooch -scikit-fem==11.0.0 - # via -r tutorial-requirements.in -scipy==1.14.1 - # via - # -c requirements.txt - # scikit-fem -scooby==0.10.0 - # via - # -c requirements.txt - # pyvista -six==1.16.0 - # via - # -c requirements.txt - # python-dateutil -typing-extensions==4.12.2 - # via - # -c requirements.txt - # pyvista -urllib3==2.2.3 - # via - # -c requirements.txt - # requests -vtk==9.3.1 - # via - # -c requirements.txt - # pyvista From 1e2a5a41b33d2feae3991b12fb61bfe684ba128b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 16:10:06 +0200 Subject: [PATCH 005/200] build: activate base to find conda-lock --- .github/actions/create_python_environment/action.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml index d72cb645a..5a1d0f6a1 100644 --- a/.github/actions/create_python_environment/action.yml +++ b/.github/actions/create_python_environment/action.yml @@ -17,6 +17,7 @@ runs: PYTHON_PACKAGE_MANAGER: conda run: | $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y + $PYTHON_PACKAGE_MANAGER activate base conda-lock install -n queens composed.conda-lock.yml $PYTHON_PACKAGE_MANAGER activate queens pip install --no-deps -e . From 662be96d3dbd7be82153560e87b80f4d71a7ef54 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 17:34:08 +0200 Subject: [PATCH 006/200] ci: clean conda cache --- .github/actions/create_python_environment/action.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml index 5a1d0f6a1..222a71809 100644 --- a/.github/actions/create_python_environment/action.yml +++ b/.github/actions/create_python_environment/action.yml @@ -18,6 +18,8 @@ runs: run: | $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y $PYTHON_PACKAGE_MANAGER activate base + # Clear potentially broken package-cache state + conda clean --packages --tarballs --index-cache --yes conda-lock install -n queens composed.conda-lock.yml $PYTHON_PACKAGE_MANAGER activate queens pip install --no-deps -e . From 5cb6568b8531f67a11aa8071c83ec9b140db33f3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 17:56:35 +0200 Subject: [PATCH 007/200] ci: use mamba for conda-lock --- .github/actions/create_python_environment/action.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml index 222a71809..03a4ceffa 100644 --- a/.github/actions/create_python_environment/action.yml +++ b/.github/actions/create_python_environment/action.yml @@ -16,11 +16,9 @@ runs: env: PYTHON_PACKAGE_MANAGER: conda run: | - $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y + $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock mamba -y $PYTHON_PACKAGE_MANAGER activate base - # Clear potentially broken package-cache state - conda clean --packages --tarballs --index-cache --yes - conda-lock install -n queens composed.conda-lock.yml + conda-lock install --conda mamba -n queens composed.conda-lock.yml $PYTHON_PACKAGE_MANAGER activate queens pip install --no-deps -e . $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml From d4438e66c70d7848569626767c1267c43836e5ad Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 18:03:12 +0200 Subject: [PATCH 008/200] ci: bump actions/checkout to v5 --- .github/workflows/tests_local.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 67f335ead..7d5a4a849 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -24,7 +24,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Install rsync run: | sudo apt-get update From dbca697c6bc3399960c7604e1db0e5660c7f2be9 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 18:14:11 +0200 Subject: [PATCH 009/200] ci: use miniforge --- .github/actions/create_python_environment/action.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml index 03a4ceffa..1a5eb39bf 100644 --- a/.github/actions/create_python_environment/action.yml +++ b/.github/actions/create_python_environment/action.yml @@ -10,14 +10,15 @@ runs: using: composite steps: - uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-version: "latest" - name: Create conda-lock environment and install QUEENS id: environment shell: bash -l {0} env: PYTHON_PACKAGE_MANAGER: conda run: | - $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock mamba -y - $PYTHON_PACKAGE_MANAGER activate base + $PYTHON_PACKAGE_MANAGER install -c conda-forge conda-lock -y conda-lock install --conda mamba -n queens composed.conda-lock.yml $PYTHON_PACKAGE_MANAGER activate queens pip install --no-deps -e . From 0927397970a480d1aa0e5baec4acdc73c7662333 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 18:52:20 +0200 Subject: [PATCH 010/200] refactor: blackify code with new black version --- src/queens/data_processors/__init__.py | 1 + src/queens/distributions/__init__.py | 1 + src/queens/drivers/__init__.py | 1 + src/queens/drivers/jobscript.py | 1 - src/queens/iterators/__init__.py | 1 + src/queens/models/__init__.py | 1 + src/queens/schedulers/__init__.py | 1 + src/queens/schedulers/cluster.py | 4 ++-- src/queens/stochastic_optimizers/__init__.py | 1 + src/queens/variational_distributions/__init__.py | 1 + .../test_variational_distributions.py | 2 +- 11 files changed, 11 insertions(+), 4 deletions(-) diff --git a/src/queens/data_processors/__init__.py b/src/queens/data_processors/__init__.py index d971049e7..3513492c1 100644 --- a/src/queens/data_processors/__init__.py +++ b/src/queens/data_processors/__init__.py @@ -16,6 +16,7 @@ Modules for extracting and processing data from simulation output files. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/distributions/__init__.py b/src/queens/distributions/__init__.py index 24075fdab..023872c52 100644 --- a/src/queens/distributions/__init__.py +++ b/src/queens/distributions/__init__.py @@ -16,6 +16,7 @@ Modules for probability distributions. """ + from __future__ import annotations from typing import TYPE_CHECKING diff --git a/src/queens/drivers/__init__.py b/src/queens/drivers/__init__.py index e92ffe561..30f56ef91 100644 --- a/src/queens/drivers/__init__.py +++ b/src/queens/drivers/__init__.py @@ -17,6 +17,7 @@ Modules for calling external simulation software. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/drivers/jobscript.py b/src/queens/drivers/jobscript.py index 7989fef9c..4cf0fa2d1 100644 --- a/src/queens/drivers/jobscript.py +++ b/src/queens/drivers/jobscript.py @@ -14,7 +14,6 @@ # """Driver to run a jobscript.""" - import logging from collections.abc import Callable from dataclasses import dataclass diff --git a/src/queens/iterators/__init__.py b/src/queens/iterators/__init__.py index c85c89ada..b2e4ee25a 100644 --- a/src/queens/iterators/__init__.py +++ b/src/queens/iterators/__init__.py @@ -17,6 +17,7 @@ Modules for parameter studies, uncertainty quantification, sensitivity analysis, Bayesian inverse analysis, and optimization. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/models/__init__.py b/src/queens/models/__init__.py index a0fa15b5f..759bfd3af 100644 --- a/src/queens/models/__init__.py +++ b/src/queens/models/__init__.py @@ -17,6 +17,7 @@ Modules for multi-query mapping of inputs to outputs, such as parameter samples to model evaluations. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/schedulers/__init__.py b/src/queens/schedulers/__init__.py index 1bbcf70b7..a3c18becf 100644 --- a/src/queens/schedulers/__init__.py +++ b/src/queens/schedulers/__init__.py @@ -16,6 +16,7 @@ Modules for scheduling and submitting computational jobs. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/schedulers/cluster.py b/src/queens/schedulers/cluster.py index b00cadb6a..157e357ae 100644 --- a/src/queens/schedulers/cluster.py +++ b/src/queens/schedulers/cluster.py @@ -63,8 +63,8 @@ def timedelta_to_str(timedelta_obj): """ # Time in seconds time_in_seconds = int(timedelta_obj.total_seconds()) - (minutes, seconds) = divmod(time_in_seconds, 60) - (hours, minutes) = divmod(minutes, 60) + minutes, seconds = divmod(time_in_seconds, 60) + hours, minutes = divmod(minutes, 60) return f"{hours:02}:{minutes:02}:{seconds:02}" diff --git a/src/queens/stochastic_optimizers/__init__.py b/src/queens/stochastic_optimizers/__init__.py index 33b1c7e9a..61d5d1b9f 100644 --- a/src/queens/stochastic_optimizers/__init__.py +++ b/src/queens/stochastic_optimizers/__init__.py @@ -16,6 +16,7 @@ Modules containing stochastic optimizers. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/src/queens/variational_distributions/__init__.py b/src/queens/variational_distributions/__init__.py index 233d836a6..7ac856019 100644 --- a/src/queens/variational_distributions/__init__.py +++ b/src/queens/variational_distributions/__init__.py @@ -16,6 +16,7 @@ Modules containing probability distributions for variational inference. """ + from typing import TYPE_CHECKING from queens.utils.imports import extract_type_checking_imports, import_class_from_class_module_map diff --git a/tests/unit_tests/variational_distributions/test_variational_distributions.py b/tests/unit_tests/variational_distributions/test_variational_distributions.py index a1d165fd9..a3c2694d9 100644 --- a/tests/unit_tests/variational_distributions/test_variational_distributions.py +++ b/tests/unit_tests/variational_distributions/test_variational_distributions.py @@ -248,7 +248,7 @@ def fixture_joint_reference_data(mean_field_reference_data, fullrank_reference_d def fixture_mixture_reference_data(mean_field_reference_data): """Reference data for the mixture distribution.""" distribution_1 = mean_field_reference_data.distribution - (mean_1, cov_1) = mean_field_reference_data.distribution_parameters + mean_1, cov_1 = mean_field_reference_data.distribution_parameters variational_parameters_1 = mean_field_reference_data.variational_parameters input_samples = mean_field_reference_data.input_samples From 201f4066edd883260c19cb65b53efd44c875f0c5 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 13 Apr 2026 19:18:04 +0200 Subject: [PATCH 011/200] test: update .pylintrc to latest pylint version --- .pylintrc | 65 +++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 49 insertions(+), 16 deletions(-) diff --git a/.pylintrc b/.pylintrc index 66ae321f7..37fbe62e7 100644 --- a/.pylintrc +++ b/.pylintrc @@ -39,7 +39,7 @@ extension-pkg-whitelist= fail-on= # Specify a score threshold under which the program will exit with error. -fail-under=10 +fail-under=10.0 # Interpret the stdin as a python script, whose filename needs to be passed as # the module_or_package argument. @@ -59,10 +59,11 @@ ignore-paths=tutorials # Emacs file locks ignore-patterns=^\.# -# List of module names for which member attributes should not be checked -# (useful for modules/projects where namespaces are manipulated during runtime -# and thus existing member attributes cannot be deduced by static analysis). It -# supports qualified module names, as well as Unix pattern matching. +# List of module names for which member attributes should not be checked and +# will not be imported (useful for modules/projects where namespaces are +# manipulated during runtime and thus existing member attributes cannot be +# deduced by static analysis). It supports qualified module names, as well as +# Unix pattern matching. ignored-modules=vtk, particles, @@ -88,6 +89,10 @@ load-plugins= # Pickle collected data for later comparisons. persistent=yes +# Resolve imports to .pyi stubs if available. May reduce no-member messages and +# increase not-an-iterable messages. +prefer-stubs=no + # Minimum Python version to use for version dependent checks. Will default to # the version used to run pylint. py-version=3.10 @@ -101,10 +106,6 @@ recursive=no # source root. source-roots= -# When enabled, pylint would attempt to guess common misconfiguration and emit -# user-friendly hints instead of false-positive error messages. -suggestion-mode=yes - # Allow loading of arbitrary C extensions. Extensions are imported into the # active Python interpreter and may run arbitrary code. unsafe-load-any-extension=no @@ -231,6 +232,11 @@ name-group= # not require a docstring. no-docstring-rgx=^_ +# Regular expression matching correct parameter specification variable names. +# If left empty, parameter specification variable names will be checked with +# the set naming style. +#paramspec-rgx= + # List of decorators that produce properties, such as abc.abstractproperty. Add # to this list to register other decorators that produce valid properties. # These decorators are taken in consideration only for invalid-name. @@ -244,6 +250,10 @@ property-classes=abc.abstractproperty # variable names will be checked with the set naming style. #typevar-rgx= +# Regular expression matching correct type variable tuple names. If left empty, +# type variable tuple names will be checked with the set naming style. +#typevartuple-rgx= + # Naming style matching correct variable names. variable-naming-style=snake_case @@ -304,6 +314,9 @@ max-locals=15 # Maximum number of parents for a class (see R0901). max-parents=7 +# Maximum number of positional arguments for function / method. +max-positional-arguments=5 + # Maximum number of public methods for a class (see R0904). max-public-methods=20 @@ -338,7 +351,9 @@ indent-after-paren=4 # tab). indent-string=' ' -# Maximum number of characters on a single line. +# Maximum number of characters on a single line. Pylint's default of 100 is +# based on PEP 8's guidance that teams may choose line lengths up to 99 +# characters. max-line-length=100 # Maximum number of lines in a module. @@ -433,7 +448,17 @@ disable=raw-checker-failed, use-symbolic-message-instead, use-implicit-booleaness-not-comparison-to-string, use-implicit-booleaness-not-comparison-to-zero, - design, + too-many-ancestors, + too-many-instance-attributes, + too-few-public-methods, + too-many-public-methods, + too-many-return-statements, + too-many-branches, + too-many-arguments, + too-many-locals, + too-many-statements, + too-many-boolean-expressions, + too-many-positional-arguments # Enable the message, report, category or checker with the given id(s). You can # either give multiple identifier separated by comma (,) or put this option @@ -451,6 +476,9 @@ timeout-methods=requests.api.delete,requests.api.get,requests.api.head,requests. [MISCELLANEOUS] +# Whether or not to search for fixme's in docstrings. +check-fixme-in-docstring=no + # List of note tags to take in consideration, separated by a comma. notes=FIXME, XXX, @@ -471,6 +499,11 @@ max-nested-blocks=5 # printed. never-returning-functions=sys.exit,argparse.parse_error +# Let 'consider-using-join' be raised when the separator to join on would be +# non-empty (resulting in expected fixes of the type: ``"- " + " - +# ".join(items)``) +suggest-join-with-non-empty-separator=yes + [REPORTS] @@ -485,10 +518,10 @@ evaluation=max(0, 0 if fatal else 10.0 - ((float(5 * error + warning + refactor # used to format the message information. See doc for all details. msg-template= -# Set the output format. Available formats are: text, parseable, colorized, -# json2 (improved json format), json (old json format) and msvs (visual -# studio). You can also give a reporter class, e.g. -# mypackage.mymodule.MyReporterClass. +# Set the output format. Available formats are: 'text', 'parseable', +# 'colorized', 'json2' (improved json format), 'json' (old json format), msvs +# (visual studio) and 'github' (GitHub actions). You can also give a reporter +# class, e.g. mypackage.mymodule.MyReporterClass. #output-format= # Tells whether to display a full report or only the messages. @@ -595,7 +628,7 @@ ignored-classes=optparse.Values, # of finding the hint is based on edit distance. missing-member-hint=yes -# The minimum edit distance a name should have in order to be considered a +# The maximum edit distance a name should have in order to be considered a # similar match for a missing member name. missing-member-hint-distance=1 From 9db683b0c7b123b7ce9642bc9652dabb2d39b506 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 10:23:06 +0200 Subject: [PATCH 012/200] build: add particles name to pypi dependency --- environment.base.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.base.yml b/environment.base.yml index 96c6e1188..a21ff3ffe 100644 --- a/environment.base.yml +++ b/environment.base.yml @@ -81,5 +81,5 @@ dependencies: - diversipy # sampling from space filling subsets # has no notable dependencies # Chopin et al. sequential Monte-Carlo, filtering/smoothing package # - particles # currently causes problem by requiring numpy<2 - - git+https://github.com/nchopin/particles.git + - particles@git+https://github.com/nchopin/particles.git - scikit-activeml>=0.4.1 From fc6e2588bf24791a9b0885eede48c70fe6c0fb1a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 23:23:23 +0200 Subject: [PATCH 013/200] build: fix import errors arviz 1.0.0 by bumping pymc version --- composed.conda-lock.yml | 420 +++++++++++++++++----------------------- environment.base.yml | 2 +- 2 files changed, 175 insertions(+), 247 deletions(-) diff --git a/composed.conda-lock.yml b/composed.conda-lock.yml index 38e236e6f..4a6262bfb 100644 --- a/composed.conda-lock.yml +++ b/composed.conda-lock.yml @@ -13,8 +13,8 @@ version: 1 metadata: content_hash: - osx-arm64: f8a8f3d8f619e3992ab90687739b623886774458833c2b4456c20e142f0a7885 - linux-64: 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https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.10.1-pyhcf101f3_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.10.2-pyhcf101f3_0.conda hash: - md5: 3718be965507e15f8c815e35b755600c - sha256: aae95f265ed767d3ba490259bf9e14ec984f15aedf7e85a67da122a327f760ea + md5: 2c07e2363c11ed772c045ef15bffe6bf + sha256: ec17b8111ef1371452093931b1791156c00ff481e64e5a9e6e98817ca9f5d50d category: main optional: false - name: cyclopts - version: 4.10.1 + version: 4.10.2 manager: conda platform: osx-arm64 dependencies: @@ -2537,10 +2435,10 @@ package: rich-rst: '>=1.3.1,<2.0.0' tomli: '>=2.0.0' typing_extensions: '>=4.8.0' - url: https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.10.1-pyhcf101f3_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.10.2-pyhcf101f3_0.conda hash: - md5: 3718be965507e15f8c815e35b755600c - sha256: aae95f265ed767d3ba490259bf9e14ec984f15aedf7e85a67da122a327f760ea + md5: 2c07e2363c11ed772c045ef15bffe6bf + sha256: 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optional: false - name: scikit-activeml diff --git a/environment.base.yml b/environment.base.yml index a21ff3ffe..653ea2f75 100644 --- a/environment.base.yml +++ b/environment.base.yml @@ -45,7 +45,7 @@ dependencies: - tensorflow-probability - tf-keras - jax - - pymc + - pymc >= 5.28.4 - stable-baselines3 # making fancy plots From 3627fc6671872c010f90e704fe9eba9c68386606 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 23:43:17 +0200 Subject: [PATCH 014/200] build: adapt pydoe name to non-camelcase --- environment.base.yml | 2 +- src/queens/iterators/latin_hypercube_sampling.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.base.yml b/environment.base.yml index 653ea2f75..5d19206f9 100644 --- a/environment.base.yml +++ b/environment.base.yml @@ -28,7 +28,7 @@ dependencies: # Others - xarray # Special array format - - pyDOE # design of experiments + - pydoe # design of experiments - SALib # for sensitivity analysis - vtk # vtk format handler - pyvista diff --git a/src/queens/iterators/latin_hypercube_sampling.py b/src/queens/iterators/latin_hypercube_sampling.py index c83226faa..6b77958dc 100644 --- a/src/queens/iterators/latin_hypercube_sampling.py +++ b/src/queens/iterators/latin_hypercube_sampling.py @@ -17,7 +17,7 @@ import logging import numpy as np -from pyDOE import lhs +from pydoe import lhs from queens.iterators._iterator import Iterator from queens.utils.logger_settings import log_init_args From 1d3fe09fecefe9295b9c41f86586f1253c7931f1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 14 Apr 2026 22:00:40 +0200 Subject: [PATCH 015/200] build: introduce base enviroment to pyproject.toml with pixi --- .gitignore | 3 ++ pyproject.toml | 103 ++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 105 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 6fb2b5617..70ffdfb07 100644 --- a/.gitignore +++ b/.gitignore @@ -82,3 +82,6 @@ venv.bak/ # best editor ever files *.swp +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/pyproject.toml b/pyproject.toml index 33515a21e..85d1c52e3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,58 @@ authors = [{ name = "QUEENS developers" }] dynamic = ["version"] description = "A general purpose framework for Uncertainty Quantification, Physics-Informed Machine Learning, Bayesian Optimization, Inverse Problems and Simulation Analytics" readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.12" +dependencies = [ + "setuptools<82", + "cython", + "numba", + "numpy", + "pandas", + "scikit-learn", + "scipy", + "dask", + "distributed", + "dask-jobqueue", + "bokeh", + "fabric", + "xarray", + "pydoe", + "salib", + "vtk", + "pyvista", + "autograd", + "chaospy", + "pyyaml", + "jinja2", + "arviz", + "gpflow>=2.9.2", + "optax", + "tensorflow>=2.19.1", + "tensorflow-probability", + "tf-keras", + "jax", + "pymc", + "stable-baselines3", + "matplotlib", + "seaborn", + "plotly", + "pytest", + "py", + "pytest-codestyle", + "pytest-cov", + "pytest-mock", + "pytest-xdist", + "mock", + "tqdm", + "tomli", + "pathos", + "black>=24.4.2", + "gnuplotlib", + "diversipy", + "particles @ git+https://github.com/nchopin/particles.git", + "scikit-activeml>=0.4.1", + "wheel>=0.46.3" +] keywords = [ "gaussian processes", "uncertainty quantification", @@ -167,3 +218,53 @@ exclude = '''(?x)( [[tool.mypy.overrides]] module = ["yaml"] follow_untyped_imports = true + +[tool.pixi.workspace] +channels = ["conda-forge", "nodefaults"] +platforms = ["linux-64", "osx-arm64"] + +[tool.pixi.dependencies] +setuptools = "<82" +cython = "*" +numba = "*" +numpy = "*" +pandas = "*" +scikit-learn = "*" +scipy = "*" +dask = "*" +distributed = "*" +dask-jobqueue = "*" +bokeh = "*" +fabric = "*" +xarray = "*" +pydoe = "*" +salib = "*" +vtk = "*" +pyvista = "*" +autograd = "*" +chaospy = "*" +pyyaml = "*" +jinja2 = "*" +arviz = "*" +gpflow = "*" +optax = "*" +tensorflow = "*" +tensorflow-probability = "*" +tf-keras = "*" +jax = "*" +pymc = "*" +stable-baselines3 = "*" +matplotlib = "*" +seaborn = "*" +plotly = "*" +pytest = "*" +py = "*" +pytest-codestyle = "*" +pytest-cov = "*" +pytest-mock = "*" +pytest-xdist = "*" +mock = "*" +tqdm = "*" +tomli = "*" +pathos = "*" +black = ">=24.4.2" From c2231c67c4d06f591ebe60c3a45d2c2ad0f8cb2f Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 14 Apr 2026 23:16:09 +0200 Subject: [PATCH 016/200] build: introduce pixi features --- pyproject.toml | 123 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 85d1c52e3..4f71d4b2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -224,6 +224,7 @@ channels = ["conda-forge", "nodefaults"] platforms = ["linux-64", "osx-arm64"] [tool.pixi.dependencies] +python = "*" setuptools = "<82" cython = "*" numba = "*" @@ -268,3 +269,125 @@ tqdm = "*" tomli = "*" pathos = "*" black = ">=24.4.2" +pip = "*" + +[tool.pixi.feature.queens] +channels = ["conda-forge", "nodefaults"] + +[tool.pixi.feature.queens.dependencies] +python = "*" +setuptools = "<82" +cython = "*" +numba = "*" +numpy = "*" +pandas = "*" +scikit-learn = "*" +scipy = "*" +dask = "*" +distributed = "*" +dask-jobqueue = "*" +bokeh = "*" +fabric = "*" +xarray = "*" +pydoe = "*" +salib = "*" +vtk = "*" +pyvista = "*" +autograd = "*" +chaospy = "*" +pyyaml = "*" +jinja2 = "*" +arviz = "*" +gpflow = "*" +optax = "*" +tensorflow = "*" +tensorflow-probability = "*" +tf-keras = "*" +jax = "*" +pymc = "*" +stable-baselines3 = "*" +matplotlib = "*" +seaborn = "*" +plotly = "*" +pytest = "*" +py = "*" +pytest-codestyle = "*" +pytest-cov = "*" +pytest-mock = "*" +pytest-xdist = "*" +mock = "*" +tqdm = "*" +tomli = "*" +pathos = "*" +black = ">=24.4.2" +pip = "*" + +[tool.pixi.feature.dev] +channels = ["conda-forge", "nodefaults"] + +[tool.pixi.feature.dev.dependencies] +pylint = ">=2.16" +isort = ">=5.0" +pre-commit = "*" +pre-commit-hooks = ">=4.4.0" +sphinx = "*" +nbsphinx = "*" +pydata-sphinx-theme = "*" +pandoc = "*" +commitizen = ">=3.12.0" +docformatter = ">=1.5.1" +yamllint = ">=1.19.0" +ruff = "*" +nbstripout = "*" +myst-parser = "*" +testbook = "*" +ipykernel = "*" +mypy = "*" +pip = "*" + +[tool.pixi.feature.tutorials] +channels = ["conda-forge", "nodefaults"] + +[tool.pixi.feature.tutorials.dependencies] +scikit-fem = "*" + +[tool.pixi.feature.fourc] +channels = ["conda-forge", "nodefaults"] + +[tool.pixi.feature.fourc.dependencies] +pip = "*" + +[tool.pixi.environments] +queens = { features = ["queens", "dev", "tutorials", "fourc"], no-default-feature = true } +queens-base = { features = []} +queens-dev = { features = ["dev"]} +queens-full = { features = ["dev", "tutorials", "fourc"]} + +[dependency-groups] +#queens = ["gnuplotlib", "diversipy", "particles @ git+https://github.com/nchopin/particles.git", "scikit-activeml>=0.4.1"] +#dev = ["liccheck", "pylint-exit", "licenseheaders"] +dev = [ "pylint>=2.16", + "isort>=5.0", + "pre-commit", + "pre-commit-hooks>=4.4.0", + "sphinx", + "nbsphinx", + "pydata-sphinx-theme", + "pandoc", + "commitizen>=3.12.0", + "docformatter>=1.5.1", + "yamllint>=1.19.0", + "ruff", + "nbstripout", + "myst-parser", + "testbook", + "ipykernel", + "mypy", + "liccheck", "pylint-exit", "licenseheaders"] +#fourc = ["fourcipp"] + +[project.optional-dependencies] +#queens = ["gnuplotlib", "diversipy", "particles @ git+https://github.com/nchopin/particles.git", "scikit-activeml>=0.4.1"] +tutorials =["scikit-fem"] +fourc = ["fourcipp"] +all = ["queens[fourc]", "queens[tutorials]"] From 719d28951fed0ae8bd691f1cfa26ce798dc26842 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 14 Apr 2026 23:17:28 +0200 Subject: [PATCH 017/200] build: remove pixi feature queens and cleanup --- pyproject.toml | 56 -------------------------------------------------- 1 file changed, 56 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4f71d4b2f..8659d31ec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -271,57 +271,6 @@ pathos = "*" black = ">=24.4.2" pip = "*" -[tool.pixi.feature.queens] -channels = ["conda-forge", "nodefaults"] - -[tool.pixi.feature.queens.dependencies] -python = "*" -setuptools = "<82" -cython = "*" -numba = "*" -numpy = "*" -pandas = "*" -scikit-learn = "*" -scipy = "*" -dask = "*" -distributed = "*" -dask-jobqueue = "*" -bokeh = "*" -fabric = "*" -xarray = "*" -pydoe = "*" -salib = "*" -vtk = "*" -pyvista = "*" -autograd = "*" -chaospy = "*" -pyyaml = "*" -jinja2 = "*" -arviz = "*" -gpflow = "*" -optax = "*" -tensorflow = "*" -tensorflow-probability = "*" -tf-keras = "*" -jax = "*" -pymc = "*" -stable-baselines3 = "*" -matplotlib = "*" -seaborn = "*" -plotly = "*" -pytest = "*" -py = "*" -pytest-codestyle = "*" -pytest-cov = "*" -pytest-mock = "*" -pytest-xdist = "*" -mock = "*" -tqdm = "*" -tomli = "*" -pathos = "*" -black = ">=24.4.2" -pip = "*" - [tool.pixi.feature.dev] channels = ["conda-forge", "nodefaults"] @@ -358,14 +307,11 @@ channels = ["conda-forge", "nodefaults"] pip = "*" [tool.pixi.environments] -queens = { features = ["queens", "dev", "tutorials", "fourc"], no-default-feature = true } queens-base = { features = []} queens-dev = { features = ["dev"]} queens-full = { features = ["dev", "tutorials", "fourc"]} [dependency-groups] -#queens = ["gnuplotlib", "diversipy", "particles @ git+https://github.com/nchopin/particles.git", "scikit-activeml>=0.4.1"] -#dev = ["liccheck", "pylint-exit", "licenseheaders"] dev = [ "pylint>=2.16", "isort>=5.0", "pre-commit", @@ -384,10 +330,8 @@ dev = [ "pylint>=2.16", "ipykernel", "mypy", "liccheck", "pylint-exit", "licenseheaders"] -#fourc = ["fourcipp"] [project.optional-dependencies] -#queens = ["gnuplotlib", "diversipy", "particles @ git+https://github.com/nchopin/particles.git", "scikit-activeml>=0.4.1"] tutorials =["scikit-fem"] fourc = ["fourcipp"] all = ["queens[fourc]", "queens[tutorials]"] From 5d544bb408d9e24032ae4d73a71b5f62fa1ec2a6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 14:36:10 +0200 Subject: [PATCH 018/200] build: add current pip-tools mininum versions --- pyproject.toml | 249 ++++++++++++++++++++++++------------------------- 1 file changed, 124 insertions(+), 125 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8659d31ec..a568cd886 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,54 +12,53 @@ readme = "README.md" requires-python = ">=3.12" dependencies = [ "setuptools<82", - "cython", - "numba", - "numpy", - "pandas", - "scikit-learn", - "scipy", - "dask", - "distributed", - "dask-jobqueue", - "bokeh", - "fabric", - "xarray", - "pydoe", - "salib", - "vtk", - "pyvista", - "autograd", - "chaospy", - "pyyaml", - "jinja2", - "arviz", + "cython>=3.0.11", + "numba>=0.60.0", + "numpy>=1.26.4", + "pandas>=2.2.3", + "scikit-learn>=1.5.2", + "scipy>=1.14.1", + "dask>=2024.10.0", + "distributed>=2024.10.0", + "dask-jobqueue>=0.9.0", + "bokeh>=3.6.1", + "fabric>=3.2.2", + "xarray>=2024.10.0", + "pydoe>=0.3.8", + "salib>=1.5.1", + "vtk>=9.3.1", + "pyvista>=0.44.1", + "autograd>=1.7.0", + "chaospy>=4.3.17", + "pyyaml>=6.0.2", + "jinja2>=3.1.4", + "arviz>=0.20.0", "gpflow>=2.9.2", - "optax", - "tensorflow>=2.19.1", - "tensorflow-probability", - "tf-keras", - "jax", - "pymc", - "stable-baselines3", - "matplotlib", - "seaborn", - "plotly", - "pytest", - "py", - "pytest-codestyle", - "pytest-cov", - "pytest-mock", - "pytest-xdist", - "mock", - "tqdm", - "tomli", - "pathos", - "black>=24.4.2", - "gnuplotlib", - "diversipy", + "optax>=0.2.3", + "tensorflow>=2.18.0", + "tensorflow-probability>=0.25.0", + "tf-keras>=2.18.0", + "jax>=0.4.35", + "pymc>=5.17.0", + "stable-baselines3>=2.4.1", + "matplotlib>=3.9.2", + "seaborn>=0.13.2", + "plotly>=5.24.1", + "pytest>=8.3.3", + "py>=1.11.0", + "pytest-codestyle>=2.0.1", + "pytest-cov>=5.0.0", + "pytest-mock>=3.14.0", + "pytest-xdist>=3.6.1", + "mock>=5.1.0", + "tqdm>=4.66.6", + "tomli>=2.0.2", + "pathos>=0.3.3", + "black>=24.10.0", + "gnuplotlib>=0.42", + "diversipy>=0.9", "particles @ git+https://github.com/nchopin/particles.git", - "scikit-activeml>=0.4.1", - "wheel>=0.46.3" + "scikit-activeml>=0.5.2", ] keywords = [ "gaussian processes", @@ -226,79 +225,79 @@ platforms = ["linux-64", "osx-arm64"] [tool.pixi.dependencies] python = "*" setuptools = "<82" -cython = "*" -numba = "*" -numpy = "*" -pandas = "*" -scikit-learn = "*" -scipy = "*" -dask = "*" -distributed = "*" -dask-jobqueue = "*" -bokeh = "*" -fabric = "*" -xarray = "*" -pydoe = "*" -salib = "*" -vtk = "*" -pyvista = "*" -autograd = "*" -chaospy = "*" -pyyaml = "*" -jinja2 = "*" -arviz = "*" -gpflow = "*" -optax = "*" -tensorflow = "*" -tensorflow-probability = "*" -tf-keras = "*" -jax = "*" -pymc = "*" -stable-baselines3 = "*" -matplotlib = "*" -seaborn = "*" -plotly = "*" -pytest = "*" -py = "*" -pytest-codestyle = "*" -pytest-cov = "*" -pytest-mock = "*" -pytest-xdist = "*" -mock = "*" -tqdm = "*" -tomli = "*" -pathos = "*" -black = ">=24.4.2" +cython = ">=3.0.11" +numba = ">=0.60.0" +numpy = ">=1.26.4" +pandas = ">=2.2.3" +scikit-learn = ">=1.5.2" +scipy = ">=1.14.1" +dask = ">=2024.10.0" +distributed = ">=2024.10.0" +dask-jobqueue = ">=0.9.0" +bokeh = ">=3.6.1" +fabric = ">=3.2.2" +xarray = ">=2024.10.0" +pydoe = ">=0.3.8" +salib = ">=1.5.1" +vtk = ">=9.3.1" +pyvista = ">=0.44.1" +autograd = ">=1.7.0" +chaospy = ">=4.3.17" +pyyaml = ">=6.0.2" +jinja2 = ">=3.1.4" +arviz = ">=0.20.0" +gpflow = ">=2.9.2" +optax = ">=0.2.3" +tensorflow = ">=2.18.0" +tensorflow-probability = ">=0.25.0" +tf-keras = ">=2.18.0" +jax = ">=0.4.35" +pymc = ">=5.17.0" +stable-baselines3 = ">=2.4.1" +matplotlib = ">=3.9.2" +seaborn = ">=0.13.2" +plotly = ">=5.24.1" +pytest = ">=8.3.3" +py = ">=1.11.0" +pytest-codestyle = ">=2.0.1" +pytest-cov = ">=5.0.0" +pytest-mock = ">=3.14.0" +pytest-xdist = ">=3.6.1" +mock = ">=5.1.0" +tqdm = ">=4.66.6" +tomli = ">=2.0.2" +pathos = ">=0.3.3" +black = ">=24.10.0" pip = "*" [tool.pixi.feature.dev] channels = ["conda-forge", "nodefaults"] [tool.pixi.feature.dev.dependencies] -pylint = ">=2.16" -isort = ">=5.0" -pre-commit = "*" -pre-commit-hooks = ">=4.4.0" -sphinx = "*" -nbsphinx = "*" -pydata-sphinx-theme = "*" -pandoc = "*" -commitizen = ">=3.12.0" -docformatter = ">=1.5.1" -yamllint = ">=1.19.0" -ruff = "*" -nbstripout = "*" -myst-parser = "*" -testbook = "*" -ipykernel = "*" -mypy = "*" +pylint = ">=3.3.1" +isort = ">=5.13.2" +pre-commit = ">=4.0.1" +pre-commit-hooks = ">=5.0.0" +sphinx = ">=8.1.3" +nbsphinx = ">=0.9.5" +pydata-sphinx-theme = ">=0.16.0" +pandoc = ">=2.4" +commitizen = ">=3.30.0" +docformatter = ">=1.7.5" +yamllint = ">=1.35.1" +ruff = ">=0.9.2" +nbstripout = ">=0.8.1" +myst-parser = ">=4.0.0" +testbook = ">=0.4.2" +ipykernel = ">=6.30.1" +mypy = ">=1.18.2" pip = "*" [tool.pixi.feature.tutorials] channels = ["conda-forge", "nodefaults"] [tool.pixi.feature.tutorials.dependencies] -scikit-fem = "*" +scikit-fem = ">=11.0.0" [tool.pixi.feature.fourc] channels = ["conda-forge", "nodefaults"] @@ -312,26 +311,26 @@ queens-dev = { features = ["dev"]} queens-full = { features = ["dev", "tutorials", "fourc"]} [dependency-groups] -dev = [ "pylint>=2.16", - "isort>=5.0", - "pre-commit", - "pre-commit-hooks>=4.4.0", - "sphinx", - "nbsphinx", - "pydata-sphinx-theme", - "pandoc", - "commitizen>=3.12.0", - "docformatter>=1.5.1", - "yamllint>=1.19.0", - "ruff", - "nbstripout", - "myst-parser", - "testbook", - "ipykernel", - "mypy", +dev = [ "pylint>=3.3.1", + "isort>=5.13.2", + "pre-commit>=4.0.1", + "pre-commit-hooks>=5.0.0", + "sphinx>=8.1.3", + "nbsphinx>=0.9.5", + "pydata-sphinx-theme>=0.16.0", + "pandoc>=2.4", + "commitizen>=3.30.0", + "docformatter>=1.7.5", + "yamllint>=1.35.1", + "ruff>=0.9.2", + "nbstripout>=0.8.1", + "myst-parser>=4.0.0", + "testbook>=0.4.2", + "ipykernel>=6.30.1", + "mypy>=1.18.2", "liccheck", "pylint-exit", "licenseheaders"] [project.optional-dependencies] -tutorials =["scikit-fem"] +tutorials =["scikit-fem>=11.0.0"] fourc = ["fourcipp"] all = ["queens[fourc]", "queens[tutorials]"] From bca335920b087f7cf70561c6ca6d77303159f363 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 14:55:18 +0200 Subject: [PATCH 019/200] build: bump versions to current conda-lock versions --- pyproject.toml | 222 ++++++++++++++++++++++++------------------------- 1 file changed, 111 insertions(+), 111 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a568cd886..f1690cfbe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,54 +11,54 @@ description = "A general purpose framework for Uncertainty Quantification, Physi readme = "README.md" requires-python = ">=3.12" dependencies = [ - "setuptools<82", - "cython>=3.0.11", - "numba>=0.60.0", - "numpy>=1.26.4", - "pandas>=2.2.3", - "scikit-learn>=1.5.2", - "scipy>=1.14.1", - "dask>=2024.10.0", - "distributed>=2024.10.0", + "setuptools>=81.0.0,<82", + "cython>=3.2.4", + "numba>=0.65.0", + "numpy>=2.4.3", + "pandas>=3.0.2", + "scikit-learn>=1.8.0", + "scipy>=1.17.1", + "dask>=2026.3.0", + "distributed>=2026.3.0", "dask-jobqueue>=0.9.0", - "bokeh>=3.6.1", - "fabric>=3.2.2", - "xarray>=2024.10.0", - "pydoe>=0.3.8", - "salib>=1.5.1", - "vtk>=9.3.1", - "pyvista>=0.44.1", - "autograd>=1.7.0", - "chaospy>=4.3.17", - "pyyaml>=6.0.2", - "jinja2>=3.1.4", - "arviz>=0.20.0", + "bokeh>=3.9.0", + "fabric>=3.2.3", + "xarray>=2026.2.0", + "pydoe>=0.9.9", + "salib>=1.5.2", + "vtk>=9.5.0", + "pyvista>=0.47.3", + "autograd>=1.8.0", + "chaospy>=4.3.20", + "pyyaml>=6.0.3", + "jinja2>=3.1.6", + "arviz>=1.0.0", "gpflow>=2.9.2", - "optax>=0.2.3", + "optax>=0.2.8", "tensorflow>=2.18.0", "tensorflow-probability>=0.25.0", "tf-keras>=2.18.0", - "jax>=0.4.35", - "pymc>=5.17.0", - "stable-baselines3>=2.4.1", - "matplotlib>=3.9.2", + "jax>=0.5.2", + "pymc>=5.28.0", + "stable-baselines3>=2.8.0", + "matplotlib>=3.10.8", "seaborn>=0.13.2", - "plotly>=5.24.1", - "pytest>=8.3.3", + "plotly>=6.6.0", + "pytest>=9.0.3", "py>=1.11.0", "pytest-codestyle>=2.0.1", - "pytest-cov>=5.0.0", - "pytest-mock>=3.14.0", - "pytest-xdist>=3.6.1", - "mock>=5.1.0", - "tqdm>=4.66.6", - "tomli>=2.0.2", - "pathos>=0.3.3", - "black>=24.10.0", - "gnuplotlib>=0.42", + "pytest-cov>=7.1.0", + "pytest-mock>=3.15.1", + "pytest-xdist>=3.8.0", + "mock>=5.2.0", + "tqdm>=4.67.3", + "tomli>=2.4.1", + "pathos>=0.3.5", + "black>=26.3.1", + "gnuplotlib>=0.46", "diversipy>=0.9", "particles @ git+https://github.com/nchopin/particles.git", - "scikit-activeml>=0.5.2", + "scikit-activeml>=1.0.0", ] keywords = [ "gaussian processes", @@ -223,81 +223,81 @@ channels = ["conda-forge", "nodefaults"] platforms = ["linux-64", "osx-arm64"] [tool.pixi.dependencies] -python = "*" -setuptools = "<82" -cython = ">=3.0.11" -numba = ">=0.60.0" -numpy = ">=1.26.4" -pandas = ">=2.2.3" -scikit-learn = ">=1.5.2" -scipy = ">=1.14.1" -dask = ">=2024.10.0" -distributed = ">=2024.10.0" +python = ">=3.12.13" +setuptools = ">=81.0.0,<82" +cython = ">=3.2.4" +numba = ">=0.65.0" +numpy = ">=2.4.3" +pandas = ">=3.0.2" +scikit-learn = ">=1.8.0" +scipy = ">=1.17.1" +dask = ">=2026.3.0" +distributed = ">=2026.3.0" dask-jobqueue = ">=0.9.0" -bokeh = ">=3.6.1" -fabric = ">=3.2.2" -xarray = ">=2024.10.0" -pydoe = ">=0.3.8" -salib = ">=1.5.1" -vtk = ">=9.3.1" -pyvista = ">=0.44.1" -autograd = ">=1.7.0" -chaospy = ">=4.3.17" -pyyaml = ">=6.0.2" -jinja2 = ">=3.1.4" -arviz = ">=0.20.0" +bokeh = ">=3.9.0" +fabric = ">=3.2.3" +xarray = ">=2026.2.0" +pydoe = ">=0.9.9" +salib = ">=1.5.2" +vtk = ">=9.5.0" +pyvista = ">=0.47.3" +autograd = ">=1.8.0" +chaospy = ">=4.3.20" +pyyaml = ">=6.0.3" +jinja2 = ">=3.1.6" +arviz = ">=1.0.0" gpflow = ">=2.9.2" -optax = ">=0.2.3" +optax = ">=0.2.8" tensorflow = ">=2.18.0" tensorflow-probability = ">=0.25.0" tf-keras = ">=2.18.0" -jax = ">=0.4.35" -pymc = ">=5.17.0" -stable-baselines3 = ">=2.4.1" -matplotlib = ">=3.9.2" +jax = ">=0.5.2" +pymc = ">=5.28.0" +stable-baselines3 = ">=2.8.0" +matplotlib = ">=3.10.8" seaborn = ">=0.13.2" -plotly = ">=5.24.1" -pytest = ">=8.3.3" +plotly = ">=6.6.0" +pytest = ">=9.0.3" py = ">=1.11.0" pytest-codestyle = ">=2.0.1" -pytest-cov = ">=5.0.0" -pytest-mock = ">=3.14.0" -pytest-xdist = ">=3.6.1" -mock = ">=5.1.0" -tqdm = ">=4.66.6" -tomli = ">=2.0.2" -pathos = ">=0.3.3" -black = ">=24.10.0" -pip = "*" +pytest-cov = ">=7.1.0" +pytest-mock = ">=3.15.1" +pytest-xdist = ">=3.8.0" +mock = ">=5.2.0" +tqdm = ">=4.67.3" +tomli = ">=2.4.1" +pathos = ">=0.3.5" +black = ">=26.3.1" +pip = ">=26.0.1" [tool.pixi.feature.dev] channels = ["conda-forge", "nodefaults"] [tool.pixi.feature.dev.dependencies] -pylint = ">=3.3.1" -isort = ">=5.13.2" -pre-commit = ">=4.0.1" +pylint = ">=4.0.5" +isort = ">=8.0.1" +pre-commit = ">=4.5.1" pre-commit-hooks = ">=5.0.0" -sphinx = ">=8.1.3" -nbsphinx = ">=0.9.5" -pydata-sphinx-theme = ">=0.16.0" -pandoc = ">=2.4" -commitizen = ">=3.30.0" -docformatter = ">=1.7.5" -yamllint = ">=1.35.1" -ruff = ">=0.9.2" -nbstripout = ">=0.8.1" -myst-parser = ">=4.0.0" +sphinx = ">=9.1.0" +nbsphinx = ">=0.9.8" +pydata-sphinx-theme = ">=0.17.0" +pandoc = ">=3.9.0.2" +commitizen = ">=4.13.10" +docformatter = ">=1.7.7" +yamllint = ">=1.38.0" +ruff = ">=0.15.10" +nbstripout = ">=0.9.1" +myst-parser = ">=5.0.0" testbook = ">=0.4.2" -ipykernel = ">=6.30.1" -mypy = ">=1.18.2" -pip = "*" +ipykernel = ">=7.2.0" +mypy = ">=1.20.1" +pip = ">=26.0.1" [tool.pixi.feature.tutorials] channels = ["conda-forge", "nodefaults"] [tool.pixi.feature.tutorials.dependencies] -scikit-fem = ">=11.0.0" +scikit-fem = ">=12.0.1" [tool.pixi.feature.fourc] channels = ["conda-forge", "nodefaults"] @@ -311,26 +311,26 @@ queens-dev = { features = ["dev"]} queens-full = { features = ["dev", "tutorials", "fourc"]} [dependency-groups] -dev = [ "pylint>=3.3.1", - "isort>=5.13.2", - "pre-commit>=4.0.1", +dev = [ "pylint>=4.0.5", + "isort>=8.0.1", + "pre-commit>=4.5.1", "pre-commit-hooks>=5.0.0", - "sphinx>=8.1.3", - "nbsphinx>=0.9.5", - "pydata-sphinx-theme>=0.16.0", - "pandoc>=2.4", - "commitizen>=3.30.0", - "docformatter>=1.7.5", - "yamllint>=1.35.1", - "ruff>=0.9.2", - "nbstripout>=0.8.1", - "myst-parser>=4.0.0", + "sphinx>=9.1.0", + "nbsphinx>=0.9.8", + "pydata-sphinx-theme>=0.17.0", + "pandoc>=3.9.0.2", + "commitizen>=4.13.10", + "docformatter>=1.7.7", + "yamllint>=1.38.0", + "ruff>=0.15.10", + "nbstripout>=0.9.1", + "myst-parser>=5.0.0", "testbook>=0.4.2", - "ipykernel>=6.30.1", - "mypy>=1.18.2", - "liccheck", "pylint-exit", "licenseheaders"] + "ipykernel>=7.2.0", + "mypy>=1.20.1", + "liccheck>=0.9.2", "pylint-exit>=1.2.0", "licenseheaders>=0.8.8"] [project.optional-dependencies] -tutorials =["scikit-fem>=11.0.0"] -fourc = ["fourcipp"] +tutorials =["scikit-fem>=12.0.1"] +fourc = ["fourcipp>=1.71.0"] all = ["queens[fourc]", "queens[tutorials]"] From c35ca172f69d654779ee72a5fcbfd88e6457637c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 14:55:52 +0200 Subject: [PATCH 020/200] build: add explicit dependency of contourpy --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index f1690cfbe..f61b30a40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,6 +55,7 @@ dependencies = [ "tomli>=2.4.1", "pathos>=0.3.5", "black>=26.3.1", + "contourpy>=1.3.3", "gnuplotlib>=0.46", "diversipy>=0.9", "particles @ git+https://github.com/nchopin/particles.git", @@ -268,6 +269,7 @@ tqdm = ">=4.67.3" tomli = ">=2.4.1" pathos = ">=0.3.5" black = ">=26.3.1" +contourpy = ">=1.3.3" pip = ">=26.0.1" [tool.pixi.feature.dev] From c15ae226f2c7ea73637ba32e81291862435ca445 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 16:12:39 +0200 Subject: [PATCH 021/200] build: first working setup with uv venv --- pyproject.toml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f61b30a40..c3bd9a94e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ dependencies = [ "setuptools>=81.0.0,<82", "cython>=3.2.4", "numba>=0.65.0", - "numpy>=2.4.3", + "numpy", "pandas>=3.0.2", "scikit-learn>=1.8.0", "scipy>=1.17.1", @@ -24,18 +24,18 @@ dependencies = [ "bokeh>=3.9.0", "fabric>=3.2.3", "xarray>=2026.2.0", - "pydoe>=0.9.9", - "salib>=1.5.2", + "pydoe", + "salib", "vtk>=9.5.0", "pyvista>=0.47.3", "autograd>=1.8.0", "chaospy>=4.3.20", "pyyaml>=6.0.3", "jinja2>=3.1.6", - "arviz>=1.0.0", - "gpflow>=2.9.2", + "arviz<1", + "gpflow", "optax>=0.2.8", - "tensorflow>=2.18.0", + "tensorflow", "tensorflow-probability>=0.25.0", "tf-keras>=2.18.0", "jax>=0.5.2", From 0bd1440ef7ea6fc22dda69f3a83641a489b92eab Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 23:33:26 +0200 Subject: [PATCH 022/200] build: update pypi dependencies based on latest conda-lock --- pyproject.toml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c3bd9a94e..ff50c7a5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ dependencies = [ "setuptools>=81.0.0,<82", "cython>=3.2.4", "numba>=0.65.0", - "numpy", + "numpy>=2.4.3", "pandas>=3.0.2", "scikit-learn>=1.8.0", "scipy>=1.17.1", @@ -23,23 +23,23 @@ dependencies = [ "dask-jobqueue>=0.9.0", "bokeh>=3.9.0", "fabric>=3.2.3", - "xarray>=2026.2.0", - "pydoe", - "salib", + "xarray>=2026.4.0", + "pydoe>=0.9.9", + "salib>=1.5.2", "vtk>=9.5.0", "pyvista>=0.47.3", "autograd>=1.8.0", "chaospy>=4.3.20", "pyyaml>=6.0.3", "jinja2>=3.1.6", - "arviz<1", + "arviz>=0.23.4,<1", "gpflow", "optax>=0.2.8", - "tensorflow", + "tensorflow>=2.18.0", "tensorflow-probability>=0.25.0", "tf-keras>=2.18.0", "jax>=0.5.2", - "pymc>=5.28.0", + "pymc>=5.28.4", "stable-baselines3>=2.8.0", "matplotlib>=3.10.8", "seaborn>=0.13.2", @@ -237,7 +237,7 @@ distributed = ">=2026.3.0" dask-jobqueue = ">=0.9.0" bokeh = ">=3.9.0" fabric = ">=3.2.3" -xarray = ">=2026.2.0" +xarray = ">=2026.4.0" pydoe = ">=0.9.9" salib = ">=1.5.2" vtk = ">=9.5.0" @@ -246,14 +246,14 @@ autograd = ">=1.8.0" chaospy = ">=4.3.20" pyyaml = ">=6.0.3" jinja2 = ">=3.1.6" -arviz = ">=1.0.0" +arviz = ">=0.23.4,<1" gpflow = ">=2.9.2" optax = ">=0.2.8" tensorflow = ">=2.18.0" tensorflow-probability = ">=0.25.0" tf-keras = ">=2.18.0" jax = ">=0.5.2" -pymc = ">=5.28.0" +pymc = ">=5.28.4" stable-baselines3 = ">=2.8.0" matplotlib = ">=3.10.8" seaborn = ">=0.13.2" @@ -334,5 +334,5 @@ dev = [ "pylint>=4.0.5", [project.optional-dependencies] tutorials =["scikit-fem>=12.0.1"] -fourc = ["fourcipp>=1.71.0"] +fourc = ["fourcipp>=1.91.0"] all = ["queens[fourc]", "queens[tutorials]"] From ad05dfe2be0d7bf85ba4e8345e519f43771d3d13 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 23:46:31 +0200 Subject: [PATCH 023/200] build: remove contourpy as explicit dependency --- pyproject.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ff50c7a5b..71900db68 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,6 @@ dependencies = [ "tomli>=2.4.1", "pathos>=0.3.5", "black>=26.3.1", - "contourpy>=1.3.3", "gnuplotlib>=0.46", "diversipy>=0.9", "particles @ git+https://github.com/nchopin/particles.git", @@ -269,7 +268,6 @@ tqdm = ">=4.67.3" tomli = ">=2.4.1" pathos = ">=0.3.5" black = ">=26.3.1" -contourpy = ">=1.3.3" pip = ">=26.0.1" [tool.pixi.feature.dev] From b3f256e751ce4d87420a1ba8e80c56fd9c09fb73 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 15 Apr 2026 23:51:37 +0200 Subject: [PATCH 024/200] build: make dev group uv installable --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 71900db68..06afd1d9a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -281,7 +281,7 @@ pre-commit-hooks = ">=5.0.0" sphinx = ">=9.1.0" nbsphinx = ">=0.9.8" pydata-sphinx-theme = ">=0.17.0" -pandoc = ">=3.9.0.2" +pandoc = "*" commitizen = ">=4.13.10" docformatter = ">=1.7.7" yamllint = ">=1.38.0" @@ -318,7 +318,7 @@ dev = [ "pylint>=4.0.5", "sphinx>=9.1.0", "nbsphinx>=0.9.8", "pydata-sphinx-theme>=0.17.0", - "pandoc>=3.9.0.2", + "pandoc", "commitizen>=4.13.10", "docformatter>=1.7.7", "yamllint>=1.38.0", From 3ac11027f71c5d0516f6b543cec08af1df058f03 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 16:56:35 +0200 Subject: [PATCH 025/200] build: add license information to metadata --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 06afd1d9a..d2a7b06c7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,6 +6,8 @@ build-backend = "setuptools.build_meta" [project] name = "queens" authors = [{ name = "QUEENS developers" }] +license = "LGPL-3.0-or-later" +license-files = ["LICENSE"] dynamic = ["version"] description = "A general purpose framework for Uncertainty Quantification, Physics-Informed Machine Learning, Bayesian Optimization, Inverse Problems and Simulation Analytics" readme = "README.md" From 3a2c7c1247a4a0973fa464fe77a3368bd85e7bbe Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 16:57:18 +0200 Subject: [PATCH 026/200] build: cleanup pixi workspace --- pyproject.toml | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d2a7b06c7..140c5ff04 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -272,9 +272,6 @@ pathos = ">=0.3.5" black = ">=26.3.1" pip = ">=26.0.1" -[tool.pixi.feature.dev] -channels = ["conda-forge", "nodefaults"] - [tool.pixi.feature.dev.dependencies] pylint = ">=4.0.5" isort = ">=8.0.1" @@ -295,22 +292,16 @@ ipykernel = ">=7.2.0" mypy = ">=1.20.1" pip = ">=26.0.1" -[tool.pixi.feature.tutorials] -channels = ["conda-forge", "nodefaults"] - [tool.pixi.feature.tutorials.dependencies] scikit-fem = ">=12.0.1" -[tool.pixi.feature.fourc] -channels = ["conda-forge", "nodefaults"] - [tool.pixi.feature.fourc.dependencies] pip = "*" [tool.pixi.environments] queens-base = { features = []} -queens-dev = { features = ["dev"]} -queens-full = { features = ["dev", "tutorials", "fourc"]} +queens-dev = { features = ["dev", "tutorials", "fourc"]} +queens-all = { features = ["tutorials", "fourc"]} [dependency-groups] dev = [ "pylint>=4.0.5", @@ -330,7 +321,9 @@ dev = [ "pylint>=4.0.5", "testbook>=0.4.2", "ipykernel>=7.2.0", "mypy>=1.20.1", - "liccheck>=0.9.2", "pylint-exit>=1.2.0", "licenseheaders>=0.8.8"] + "liccheck>=0.9.2", + "pylint-exit>=1.2.0", + "licenseheaders>=0.8.8"] [project.optional-dependencies] tutorials =["scikit-fem>=12.0.1"] From 5ffa9dfdaebf4b97dc522d89a47cf588e28f573c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 17:12:49 +0200 Subject: [PATCH 027/200] build: prepare switch from liccheck to pip-licenses --- pyproject.toml | 80 ++++++++++++++------------------------------------ 1 file changed, 22 insertions(+), 58 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 140c5ff04..66c98d7d6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -144,61 +144,25 @@ show_missing = false [tool.coverage.html] directory = "html_coverage_report" -[tool.liccheck] -authorized_licenses = [ - "apache", - "apache 2.0", - "Apache-2.0", - "apache software license", - "apache license, version 2.0", - "apache license version 2.0", - "apache license 2.0", - "apache software", - "bsd", - "new bsd", - "bsd license", - "new bsd license", - "3-clause bsd", - "BSD 3-Clause", - "BSD-3-Clause", - "simplified bsd", - "CMU License (MIT-CMU)", - "gnu lgpl", - "GNU Library or Lesser General Public License (LGPL)", - "lgpl", - "historical permission notice and disclaimer (hpnd)", - "isc", - "isc license", - "isc license (iscl)", - "mit", - "mit license", - "mozilla public license 2.0", - "mozilla public license 2.0 (mpl 2.0)", - "python software foundation", - "python software foundation license", - "University of Illinois/NCSA Open Source", - "zlib/libpng", +[tool.pip-licenses] +from = "mixed" +ignore-packages = [ + # cons is under LGPL-3 + "cons", + # queens (this library) is under a LGPL-3-or-later + "queens", + # fourcipp is under MIT + "fourcipp", + # scikit-activeml is under BSD 3-Clause License + "scikit-activeml", + # namex is under Apache 2.0 see https://github.com/fchollet/namex?tab=License-1-ov-file + "namex", + # miniKanren is under a BSD-3-Clause (sligthly modified a,b,c instead of 1.,2.,3. see https://github.com/pythological/kanren/blob/main/LICENSE.txt + "miniKanren", + # vtk is under BSD-3-Clause see https://gitlab.kitware.com/vtk/vtk/-/blob/master/Copyright.txt?ref_type=heads + "vtk", ] -unauthorized_licenses = [ - "gpl v3", - "gpl v2", - "gpl", - "GNU general public license (gpl)", - "IBM Public License", - "RPL", - "Reciprocal Public License", - "Sleepycat License", -] -[tool.liccheck.authorized_packages] -# filelock has public domain license without restrictions -# see https://github.com/tox-dev/py-filelock -filelock = ">=3" -# cons is under LGPL-3 -cons = ">=0.4.5" -# namex is under Apache 2.0 see https://github.com/fchollet/namex?tab=License-1-ov-file -namex = "==0.0.8" -# setuptools is under MIT License -setuptools = ">=79.0.0" +allow-only="MIT;MIT License;MIT-CMU;BSD;BSD License;BSD-2-Clause;BSD-3-Clause;BSD 3-Clause;3-Clause BSD License;BSD-2-Clause AND Apache-2.0 WITH LLVM-exception;BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0;Apache-2.0;Apache License 2.0;Apache Software License;Apache-2.0 OR BSD-3-Clause;Apache-2.0 OR BSD-2-Clause;Apache-2.0 AND CNRI-Python;Apache-2.0 AND MIT;ISC;PSF-2.0;Python Software Foundation License;MPL-2.0;Mozilla Public License 2.0;Mozilla Public License 2.0 (MPL 2.0);MPL-2.0 AND MIT;LGPL;LGPL-2.1;LGPL-3.0;LGPL-3.0-or-later;Zlib;0BSD;CC0-1.0" [tool.mypy] check_untyped_defs = true @@ -290,13 +254,12 @@ myst-parser = ">=5.0.0" testbook = ">=0.4.2" ipykernel = ">=7.2.0" mypy = ">=1.20.1" -pip = ">=26.0.1" +pip-licenses = ">=5.5" [tool.pixi.feature.tutorials.dependencies] scikit-fem = ">=12.0.1" [tool.pixi.feature.fourc.dependencies] -pip = "*" [tool.pixi.environments] queens-base = { features = []} @@ -321,9 +284,10 @@ dev = [ "pylint>=4.0.5", "testbook>=0.4.2", "ipykernel>=7.2.0", "mypy>=1.20.1", - "liccheck>=0.9.2", "pylint-exit>=1.2.0", - "licenseheaders>=0.8.8"] + "licenseheaders>=0.8.8", + "pip-licenses>=5.5", +] [project.optional-dependencies] tutorials =["scikit-fem>=12.0.1"] From baeb0b465b72db0dd2c7a4906f3aa2ffaa96fe38 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 19:11:14 +0200 Subject: [PATCH 028/200] build: add pixi.lock --- .pre-commit-config.yaml | 2 +- pixi.lock | 17092 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 17093 insertions(+), 1 deletion(-) create mode 100644 pixi.lock diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 818b7eb79..4c87e917b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,7 +25,7 @@ repos: entry: check-added-large-files language: python types: [text] - exclude: '^composed\.conda-lock\.yml$' + exclude: '^(composed\.conda-lock\.yml|pixi\.lock)$' - id: check-license-header name: check for correct license header entry: licenseheaders diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 000000000..3257c326d --- /dev/null +++ b/pixi.lock @@ -0,0 +1,17092 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/nodefaults/ + indexes: + - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/_x86_64-microarch-level-1-3_x86_64.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-49.0-unix_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.5-py312h5d8c7f2_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/arviz-0.23.4-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_3.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/autograd-1.8.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.7-ha8fc4e3_5.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-hdaf4b65_5.conda + - conda: 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prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + auth-host: prefix.dev + auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} + environments: queens-dev + frozen: true + activate-environment: queens-dev - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" @@ -34,26 +43,18 @@ jobs: - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build - - name: Create Python environment - id: environment - uses: ./.github/actions/create_python_environment - name: Register Jupyter kernel - env: - PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}} run: | - $PYTHON_PACKAGE_MANAGER activate queens - python -m ipykernel install --user --name queens --display-name "Python (queens)" + python -m ipykernel install --user --name queens --display-name "Python (queens)" - name: Install xvfb run: | apt-get update apt-get install -y xvfb - name: Sphinx build env: - PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}} PYTHONPATH: ${{ github.workspace }} run: | set -euxo pipefail - $PYTHON_PACKAGE_MANAGER activate queens sphinx-apidoc -o doc/source src/ -fMT cd doc xvfb-run -a sphinx-build -b html -d build/doctrees source build/html -W diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 7d5a4a849..0b1145ccf 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -25,6 +25,18 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v5 + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + auth-host: prefix.dev + auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} + environments: >- + queens-base + queens-all + queens-dev + frozen: true + activate-environment: queens-dev - name: Install rsync run: | sudo apt-get update @@ -32,15 +44,11 @@ jobs: - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build - - name: Create Python environment - id: environment - uses: ./.github/actions/create_python_environment - - name: Get Python package manager - run: echo "PYTHON_PACKAGE_MANAGER=${{steps.environment.outputs.ppm}}" >> $GITHUB_ENV + - name: Show resolved pixi environment + run: | + pixi list --locked - name: Code checks run: | - $PYTHON_PACKAGE_MANAGER activate queens - echo "::group::Run isort..." isort --check-only src/* tests echo "::endgroup::" @@ -71,8 +79,7 @@ jobs: # echo "::endgroup::" echo "::group::Check compatibility with licenses of dependencies..." - pip freeze --exclude-editable > python_requirements_for_liccheck.txt - liccheck -r python_requirements_for_liccheck.txt + pip-licenses --python=.pixi/envs/queens-all/bin/python echo "::endgroup::" echo "::group::Create an rc file for the license header check..." @@ -88,12 +95,10 @@ jobs: uses: webiny/action-conventional-commits@v1.3.0 - name: Run pytest run: | - $PYTHON_PACKAGE_MANAGER activate queens pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - name: Run pytest for tutorials run: | - $PYTHON_PACKAGE_MANAGER activate queens pytest -v -m "tutorial_tests" - name: Upload coverage report uses: actions/upload-pages-artifact@v3 From 68f5641391e8bdd7b30fa7cc03f93194e8c2cb4b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 19:16:55 +0200 Subject: [PATCH 030/200] build: add editable install of QUEENS to pixi default feature/ environment --- pixi.lock | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 3 +++ 2 files changed, 69 insertions(+) diff --git a/pixi.lock b/pixi.lock index 3257c326d..e10b6d102 100644 --- a/pixi.lock +++ b/pixi.lock @@ -521,6 +521,7 @@ environments: - pypi: git+https://github.com/nchopin/particles.git#f71e94a21a11c73b58e2d694775b1b1d379b8854 - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ osx-arm64: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda @@ -941,6 +942,7 @@ environments: - pypi: git+https://github.com/nchopin/particles.git#f71e94a21a11c73b58e2d694775b1b1d379b8854 - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ queens-all: channels: - url: https://conda.anaconda.org/conda-forge/ @@ -1475,6 +1477,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/11/0e/a9f6f81013e0deaf559b25711623864970fe6a098314e374ccb1540a4152/regex-2026.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ osx-arm64: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda @@ -1905,6 +1908,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/62/c8/3baa06d75c98c46d4cc4262b71fd2edb9062b5665e868bca57859dadf93a/regex-2026.4.4-cp312-cp312-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ queens-base: channels: - url: https://conda.anaconda.org/conda-forge/ @@ -2426,6 +2430,7 @@ environments: - pypi: git+https://github.com/nchopin/particles.git#f71e94a21a11c73b58e2d694775b1b1d379b8854 - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ osx-arm64: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda @@ -2846,6 +2851,7 @@ environments: - pypi: git+https://github.com/nchopin/particles.git#f71e94a21a11c73b58e2d694775b1b1d379b8854 - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ queens-dev: channels: - url: https://conda.anaconda.org/conda-forge/ @@ -3476,6 +3482,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/11/0e/a9f6f81013e0deaf559b25711623864970fe6a098314e374ccb1540a4152/regex-2026.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ osx-arm64: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda @@ -4005,6 +4012,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/62/c8/3baa06d75c98c46d4cc4262b71fd2edb9062b5665e868bca57859dadf93a/regex-2026.4.4-cp312-cp312-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/fe/b6/e116761ceeb880b7ad4c6a7e1203538754dd7dda42538f08d6daaf8dfa4d/tensorflow_probability-0.25.0-py2.py3-none-any.whl + - pypi: ./ packages: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda build_number: 7 @@ -14547,6 +14555,64 @@ packages: purls: [] size: 45982348 timestamp: 1759266212707 +- pypi: ./ + name: queens + version: '1.1' + sha256: 7dea89b0168cdbdd1cf70f2f4dff09d3707423c52cc03ec73a13d01b1c06f1c0 + requires_dist: + - setuptools>=81.0.0,<82 + - cython>=3.2.4 + - numba>=0.65.0 + - numpy>=2.4.3 + - pandas>=3.0.2 + - scikit-learn>=1.8.0 + - scipy>=1.17.1 + - dask>=2026.3.0 + - distributed>=2026.3.0 + - dask-jobqueue>=0.9.0 + - bokeh>=3.9.0 + - fabric>=3.2.3 + - xarray>=2026.4.0 + - pydoe>=0.9.9 + - salib>=1.5.2 + - vtk>=9.5.0 + - pyvista>=0.47.3 + - autograd>=1.8.0 + - chaospy>=4.3.20 + - pyyaml>=6.0.3 + - jinja2>=3.1.6 + - arviz>=0.23.4,<1 + - gpflow + - optax>=0.2.8 + - tensorflow>=2.18.0 + - tensorflow-probability>=0.25.0 + - tf-keras>=2.18.0 + - jax>=0.5.2 + - pymc>=5.28.4 + - stable-baselines3>=2.8.0 + - matplotlib>=3.10.8 + - seaborn>=0.13.2 + - plotly>=6.6.0 + - pytest>=9.0.3 + - py>=1.11.0 + - pytest-codestyle>=2.0.1 + - pytest-cov>=7.1.0 + - pytest-mock>=3.15.1 + - pytest-xdist>=3.8.0 + - mock>=5.2.0 + - tqdm>=4.67.3 + - tomli>=2.4.1 + - pathos>=0.3.5 + - black>=26.3.1 + - gnuplotlib>=0.46 + - diversipy>=0.9 + - particles @ git+https://github.com/nchopin/particles.git + - scikit-activeml>=1.0.0 + - scikit-fem>=12.0.1 ; extra == 'tutorials' + - fourcipp>=1.91.0 ; extra == 'fourc' + - queens[fourc] ; extra == 'all' + - queens[tutorials] ; extra == 'all' + requires_python: '>=3.12' - conda: https://conda.anaconda.org/conda-forge/noarch/questionary-2.1.1-pyhd8ed1ab_0.conda sha256: 0604c6dff3af5f53e34fceb985395d08287137f220450108a795bcd1959caf14 md5: 34fa231b5c5927684b03bb296bb94ddc diff --git a/pyproject.toml b/pyproject.toml index 66c98d7d6..e1132f7b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -236,6 +236,9 @@ pathos = ">=0.3.5" black = ">=26.3.1" pip = ">=26.0.1" +[tool.pixi.pypi-dependencies] +queens = { path = ".", editable = true } + [tool.pixi.feature.dev.dependencies] pylint = ">=4.0.5" isort = ">=8.0.1" From 97e80b4eb458caf14a6240c7716b75e13261f6d4 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 19:48:22 +0200 Subject: [PATCH 031/200] ci: pixi list is called after install anyway --- .github/workflows/tests_local.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 0b1145ccf..f4ff702a3 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -44,9 +44,6 @@ jobs: - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build - - name: Show resolved pixi environment - run: | - pixi list --locked - name: Code checks run: | echo "::group::Run isort..." From df13f3eae3156a239f0c2b65cd251b3de89fbe64 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 20:15:17 +0200 Subject: [PATCH 032/200] build: fix black python version warning --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index e1132f7b0..561924646 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -96,6 +96,7 @@ Changelog = "https://github.com/queens-py/queens/blob/main/CHANGELOG.md" # Tools section [tool.black] line-length = 100 +target-version = ["py312"] [tool.isort] profile = "black" From 8cf1b5df521383870142495cc6a8d7b9649f44be Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 20:15:30 +0200 Subject: [PATCH 033/200] ci: ensure that pipline fails if one code check fails set -euo pipefail is a Bash shell option line. It changes how the shell handles errors inside a multi-line script block. What each part does: -e: exit immediately if a command returns non-zero -u: treat unset variables as errors -o pipefail: if any command in a pipeline fails, the pipeline fails --- .github/workflows/tests_local.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index f4ff702a3..8d14913bf 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -46,6 +46,8 @@ jobs: ln -s /home/user/4C/bin/ config/4C_build - name: Code checks run: | + set -euo pipefail + echo "::group::Run isort..." isort --check-only src/* tests echo "::endgroup::" @@ -92,10 +94,14 @@ jobs: uses: webiny/action-conventional-commits@v1.3.0 - name: Run pytest run: | + set -euo pipefail + pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - name: Run pytest for tutorials run: | + set -euo pipefail + pytest -v -m "tutorial_tests" - name: Upload coverage report uses: actions/upload-pages-artifact@v3 From 3b4b8d2bd7bf42e1539d1c6888256f3f062c1b15 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 20:34:36 +0200 Subject: [PATCH 034/200] ci: deactivate caching --- .github/workflows/build_documentation.yml | 2 +- .github/workflows/tests_local.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index ca8e4a563..72ec7c854 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -27,7 +27,7 @@ jobs: - uses: prefix-dev/setup-pixi@v0.9.4 with: pixi-version: v0.67.0 - cache: true + #cache: true auth-host: prefix.dev auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} environments: queens-dev diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 8d14913bf..0dff037f4 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -28,7 +28,7 @@ jobs: - uses: prefix-dev/setup-pixi@v0.9.4 with: pixi-version: v0.67.0 - cache: true + #cache: true auth-host: prefix.dev auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} environments: >- From 2ca19cdb637cf28d8606a50ec51aeec3919b57c0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 20:46:50 +0200 Subject: [PATCH 035/200] ci: skip .pixi path for nbstripout --- .github/workflows/tests_local.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 0dff037f4..90fee5b1d 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -69,7 +69,8 @@ jobs: echo "::endgroup::" echo "::group::Run nbstripout..." - find . -name '*.ipynb' -exec nbstripout --verify {} + + find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + + echo "::endgroup::" # echo "::group::Create code quality report..." From abf5121e15b3cbca8898ffde9f9e7f167f31248f Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 21:18:27 +0200 Subject: [PATCH 036/200] build: add license exception for torch --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 561924646..90858ff5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -162,6 +162,8 @@ ignore-packages = [ "miniKanren", # vtk is under BSD-3-Clause see https://gitlab.kitware.com/vtk/vtk/-/blob/master/Copyright.txt?ref_type=heads "vtk", + # torch is under BSD-3-Clause + "torch", ] allow-only="MIT;MIT License;MIT-CMU;BSD;BSD License;BSD-2-Clause;BSD-3-Clause;BSD 3-Clause;3-Clause BSD License;BSD-2-Clause AND Apache-2.0 WITH LLVM-exception;BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0;Apache-2.0;Apache License 2.0;Apache Software License;Apache-2.0 OR BSD-3-Clause;Apache-2.0 OR BSD-2-Clause;Apache-2.0 AND CNRI-Python;Apache-2.0 AND MIT;ISC;PSF-2.0;Python Software Foundation License;MPL-2.0;Mozilla Public License 2.0;Mozilla Public License 2.0 (MPL 2.0);MPL-2.0 AND MIT;LGPL;LGPL-2.1;LGPL-3.0;LGPL-3.0-or-later;Zlib;0BSD;CC0-1.0" From d2d5b68c824e471aa6a27a6c7b2cab43a15d8111 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 21:25:08 +0200 Subject: [PATCH 037/200] feat: rework remote env build and remote tests with using pixi --- .gitlab/.gitlab-ci.yml | 145 +++++++++++--------------- src/queens/utils/remote_build.py | 26 +---- src/queens/utils/remote_operations.py | 85 ++++----------- 3 files changed, 86 insertions(+), 170 deletions(-) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index c921f8648..4f572c0d1 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -8,21 +8,26 @@ variables: IMCS_TESTS: value: "1" description: "Run cluster tests at IMCS" + REMOTE_BUILD_DIR: + value: "/home/queens/builds/queens-$CI_PIPELINE_ID" LNM_REMOTE_PYTHON: - value: "/home/queens/miniforge3/envs/queens-$CI_PIPELINE_ID/bin/python" + value: "$REMOTE_BUILD_DIR/.pixi/envs/queens-dev/bin/python" description: "Python path on LNM clusters" LNM_REMOTE_ADDRESS: value: "thought" description: "Hostname of LNM cluster" IMCS_REMOTE_PYTHON: - value: "/home/queens/miniforge3/envs/queens-$CI_PIPELINE_ID/bin/python" + value: "$REMOTE_BUILD_DIR/.pixi/envs/queens-dev/bin/python" description: "Python path on IMCS clusters" IMCS_REMOTE_ADDRESS: value: "charon.bauv.unibw-muenchen.de" description: "Hostname of IMCS cluster" - PYTHON_PACKAGE_MANAGER: - value: "mamba" - description: "Python package manager to create the python environments" + PIXI_VERSION: + value: "v0.67.0" + description: "Pinned pixi version used by the CI pipeline" + PIXI_ENVIRONMENT: + value: "queens-dev" + description: "Pixi workspace environment used in CI jobs" #--------------------------------------------------------------------------------------------------- # Define stages #--------------------------------------------------------------------------------------------------- @@ -42,63 +47,66 @@ workflow: #--------------------------------------------------------------------------------------------------- # Define platform specific settings #--------------------------------------------------------------------------------------------------- -.ubuntu_settings: +.check_pixi_available: before_script: - - $PYTHON_PACKAGE_MANAGER activate queens-$CI_PIPELINE_ID - # This ensures that the correct queens source is used - - pip install --no-deps -e . - - echo Queens source for testing is $(pip list | grep -o '/.*') + - | + export PATH="$HOME/.pixi/bin:$PATH" + if ! command -v pixi >/dev/null 2>&1; then + curl -fsSL https://pixi.sh/install.sh | PIXI_VERSION="$PIXI_VERSION" PIXI_HOME="$HOME/.pixi" bash + fi + pixi --version #--------------------------------------------------------------------------------------------------- # Jobs of stage: build #--------------------------------------------------------------------------------------------------- -.build_conda_env: +.build_pixi_env: + extends: + - .check_pixi_available stage: build - before_script: - - 'echo "Using python environment manager: `$PYTHON_PACKAGE_MANAGER --version`"' script: - - $PYTHON_PACKAGE_MANAGER install -n base -c conda-forge conda-lock -y - - conda-lock install -n queens-$CI_PIPELINE_ID composed.conda-lock.yml - - $PYTHON_PACKAGE_MANAGER activate queens-$CI_PIPELINE_ID - - pip install --no-deps -e . - - $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml + - pixi install --frozen -e "$PIXI_ENVIRONMENT" + - pixi list --frozen -e "$PIXI_ENVIRONMENT" > pipeline_pixi_environment.txt artifacts: - name: "conda_env-$CI_PIPELINE_ID.yml" + name: "pixi_env-$CI_PIPELINE_ID.txt" paths: - - pipeline_conda_environment.yml + - pipeline_pixi_environment.txt when: always expire_in: 4 weeks -lnm-build_conda_env: +lnm-build_pixi_env: extends: - - .build_conda_env + - .build_pixi_env tags: - lnm-build rules: - if: $LNM_TESTS == "1" -imcs-build_conda_env: +imcs-build_pixi_env: extends: - - .build_conda_env + - .build_pixi_env tags: - imcs-build rules: - if: $IMCS_TESTS == "1" #---------------------------------------------------------------------------------------------- -.build_conda_env_cluster: +.build_pixi_env_cluster: stage: build script: - - ENV_PREFIX=queens-$CI_PIPELINE_ID - - $PYTHON_PACKAGE_MANAGER create -y --prefix ./$ENV_PREFIX python=3.11 cloudpickle fabric - - $PYTHON_PACKAGE_MANAGER activate ./$ENV_PREFIX - - pip install --no-deps -e . - - python src/queens/utils/remote_build.py - --host=$REMOTE_ADDRESS --user=queens --remote-python=$REMOTE_PYTHON - --remote-queens-repository=/home/queens/builds/queens-$CI_PIPELINE_ID --package-manager - $PYTHON_PACKAGE_MANAGER --use-conda-lock + - | + ssh queens@$REMOTE_ADDRESS "bash -lc ' + export PATH=\"\$HOME/.pixi/bin:\$PATH\" + if ! command -v pixi >/dev/null 2>&1; then + curl -fsSL https://pixi.sh/install.sh | PIXI_VERSION=\"$PIXI_VERSION\" PIXI_HOME=\"\$HOME/.pixi\" bash + fi + pixi --version + '" + - pixi run --frozen -e "$PIXI_ENVIRONMENT" python src/queens/utils/remote_build.py + --host=$REMOTE_ADDRESS --user=queens + --remote-queens-repository=$REMOTE_BUILD_DIR + --pixi-environment=$PIXI_ENVIRONMENT -thought-build_conda_env: +thought-build_pixi_env: extends: - - .build_conda_env_cluster + - .build_pixi_env_cluster variables: REMOTE_ADDRESS: $LNM_REMOTE_ADDRESS REMOTE_PYTHON: $LNM_REMOTE_PYTHON @@ -107,9 +115,9 @@ thought-build_conda_env: rules: - if: $LNM_TESTS == "1" -charon-build_conda_env: +charon-build_pixi_env: extends: - - .build_conda_env_cluster + - .build_pixi_env_cluster variables: REMOTE_ADDRESS: $IMCS_REMOTE_ADDRESS REMOTE_PYTHON: $IMCS_REMOTE_PYTHON @@ -177,14 +185,14 @@ charon-build_4C: #--------------------------------------------------------------------------------------------------- .cluster_tests: extends: - - .ubuntu_settings + - .check_pixi_available stage: tests script: - - pytest tests/integration_tests/cluster/ + - pixi run --locked -e "$PIXI_ENVIRONMENT" pytest tests/integration_tests/cluster/ -v -m $CLUSTER_MARKER --no-cov -o log_cli=true --log-cli-level=DEBUG --remote-user=queens --remote-python=$REMOTE_PYTHON - --remote-queens-repository=/home/queens/builds/queens-$CI_PIPELINE_ID + --remote-queens-repository=$REMOTE_BUILD_DIR --color=yes --pipeline-id=$CI_PIPELINE_ID --junitxml=test_junit.xml @@ -204,8 +212,8 @@ lnm-cluster_tests: CLUSTER_MARKER: "lnm_cluster" REMOTE_PYTHON: $LNM_REMOTE_PYTHON needs: - - lnm-build_conda_env - - thought-build_conda_env + - lnm-build_pixi_env + - thought-build_pixi_env - thought-build_4C tags: - lnm-ubuntu @@ -219,8 +227,8 @@ imcs-cluster_tests: CLUSTER_MARKER: "imcs_cluster" REMOTE_PYTHON: $IMCS_REMOTE_PYTHON needs: - - imcs-build_conda_env - - charon-build_conda_env + - imcs-build_pixi_env + - charon-build_pixi_env - charon-build_4C tags: - imcs-ubuntu @@ -230,49 +238,18 @@ imcs-cluster_tests: #--------------------------------------------------------------------------------------------------- # Jobs of stage: cleanup #--------------------------------------------------------------------------------------------------- -# Remove conda env on ubuntu runners -.remove_conda_env: - stage: cleanup - script: - - $PYTHON_PACKAGE_MANAGER env remove -n queens-$CI_PIPELINE_ID - when: always - variables: - GIT_STRATEGY: none - -lnm-remove_conda_env: - extends: - - .remove_conda_env - dependencies: - - lnm-build_conda_env - tags: - - lnm-build - rules: - - if: $LNM_TESTS == "1" - -imcs-remove_conda_env: - extends: - - .remove_conda_env - dependencies: - - imcs-build_conda_env - tags: - - imcs-build - rules: - - if: $IMCS_TESTS == "1" - -#--------------------------------------------------------------------------------------------------- -# Remove conda env and repository on cluster -.remove_conda_env_cluster: +# Remove pixi environment and repository on cluster +.remove_build_dir_cluster: stage: cleanup script: - - ssh queens@$REMOTE_ADDRESS "$PYTHON_PACKAGE_MANAGER env remove -n queens-$CI_PIPELINE_ID; - rm -rf /home/queens/builds/queens-$CI_PIPELINE_ID" + - ssh queens@$REMOTE_ADDRESS "rm -rf $REMOTE_BUILD_DIR;" when: always -thought-cluster-remove_conda_env: +thought-cluster-remove_build_dir: extends: - - .remove_conda_env_cluster + - .remove_build_dir_cluster dependencies: - - thought-build_conda_env + - thought-build_pixi_env variables: REMOTE_ADDRESS: $LNM_REMOTE_ADDRESS tags: @@ -280,11 +257,11 @@ thought-cluster-remove_conda_env: rules: - if: $LNM_TESTS == "1" -charon-cluster-remove_conda_env: +charon-cluster-remove_build_dir: extends: - - .remove_conda_env_cluster + - .remove_build_dir_cluster dependencies: - - charon-build_conda_env + - charon-build_pixi_env variables: REMOTE_ADDRESS: $IMCS_REMOTE_ADDRESS tags: diff --git a/src/queens/utils/remote_build.py b/src/queens/utils/remote_build.py index a8bd84e1b..ae42f8170 100644 --- a/src/queens/utils/remote_build.py +++ b/src/queens/utils/remote_build.py @@ -20,20 +20,12 @@ from queens.utils.remote_operations import RemoteConnection -DEFAULT_PACKAGE_MANAGER = "mamba" -FALLBACK_PACKAGE_MANAGER = "conda" -SUPPORTED_PACKAGE_MANAGERS = [DEFAULT_PACKAGE_MANAGER, FALLBACK_PACKAGE_MANAGER] - - if __name__ == "__main__": parser = argparse.ArgumentParser(description="Build queens environment on remote machine.") parser.add_argument( "--host", type=str, required=True, help="hostname or ip address of remote host" ) parser.add_argument("--user", type=str, default=None, required=False, help="remote username") - parser.add_argument( - "--remote-python", type=str, required=True, help="path to python environment on remote host" - ) parser.add_argument( "--remote-queens-repository", type=str, @@ -51,16 +43,10 @@ ), ) parser.add_argument( - "--package-manager", + "--pixi-environment", type=str, - default=DEFAULT_PACKAGE_MANAGER, - choices=SUPPORTED_PACKAGE_MANAGERS, - help="package manager used for the creation of the remote environment", - ) - parser.add_argument( - "--use-conda-lock", - action="store_true", - help="install the remote environment from composed.conda-lock.yml", + default="queens-all", + help="pixi workspace environment to install on the remote host", ) args = parser.parse_args(sys.argv[1:]) @@ -68,12 +54,10 @@ remote_connection = RemoteConnection( host=args.host, user=args.user, - remote_python=args.remote_python, + remote_python="", remote_queens_repository=args.remote_queens_repository, gateway=args.gateway if args.gateway is None else json.loads(args.gateway), ) remote_connection.open() remote_connection.sync_remote_repository() - remote_connection.build_remote_environment( - package_manager=args.package_manager, use_conda_lock=args.use_conda_lock - ) + remote_connection.build_remote_environment(pixi_environment=args.pixi_environment) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 3ea40e1d2..6c8639c93 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -35,10 +35,6 @@ _logger = logging.getLogger(__name__) -DEFAULT_PACKAGE_MANAGER = "mamba" -FALLBACK_PACKAGE_MANAGER = "conda" -SUPPORTED_PACKAGE_MANAGERS = [DEFAULT_PACKAGE_MANAGER, FALLBACK_PACKAGE_MANAGER] - class RemoteConnection(Connection): """This is class wrapper around the Connection class of fabric. @@ -334,75 +330,34 @@ def copy_from_remote( def build_remote_environment( self, - package_manager: str = DEFAULT_PACKAGE_MANAGER, - use_conda_lock: bool = False, + pixi_environment: str = "queens-all", ) -> None: - """Build remote QUEENS environment. + """Build the remote QUEENS pixi environment. Args: - package_manager: Package manager used for the creation of the environment ("mamba" or - "conda") - use_conda_lock: Install the environment from composed.conda-lock.yml instead of the - layered environment files + pixi_environment: Pixi workspace environment to install on the remote host """ - if package_manager not in SUPPORTED_PACKAGE_MANAGERS: - raise ValueError( - f"The package manager '{package_manager}' is not supported.\n" - f"Supported package managers are: {SUPPORTED_PACKAGE_MANAGERS}" - ) remote_connect = f"{self.user}@{self.host}" - - # check if requested package_manager is installed on remote machine: - def package_manager_exists_remote(package_manager_name: str) -> bool: - """Check if requested package manager exists on remote. - - Args: - package_manager_name: name of package manager - """ - result_which = self.run(f"which {package_manager_name}") - if result_which.stderr: - message = ( - f"Could not find requested package manager '{package_manager_name}' " - f"on '{remote_connect}'." - ) - if package_manager_name == DEFAULT_PACKAGE_MANAGER: - _logger.warning(message) - _logger.warning( - "Trying to fall back to the '%s' package manager.", FALLBACK_PACKAGE_MANAGER - ) - package_manager_exists_remote(package_manager_name=FALLBACK_PACKAGE_MANAGER) - else: - raise RuntimeError(message) - return False - return True - - if not package_manager_exists_remote(package_manager_name=package_manager): - package_manager = FALLBACK_PACKAGE_MANAGER + result_which = self.run("which pixi", warn=True, in_stream=False) + if not result_which.ok: + _logger.warning( + "Could not find 'pixi' on '%s'. " + "The remote environment was not built automatically.", + remote_connect, + ) + _logger.warning( + "Either install pixi or install the Python environment manually on the remote host." + "See the README.md for environment setup details." + ) + return _logger.info("Build remote QUEENS environment...") start_time = time.time() - environment_name = Path(self.remote_python).parents[1].name - if use_conda_lock: - command_string = ( - f"cd {self.remote_queens_repository}; " - f"{package_manager} install -n base -c conda-forge conda-lock -y;" - f"{package_manager} remove --name {environment_name} --all -y;" - f"conda-lock install -n {environment_name} composed.conda-lock.yml; " - f"{package_manager} activate {environment_name};" - f"pip install --no-deps -e ." - ) - else: - command_string = ( - f"cd {self.remote_queens_repository}; " - f"{package_manager} remove --name {environment_name} --all -y;" - f"{package_manager} env create -f environment.base.yml --name {environment_name}; " - f"{package_manager} env update -f environment.dev.yml --name {environment_name}; " - f"{package_manager} env update -f environment.tutorials.yml" - f"--name {environment_name}; " - f"{package_manager} env update -f environment.fourc.yml --name {environment_name}; " - f"{package_manager} activate {environment_name};" - f"pip install --no-deps -e ." - ) + command_string = ( + f"cd {self.remote_queens_repository}; " + f"rm -rf .pixi/envs/{pixi_environment}; " + f"pixi install --frozen --environment {pixi_environment}; " + ) result = self.run(command_string, in_stream=False) _logger.debug(result.stdout) From e436d4f8ab2f03a98540ffd3dd43fb62fb7204cd Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 21:35:44 +0200 Subject: [PATCH 038/200] build: add license exception for PySide6 --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 90858ff5b..6e75b3da9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -164,6 +164,8 @@ ignore-packages = [ "vtk", # torch is under BSD-3-Clause "torch", + # PySide6 is under (LGPLv3 or GPLv2 or GPLv3) see https://code.qt.io/cgit/pyside/pyside-setup.git/tree/README.pyside6.md + "PySide6", ] allow-only="MIT;MIT License;MIT-CMU;BSD;BSD License;BSD-2-Clause;BSD-3-Clause;BSD 3-Clause;3-Clause BSD License;BSD-2-Clause AND Apache-2.0 WITH LLVM-exception;BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0;Apache-2.0;Apache License 2.0;Apache Software License;Apache-2.0 OR BSD-3-Clause;Apache-2.0 OR BSD-2-Clause;Apache-2.0 AND CNRI-Python;Apache-2.0 AND MIT;ISC;PSF-2.0;Python Software Foundation License;MPL-2.0;Mozilla Public License 2.0;Mozilla Public License 2.0 (MPL 2.0);MPL-2.0 AND MIT;LGPL;LGPL-2.1;LGPL-3.0;LGPL-3.0-or-later;Zlib;0BSD;CC0-1.0" From 36c95fe20511bdbf345d36cdf7f2871adf7eefdd Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 21:39:16 +0200 Subject: [PATCH 039/200] feat: format warning --- src/queens/utils/remote_operations.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 6c8639c93..8b069a9c7 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -341,14 +341,12 @@ def build_remote_environment( result_which = self.run("which pixi", warn=True, in_stream=False) if not result_which.ok: _logger.warning( - "Could not find 'pixi' on '%s'. " - "The remote environment was not built automatically.", + "\nCould not find 'pixi' on '%s'. " + "The remote environment was not built automatically.\n" + "Either install pixi and retry or install the Python environment manually on " + "the remote host. See the README.md for environment setup details.\n", remote_connect, ) - _logger.warning( - "Either install pixi or install the Python environment manually on the remote host." - "See the README.md for environment setup details." - ) return _logger.info("Build remote QUEENS environment...") From 62d8beffcb987d11c30b9eaf687454658d847a96 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 21:52:56 +0200 Subject: [PATCH 040/200] feat: fix checking pixi availability --- src/queens/utils/remote_operations.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 8b069a9c7..c1465c099 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -339,7 +339,9 @@ def build_remote_environment( """ remote_connect = f"{self.user}@{self.host}" result_which = self.run("which pixi", warn=True, in_stream=False) - if not result_which.ok: + _logger.debug(result_which.stdout) + if result_which.exited: + _logger.debug(result_which.stderr) _logger.warning( "\nCould not find 'pixi' on '%s'. " "The remote environment was not built automatically.\n" From 1165f389bded2264e788f583eb31622948c9a4ef Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 22:25:50 +0200 Subject: [PATCH 041/200] feat: fix checking pixi availabnility without warning --- src/queens/utils/remote_operations.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index c1465c099..3303280af 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -338,10 +338,14 @@ def build_remote_environment( pixi_environment: Pixi workspace environment to install on the remote host """ remote_connect = f"{self.user}@{self.host}" - result_which = self.run("which pixi", warn=True, in_stream=False) - _logger.debug(result_which.stdout) + _logger.info("Check availability of pixi on %s...", remote_connect) + result_which = self.run( + "bash -lc 'export PATH=\"$HOME/.pixi/bin:$PATH\"; command -v pixi'", + warn=True, + echo=True, + in_stream=False, + ) if result_which.exited: - _logger.debug(result_which.stderr) _logger.warning( "\nCould not find 'pixi' on '%s'. " "The remote environment was not built automatically.\n" @@ -354,11 +358,12 @@ def build_remote_environment( _logger.info("Build remote QUEENS environment...") start_time = time.time() command_string = ( - f"cd {self.remote_queens_repository}; " + 'bash -lc \'export PATH="$HOME/.pixi/bin:$PATH";' + f" cd {self.remote_queens_repository}; " f"rm -rf .pixi/envs/{pixi_environment}; " - f"pixi install --frozen --environment {pixi_environment}; " + f"pixi install --frozen --environment {pixi_environment};'" ) - result = self.run(command_string, in_stream=False) + result = self.run(command_string, echo=True, in_stream=False) _logger.debug(result.stdout) _logger.info("Build of remote queens environment was successful.") From 4b88697805265bb7e2c8bae03e666af1cda5bcc0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 17 Apr 2026 22:26:39 +0200 Subject: [PATCH 042/200] build: add license exception for shiboken6 --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 6e75b3da9..fd4304b16 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -166,6 +166,8 @@ ignore-packages = [ "torch", # PySide6 is under (LGPLv3 or GPLv2 or GPLv3) see https://code.qt.io/cgit/pyside/pyside-setup.git/tree/README.pyside6.md "PySide6", + # shiboken6 is under (LGPLv3 or GPLv2 or GPLv3) see https://code.qt.io/cgit/pyside/pyside-setup.git/tree/README.pyside6.md + "shiboken6", ] allow-only="MIT;MIT License;MIT-CMU;BSD;BSD License;BSD-2-Clause;BSD-3-Clause;BSD 3-Clause;3-Clause BSD License;BSD-2-Clause AND Apache-2.0 WITH LLVM-exception;BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0;Apache-2.0;Apache License 2.0;Apache Software License;Apache-2.0 OR BSD-3-Clause;Apache-2.0 OR BSD-2-Clause;Apache-2.0 AND CNRI-Python;Apache-2.0 AND MIT;ISC;PSF-2.0;Python Software Foundation License;MPL-2.0;Mozilla Public License 2.0;Mozilla Public License 2.0 (MPL 2.0);MPL-2.0 AND MIT;LGPL;LGPL-2.1;LGPL-3.0;LGPL-3.0-or-later;Zlib;0BSD;CC0-1.0" From ab985db53ee554db8723217a3cfd6ada434a6627 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 18 Apr 2026 13:49:23 +0200 Subject: [PATCH 043/200] feat: check integrity of dependencies in pyproject --- .pre-commit-config.yaml | 6 + .../check_pyproject_dependency_integrity.py | 336 ++++++++++++++++++ 2 files changed, 342 insertions(+) create mode 100644 tools/dependencies/check_pyproject_dependency_integrity.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4c87e917b..bb4e8bb64 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,6 +33,12 @@ repos: language: python types: ["python"] pass_filenames: true + - id: check-pyproject-dependency-integrity + name: check pyproject dependency integrity + entry: python3 tools/dependencies/check_pyproject_dependency_integrity.py --path + language: system + files: '^pyproject\.toml$' + pass_filenames: true - id: docformatter name: docformatter entry: docformatter diff --git a/tools/dependencies/check_pyproject_dependency_integrity.py b/tools/dependencies/check_pyproject_dependency_integrity.py new file mode 100644 index 000000000..c8108ed48 --- /dev/null +++ b/tools/dependencies/check_pyproject_dependency_integrity.py @@ -0,0 +1,336 @@ +#!/usr/bin/env python3 +# +# SPDX-License-Identifier: LGPL-3.0-or-later +# Copyright (c) 2024-2025, QUEENS contributors. +# +# This file is part of QUEENS. +# +# QUEENS is free software: you can redistribute it and/or modify it under the terms of the GNU +# Lesser General Public License as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. QUEENS is distributed in the hope that it will +# be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You +# should have received a copy of the GNU Lesser General Public License along with QUEENS. If not, +# see . +# +"""Check consistency between PEP-style and pixi dependency declarations.""" + +import argparse +import difflib +import re +import sys +import tomllib +from pathlib import Path +from typing import Any + +META_EXTRA_PATTERN = re.compile(r"^queens\[(?P[A-Za-z0-9_.-]+)\]$") +PACKAGE_NAME_PATTERN = re.compile(r"^\s*([A-Za-z0-9_.-]+)") + + +def _load_pyproject(path: str) -> dict[str, Any]: + """Load pyproject.toml.""" + with Path(path).open("rb") as file: + return tomllib.load(file) + + +def _pixi_dependency_to_pep(name: str, spec: Any) -> str: + """Convert a pixi dependency entry to a PEP-style requirement string.""" + if isinstance(spec, str): + return name if spec in {"", "*"} else f"{name}{spec}" + + if isinstance(spec, dict): + if "git" in spec: + git_url = spec["git"] + if not str(git_url).startswith("git+"): + git_url = f"git+{git_url}" + return f"{name} @ {git_url}" + if "version" in spec: + version_spec = spec["version"] + return name if version_spec in {"", "*"} else f"{name}{version_spec}" + if "path" in spec: + editable = bool(spec.get("editable", False)) + if editable: + return f"{name} @ editable:{spec['path']}" + return f"{name} @ path:{spec['path']}" + + raise ValueError(f"Unsupported pixi dependency format for '{name}': {spec!r}") + + +def _combine_pixi_dependencies( + dependencies: dict[str, Any] | None, pypi_dependencies: dict[str, Any] | None +) -> list[tuple[str, Any]]: + """Combine conda and PyPI pixi dependencies (preserve order).""" + combined: list[tuple[str, Any]] = [] + if dependencies: + combined.extend(dependencies.items()) + if pypi_dependencies: + combined.extend(pypi_dependencies.items()) + return combined + + +def _diff_lines(expected: list[str], actual: list[str], name: str) -> str: + """Create a readable unified diff for two lists.""" + return "\n".join( + difflib.unified_diff( + expected, + actual, + fromfile=f"{name} (PEP)", + tofile=f"{name} (pixi)", + lineterm="", + ) + ) + + +def _extract_requirement_name(requirement: str) -> str: + """Extract the package name from a requirement string.""" + match = PACKAGE_NAME_PATTERN.match(requirement) + if match is None: + raise ValueError(f"Could not extract package name from requirement {requirement!r}") + return match.group(1) + + +def _compare_dependency_lists( + name: str, + pep_dependencies: list[str], + pixi_dependencies: list[tuple[str, Any]], + allowed_version_mismatches: set[str] | None = None, +) -> list[str]: + """Compare PEP dependency list to pixi dependency list.""" + allowed_version_mismatches = allowed_version_mismatches or set() + actual = [ + _pixi_dependency_to_pep(dep_name, dep_spec) for dep_name, dep_spec in pixi_dependencies + ] + + if len(pep_dependencies) != len(actual): + return [f"Dependency mismatch for '{name}':\n{_diff_lines(pep_dependencies, actual, name)}"] + + for index, (pep_requirement, pixi_requirement) in enumerate( + zip(pep_dependencies, actual, strict=True) + ): + pep_name = _extract_requirement_name(pep_requirement) + pixi_name = _extract_requirement_name(pixi_requirement) + if pep_name != pixi_name: + return [ + f"Dependency order/name mismatch for '{name}' at position {index}: " + f"{pep_name!r} != {pixi_name!r}\n{_diff_lines(pep_dependencies, actual, name)}" + ] + if pep_requirement != pixi_requirement and pep_name not in allowed_version_mismatches: + return [ + f"Dependency mismatch for '{name}':\n{_diff_lines(pep_dependencies, actual, name)}" + ] + + return [] + + +def _validate_base_dependencies( + pyproject: dict[str, Any], allowed_version_mismatches: set[str] | None = None +) -> list[str]: + """Validate matching base dependencies between PEP and pixi.""" + error_messages: list[str] = [] + + project = pyproject.get("project", {}) + tool_pixi = pyproject.get("tool", {}).get("pixi", {}) + pixi_dependencies = tool_pixi.get("dependencies", {}) + pixi_pypi_dependencies = tool_pixi.get("pypi-dependencies", {}) + + ordered_conda = list(pixi_dependencies.items()) + + if not ordered_conda: + return ["[tool.pixi.dependencies] is empty; expected at least python and pip."] + + if ordered_conda[0][0] != "python": + error_messages.append("The first entry in [tool.pixi.dependencies] must be 'python'.") + else: + requires_python = project.get("requires-python") + if ordered_conda[0][1] != requires_python: + error_messages.append( + "Mismatch between project.requires-python and tool.pixi.dependencies.python: " + f"{requires_python!r} != {ordered_conda[0][1]!r}" + ) + + if len(ordered_conda) < 2 or ordered_conda[1][0] != "pip": + error_messages.append("The second entry in [tool.pixi.dependencies] must be 'pip'.") + + combined = _combine_pixi_dependencies(pixi_dependencies, pixi_pypi_dependencies) + if not combined: + return error_messages + + if combined[-1][0] != "queens": + error_messages.append( + "The last combined pixi dependency entry must be the local editable 'queens' package." + ) + else: + queens_spec = combined[-1][1] + if not ( + isinstance(queens_spec, dict) + and queens_spec.get("path") == "." + and queens_spec.get("editable") is True + ): + error_messages.append( + "The final 'queens' pixi dependency must be declared as " + "{ path = '.', editable = true }." + ) + + stripped_combined = [ + (name, spec) for name, spec in combined if name not in {"python", "pip", "queens"} + ] + pep_dependencies = project.get("dependencies", []) + error_messages.extend( + _compare_dependency_lists( + "project.dependencies", + pep_dependencies, + stripped_combined, + allowed_version_mismatches, + ) + ) + + return error_messages + + +def _is_meta_optional_dependency(requirements: list[str]) -> bool: + """Return whether an optional dependency group is a composed meta-extra.""" + return bool(requirements) and all( + META_EXTRA_PATTERN.fullmatch(requirement) for requirement in requirements + ) + + +def _validate_meta_optional_dependency( + name: str, + requirements: list[str], + optional_dependencies: dict[str, list[str]], + pixi_features: dict[str, Any], +) -> list[str]: + """Validate a composed optional dependency such as 'all'.""" + error_messages: list[str] = [] + referenced_extras = [ + match.group("extra") + for requirement in requirements + if (match := META_EXTRA_PATTERN.fullmatch(requirement)) + ] + + for referenced_extra in referenced_extras: + if referenced_extra not in optional_dependencies: + error_messages.append( + f"Meta optional dependency '{name}' references unknown extra '{referenced_extra}'." + ) + if referenced_extra not in pixi_features: + error_messages.append( + f"Meta optional dependency '{name}' references '{referenced_extra}', but no " + f"[tool.pixi.feature.{referenced_extra}] exists." + ) + + return error_messages + + +def _validate_feature_groups( + pyproject: dict[str, Any], allowed_version_mismatches: set[str] | None = None +) -> list[str]: + """Validate dependency groups and optional dependencies against pixi. + + For each dependency group and each optional-depedencies group a pixi + feature with identical requirements should exist. + """ + error_messages: list[str] = [] + + dependency_groups = pyproject.get("dependency-groups", {}) + optional_dependencies = pyproject.get("project", {}).get("optional-dependencies", {}) + pixi_features = pyproject.get("tool", {}).get("pixi", {}).get("feature", {}) + + for name, pep_dependencies in dependency_groups.items(): + feature = pixi_features.get(name) + if feature is None: + error_messages.append( + f"Missing [tool.pixi.feature.{name}] for dependency group '{name}'." + ) + continue + pixi_dependencies_combined = _combine_pixi_dependencies( + feature.get("dependencies"), + feature.get("pypi-dependencies"), + ) + error_messages.extend( + _compare_dependency_lists( + f"dependency-groups.{name}", + pep_dependencies, + pixi_dependencies_combined, + allowed_version_mismatches, + ) + ) + + for name, pep_dependencies in optional_dependencies.items(): + if _is_meta_optional_dependency(pep_dependencies): + error_messages.extend( + _validate_meta_optional_dependency( + name, + pep_dependencies, + optional_dependencies, + pixi_features, + ) + ) + continue + + feature = pixi_features.get(name) + if feature is None: + error_messages.append( + f"Missing [tool.pixi.feature.{name}] for optional dependency group '{name}'." + ) + continue + pixi_dependencies_combined = _combine_pixi_dependencies( + feature.get("dependencies"), + feature.get("pypi-dependencies"), + ) + error_messages.extend( + _compare_dependency_lists( + f"project.optional-dependencies.{name}", + pep_dependencies, + pixi_dependencies_combined, + allowed_version_mismatches, + ) + ) + + return error_messages + + +def main() -> int: + """Validate pyproject.toml integrity.""" + parser = argparse.ArgumentParser( + description="Check consistency between PEP-style and pixi dependency declarations." + ) + parser.add_argument("--path", default="pyproject.toml", help="Path to pyproject.toml") + parser.add_argument( + "--allow-version-mismatch", + action="append", + default=None, + help=( + "Package name for which version mismatches are allowed as long as the package name " + "and position are identical between the PEP and pixi declarations." + ), + ) + args = parser.parse_args() + + try: + pyproject = _load_pyproject(args.path) + except (OSError, tomllib.TOMLDecodeError) as error: + print(f"Failed to load {args.path}: {error}", file=sys.stderr) + return 2 + + allowed_version_mismatches = set(args.allow_version_mismatch or []) + + error_messages = [] + error_messages.extend(_validate_base_dependencies(pyproject, allowed_version_mismatches)) + error_messages.extend(_validate_feature_groups(pyproject, allowed_version_mismatches)) + + if not error_messages: + print( + "Dependency declarations in pyproject.toml are consistent " + "between PEP and pixi sections." + ) + return 0 + + print("Dependency integrity check failed:\n", file=sys.stderr) + for error_message in error_messages: + print(f"- {error_message}\n", file=sys.stderr) + return 1 + + +if __name__ == "__main__": + raise SystemExit(main()) From 7f02edb81a58519c2bb7c05c372390380fb09d9c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 18 Apr 2026 13:59:49 +0200 Subject: [PATCH 044/200] build: make pyproject dependencies consistent --- .pre-commit-config.yaml | 7 +++++-- pyproject.toml | 15 ++++++++++++--- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bb4e8bb64..1955bcd7c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,7 @@ default_stages: [pre-commit, pre-merge-commit, pre-push, manual] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.2 # Ruff version + rev: v0.9.2 # Ruff version hooks: # Run the linter. # Needs to placed before black, isort, and other formatters @@ -35,7 +35,10 @@ repos: pass_filenames: true - id: check-pyproject-dependency-integrity name: check pyproject dependency integrity - entry: python3 tools/dependencies/check_pyproject_dependency_integrity.py --path + entry: > + python3 tools/dependencies/check_pyproject_dependency_integrity.py + --allow-version-mismatch gpflow + --path language: system files: '^pyproject\.toml$' pass_filenames: true diff --git a/pyproject.toml b/pyproject.toml index fd4304b16..888f24ea3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -196,7 +196,8 @@ channels = ["conda-forge", "nodefaults"] platforms = ["linux-64", "osx-arm64"] [tool.pixi.dependencies] -python = ">=3.12.13" +python = ">=3.12" +pip = ">=26.0.1" setuptools = ">=81.0.0,<82" cython = ">=3.2.4" numba = ">=0.65.0" @@ -241,9 +242,12 @@ tqdm = ">=4.67.3" tomli = ">=2.4.1" pathos = ">=0.3.5" black = ">=26.3.1" -pip = ">=26.0.1" [tool.pixi.pypi-dependencies] +gnuplotlib = ">=0.46" +diversipy = ">=0.9" +particles = { git = "https://github.com/nchopin/particles.git"} +scikit-activeml= ">=1.0.0" queens = { path = ".", editable = true } [tool.pixi.feature.dev.dependencies] @@ -265,11 +269,16 @@ testbook = ">=0.4.2" ipykernel = ">=7.2.0" mypy = ">=1.20.1" pip-licenses = ">=5.5" +[tool.pixi.feature.dev.pypi-dependencies] +pylint-exit = ">=1.2.0" +licenseheaders = ">=0.8.8" [tool.pixi.feature.tutorials.dependencies] scikit-fem = ">=12.0.1" [tool.pixi.feature.fourc.dependencies] +[tool.pixi.feature.fourc.pypi-dependencies] +fourcipp = ">=1.91.0" [tool.pixi.environments] queens-base = { features = []} @@ -294,9 +303,9 @@ dev = [ "pylint>=4.0.5", "testbook>=0.4.2", "ipykernel>=7.2.0", "mypy>=1.20.1", + "pip-licenses>=5.5", "pylint-exit>=1.2.0", "licenseheaders>=0.8.8", - "pip-licenses>=5.5", ] [project.optional-dependencies] From 6151615d838e06800be723840aca427afd0f896d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 18 Apr 2026 14:36:33 +0200 Subject: [PATCH 045/200] ci: add dependency integrity checks to ci pipeline 1. check integrity of the pyproject.toml dependency sections for consistency between pep definitions and pixi sections 2. check whether the dependencies have been added and the pixi.lock file would thus be changed (but has not) --- .github/workflows/tests_local.yml | 88 +++++++++++++++++++ .../diff_pyproject_dependency_declarations.py | 81 +++++++++++++++++ 2 files changed, 169 insertions(+) create mode 100644 tools/dependencies/diff_pyproject_dependency_declarations.py diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 90fee5b1d..a8c04af67 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -10,6 +10,10 @@ on: - main workflow_dispatch: +permissions: + contents: read + pull-requests: write + env: # Set TEST_TIMING_OPTION if local test should be timed. Default is off. TEST_TIMING_OPTION: "" @@ -37,6 +41,9 @@ jobs: queens-dev frozen: true activate-environment: queens-dev + - name: Mark repo as safe for git + run: | + git config --global --add safe.directory "$GITHUB_WORKSPACE" - name: Install rsync run: | sudo apt-get update @@ -44,10 +51,91 @@ jobs: - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build + - name: Check dependency declaration integrity + run: | + set -euo pipefail + # Validate that the PEP-style dependency declarations in pyproject.toml + # stay aligned with the pixi dependency sections. + python3 tools/dependencies/check_pyproject_dependency_integrity.py \ + --path pyproject.toml \ + --allow-version-mismatch gpflow + - name: Check pixi environment integrity + id: environment_integrity + run: | + set -euo pipefail + + base_ref="main" + pyproject_diff_file="$(mktemp)" + git fetch --no-tags --depth=1 origin "${base_ref}" + + pyproject_changed=false + # The diff helper returns: + # 0 if dependency-related declarations are unchanged, + # 1 if there is a relevant dependency diff, + # >1 if the diff command itself failed. + if python3 tools/dependencies/diff_pyproject_dependency_declarations.py \ + --base-ref "origin/${base_ref}" \ + --head-ref HEAD \ + > "${pyproject_diff_file}"; then + pyproject_changed=false + else + # $? is the exit status of the last command. + # when arriving here, the diff command found a diff (exit status 1) or + # the diff command itself failed (exit status >1). + pyproject_check_status=$? + if [ "${pyproject_check_status}" -eq 1 ]; then + pyproject_changed=true + else + echo "Failed to compare dependency-related pyproject.toml sections." + exit "${pyproject_check_status}" + fi + fi + + lock_update_possible=false + # `pixi lock --check` exits non-zero when the current pyproject.toml + # would produce a different pixi.lock. + if ! pixi lock --check >/dev/null 2>&1; then + lock_update_possible=true + fi + + { + echo "pyproject_changed=${pyproject_changed}" + echo "lock_update_possible=${lock_update_possible}" + echo "compare_ref=${base_ref}" + } >> "$GITHUB_OUTPUT" + + { + echo "### Pixi Environment Integrity" + echo "" + echo "- dependency-relevant \`pyproject.toml\` changes vs \`${base_ref}\`: ${pyproject_changed}" + echo "- \`pixi.lock\` would change if refreshed: ${lock_update_possible}" + if [ "${pyproject_changed}" = "true" ]; then + echo "" + echo "
" + echo "Dependency diff" + echo "" + echo '```diff' + cat "${pyproject_diff_file}" + echo '```' + echo "
" + fi + } >> "$GITHUB_STEP_SUMMARY" + + # Only fail if the dependency declarations changed and the lockfile is + # stale. A stale lockfile without dependency declaration changes is + # reported in the summary but does not block the workflow here. + if [ "${pyproject_changed}" = "true" ] && [ "${lock_update_possible}" = "true" ]; then + echo "pyproject.toml dependency sections changed compared to main" + echo "AND pixi.lock would be updated by pixi lock." + echo "Please regenerate and commit pixi.lock for this change." + exit 1 + fi - name: Code checks run: | set -euo pipefail + # Run all checks in one fail-fast block so a tool failure is not + # hidden by later bookkeeping commands such as echo/endgroup lines. echo "::group::Run isort..." isort --check-only src/* tests echo "::endgroup::" diff --git a/tools/dependencies/diff_pyproject_dependency_declarations.py b/tools/dependencies/diff_pyproject_dependency_declarations.py new file mode 100644 index 000000000..78328e1e2 --- /dev/null +++ b/tools/dependencies/diff_pyproject_dependency_declarations.py @@ -0,0 +1,81 @@ +#!/usr/bin/env python3 +# +# SPDX-License-Identifier: LGPL-3.0-or-later +# Copyright (c) 2024-2025, QUEENS contributors. +# +# This file is part of QUEENS. +# +# QUEENS is free software: you can redistribute it and/or modify it under the terms of the GNU +# Lesser General Public License as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. QUEENS is distributed in the hope that it will +# be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You +# should have received a copy of the GNU Lesser General Public License along with QUEENS. If not, +# see . +# +"""Diff dependency-related pyproject.toml declarations between two git refs.""" + +import argparse +import difflib +import json +import subprocess +import sys +import tomllib +from typing import Any + + +def _load_pyproject_sections(ref: str, path: str) -> dict[str, Any]: + """Load relevant dependency declarations from a git ref.""" + content = subprocess.check_output(["git", "show", f"{ref}:{path}"], text=False) + parsed = tomllib.loads(content.decode("utf-8")) + return { + "project.dependencies": parsed.get("project", {}).get("dependencies", []), + "dependency-groups": parsed.get("dependency-groups", {}), + "project.optional-dependencies": parsed.get("project", {}).get("optional-dependencies", {}), + "tool.pixi.workspace": parsed.get("tool", {}).get("pixi", {}).get("workspace", {}), + "tool.pixi.dependencies": parsed.get("tool", {}).get("pixi", {}).get("dependencies", {}), + "tool.pixi.pypi-dependencies": parsed.get("tool", {}) + .get("pixi", {}) + .get("pypi-dependencies", {}), + "tool.pixi.feature": parsed.get("tool", {}).get("pixi", {}).get("feature", {}), + } + + +def main() -> int: + """Run the diff and return a status code.""" + parser = argparse.ArgumentParser( + description="Compare dependency-related pyproject.toml declarations between two refs." + ) + parser.add_argument("--base-ref", required=True, help="Base git ref") + parser.add_argument("--head-ref", default="HEAD", help="Head git ref") + parser.add_argument("--path", default="pyproject.toml", help="Path to pyproject.toml") + args = parser.parse_args() + + try: + base_content = _load_pyproject_sections(args.base_ref, args.path) + head_content = _load_pyproject_sections(args.head_ref, args.path) + except subprocess.CalledProcessError as error: + print(error.stderr.decode("utf-8") if error.stderr else str(error), file=sys.stderr) + return 2 + + base_json = json.dumps(base_content, indent=2, sort_keys=True).splitlines() + head_json = json.dumps(head_content, indent=2, sort_keys=True).splitlines() + diff = list( + difflib.unified_diff( + base_json, + head_json, + fromfile=f"{args.base_ref}:{args.path}", + tofile=f"{args.head_ref}:{args.path}", + lineterm="", + ) + ) + + if not diff: + return 0 + + print("\n".join(diff)) + return 1 + + +if __name__ == "__main__": + raise SystemExit(main()) From 066fee39adbfc6398ac7a5879523e5c2d5a19fce Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 18 Apr 2026 17:04:00 +0200 Subject: [PATCH 046/200] ci: use cache only on main --- .github/workflows/tests_local.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index a8c04af67..11a9d9449 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -32,7 +32,8 @@ jobs: - uses: prefix-dev/setup-pixi@v0.9.4 with: pixi-version: v0.67.0 - #cache: true + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} auth-host: prefix.dev auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} environments: >- From 3fc045ac8c994891ab4866ae83fe40b795d2c479 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 15:04:23 +0200 Subject: [PATCH 047/200] ci: improve logs of pixi integrity checks --- .github/workflows/tests_local.yml | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 11a9d9449..6c67d8430 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -69,6 +69,7 @@ jobs: pyproject_diff_file="$(mktemp)" git fetch --no-tags --depth=1 origin "${base_ref}" + echo "::group::Check if dependency declarations changed..." pyproject_changed=false # The diff helper returns: # 0 if dependency-related declarations are unchanged, @@ -91,13 +92,18 @@ jobs: exit "${pyproject_check_status}" fi fi + echo "Pyproject.toml dependency sections changed compared to ${base_ref}: ${pyproject_changed}" + echo "::endgroup::" + echo "::group::Check if pixi.lock would be updated by pixi lock..." lock_update_possible=false # `pixi lock --check` exits non-zero when the current pyproject.toml # would produce a different pixi.lock. - if ! pixi lock --check >/dev/null 2>&1; then + if ! pixi lock --check; then lock_update_possible=true fi + echo "pixi.lock would be updated by pixi lock: ${lock_update_possible}" + echo "::endgroup::" { echo "pyproject_changed=${pyproject_changed}" @@ -105,11 +111,14 @@ jobs: echo "compare_ref=${base_ref}" } >> "$GITHUB_OUTPUT" + + # ---- Write rich Markdown to Step Summary ---- { echo "### Pixi Environment Integrity" echo "" echo "- dependency-relevant \`pyproject.toml\` changes vs \`${base_ref}\`: ${pyproject_changed}" echo "- \`pixi.lock\` would change if refreshed: ${lock_update_possible}" + if [ "${pyproject_changed}" = "true" ]; then echo "" echo "
" @@ -122,6 +131,21 @@ jobs: fi } >> "$GITHUB_STEP_SUMMARY" + + # ---- Write clean, readable logs ---- + echo "::group::Summary Pixi Environment Integrity" + echo "----------------------------------------" + echo "pyproject changes vs ${base_ref}: ${pyproject_changed}" + echo "pixi.lock update possible: ${lock_update_possible}" + + if [ "${pyproject_changed}" = "true" ]; then + echo "::group::Dependency diff" + cat "${pyproject_diff_file}" + echo "::endgroup::" + fi + echo "::endgroup::" + + echo "::group::Do integrity check..." # Only fail if the dependency declarations changed and the lockfile is # stale. A stale lockfile without dependency declaration changes is # reported in the summary but does not block the workflow here. @@ -130,7 +154,10 @@ jobs: echo "AND pixi.lock would be updated by pixi lock." echo "Please regenerate and commit pixi.lock for this change." exit 1 + else + echo "Pixi environment integrity is OK." fi + echo "::endgroup::" - name: Code checks run: | set -euo pipefail From 80137ed8cca6de10734dacfcc7ee440edae5113d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 16:19:48 +0200 Subject: [PATCH 048/200] ci: make sure that pixi.lock not already changed --- .github/workflows/tests_local.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 6c67d8430..2255e9c62 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -96,6 +96,11 @@ jobs: echo "::endgroup::" echo "::group::Check if pixi.lock would be updated by pixi lock..." + # Detect any change (modified, deleted, untracked, etc.) + if [ -n "$(git status --porcelain -- pixi.lock)" ]; then + echo "Restoring pixi.lock from HEAD..." + git restore --source=HEAD --staged --worktree pixi.lock 2>/dev/null + fi lock_update_possible=false # `pixi lock --check` exits non-zero when the current pyproject.toml # would produce a different pixi.lock. From 9ba2b2e6cf4c013a689da37754e148e3bca8c818 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 16:38:39 +0200 Subject: [PATCH 049/200] ci: fix pixi lock --- .github/workflows/tests_local.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 2255e9c62..1586b4bd6 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -102,9 +102,12 @@ jobs: git restore --source=HEAD --staged --worktree pixi.lock 2>/dev/null fi lock_update_possible=false - # `pixi lock --check` exits non-zero when the current pyproject.toml - # would produce a different pixi.lock. - if ! pixi lock --check; then + # `pixi lock --check --dry-run` exits non-zero when the current pyproject.toml + # would produce a different pixi.lock without writing the lockfile to disk. + pixi lock --check --dry-run + exit_code_pixi_lock_check=$? + echo "exit code: $exit_code_pixi_lock_check" + if [ $exit_code_pixi_lock_check -ne 0 ]; then lock_update_possible=true fi echo "pixi.lock would be updated by pixi lock: ${lock_update_possible}" From 795e7eea96bbe875624b6ed7500c873a0b205576 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 16:56:12 +0200 Subject: [PATCH 050/200] ci: allow pixi lock to fail --- .github/workflows/tests_local.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 1586b4bd6..c4a10c1e6 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -102,10 +102,14 @@ jobs: git restore --source=HEAD --staged --worktree pixi.lock 2>/dev/null fi lock_update_possible=false + # deactivate exit on error to allow `pixi lock --check --dry-run` to fail + set +e # `pixi lock --check --dry-run` exits non-zero when the current pyproject.toml # would produce a different pixi.lock without writing the lockfile to disk. pixi lock --check --dry-run exit_code_pixi_lock_check=$? + # reactivate exit on error + set -e echo "exit code: $exit_code_pixi_lock_check" if [ $exit_code_pixi_lock_check -ne 0 ]; then lock_update_possible=true From 644422349969f461a95b38b8a80c83bafab15924 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 19:48:29 +0200 Subject: [PATCH 051/200] ci: remove authentication to prefix dev --- .github/workflows/tests_local.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index c4a10c1e6..554b63fe5 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -34,8 +34,6 @@ jobs: pixi-version: v0.67.0 cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - auth-host: prefix.dev - auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} environments: >- queens-base queens-all From e935aaaee59347c50e12fc3d6e375c3c53544ee0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 19 Apr 2026 19:56:24 +0200 Subject: [PATCH 052/200] ci: reactivate cache and deactivate auth --- .github/workflows/build_documentation.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 72ec7c854..d7a2e7d6e 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -27,9 +27,8 @@ jobs: - uses: prefix-dev/setup-pixi@v0.9.4 with: pixi-version: v0.67.0 - #cache: true - auth-host: prefix.dev - auth-token: ${{ secrets.PREFIX_DEV_TOKEN }} + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: queens-dev frozen: true activate-environment: queens-dev From c9f4cc4e1c1435ac68d75b5c1f1691f189d1db50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lea=20H=C3=A4usel?= Date: Mon, 20 Apr 2026 17:18:28 +0200 Subject: [PATCH 053/200] fix: mypy errors --- .../parameters/random_fields/karhunen_loeve.py | 2 +- src/queens/utils/iterative_averaging.py | 16 ++++++++-------- .../plot_results.py | 4 +++- .../plot_input_random_field.py | 5 ++++- 4 files changed, 16 insertions(+), 11 deletions(-) diff --git a/src/queens/parameters/random_fields/karhunen_loeve.py b/src/queens/parameters/random_fields/karhunen_loeve.py index 790eb19d0..68181ccd7 100644 --- a/src/queens/parameters/random_fields/karhunen_loeve.py +++ b/src/queens/parameters/random_fields/karhunen_loeve.py @@ -197,7 +197,7 @@ def eigendecomp_cov_matrix(self, latent_dimension: int | None = None) -> int: dimension = latent_dimension else: eigenvalues_normed = eigenvalues / np.sum(eigenvalues) - dimension = (np.cumsum(eigenvalues_normed) < self.explained_variance).argmin() + 1 + dimension = int((np.cumsum(eigenvalues_normed) < self.explained_variance).argmin()) + 1 if dimension == 1 and eigenvalues_normed[0] <= self.explained_variance: raise ValueError("Expansion failed.") diff --git a/src/queens/utils/iterative_averaging.py b/src/queens/utils/iterative_averaging.py index 5c271e1d1..86c989d43 100644 --- a/src/queens/utils/iterative_averaging.py +++ b/src/queens/utils/iterative_averaging.py @@ -273,11 +273,11 @@ def l1_norm(vector: NumericalValue, averaged: bool = False) -> float | np.floati Returns: L1 norm of the vector """ - vector = np.array(vector).flatten() - vector = np.nan_to_num(vector) - norm = np.sum(np.abs(vector)) + vector_array = np.array(vector).flatten() + vector_array = np.nan_to_num(vector_array) + norm = np.sum(np.abs(vector_array)) if averaged: - norm /= len(vector) + norm /= vector_array.size return norm @@ -291,11 +291,11 @@ def l2_norm(vector: NumericalValue, averaged: bool = False) -> float | np.floati Returns: L2 norm of the vector """ - vector = np.array(vector).flatten() - vector = np.nan_to_num(vector) - norm = np.sum(vector**2) ** 0.5 + vector_array = np.array(vector).flatten() + vector_array = np.nan_to_num(vector_array) + norm = np.sum(vector_array**2) ** 0.5 if averaged: - norm /= len(vector) ** 0.5 + norm /= vector_array.size**0.5 return norm diff --git a/tutorials/3_orchestrating_4c_simulations/plot_results.py b/tutorials/3_orchestrating_4c_simulations/plot_results.py index 11a720716..8990febc7 100644 --- a/tutorials/3_orchestrating_4c_simulations/plot_results.py +++ b/tutorials/3_orchestrating_4c_simulations/plot_results.py @@ -13,7 +13,9 @@ # see . # """Plotting functions for tutorial 3.""" + import os +from typing import Any, cast os.environ["PYVISTA_OFF_SCREEN"] = "true" os.environ["VTK_DEFAULT_RENDER_WINDOW_OFFSCREEN"] = "1" @@ -21,7 +23,7 @@ import pyvista as pv -fe_mesh = pv.read("beam_coarse.exo") +fe_mesh = cast(pv.DataSet, cast(Any, pv.read("beam_coarse.exo"))) def plot_results( diff --git a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/plot_input_random_field.py b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/plot_input_random_field.py index ba7e4e7dc..83c31d42d 100644 --- a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/plot_input_random_field.py +++ b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/plot_input_random_field.py @@ -13,6 +13,9 @@ # see . # """Plotting functions for tutorial 4.""" + +from typing import Any, cast + import matplotlib.pyplot as plt import numpy as np import pyvista as pv @@ -29,7 +32,7 @@ def plot_field(file_path: str, field: np.ndarray, ax: Axes3D, color_bar_title: s ax: 3D Matplotlib axis to plot into. color_bar_title: Label shown next to the color bar. """ - mesh = pv.read(file_path)[0][0] + mesh = cast(pv.DataSet, cast(Any, pv.read(file_path))[0][0]) mesh.cell_data["field"] = field cell_values = field From d4ceb111dbc94b7db63ee3eb44b8730d12ea8fda Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 20 Apr 2026 21:49:49 +0200 Subject: [PATCH 054/200] ci: bump version of skywalking eyes (license header checks) up to 0.8.0 --- .github/workflows/tests_local.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 554b63fe5..1ccafd8ca 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -216,7 +216,7 @@ jobs: mypy . echo "::endgroup::" - name: Check license headers - uses: apache/skywalking-eyes/header@v0.4.0 + uses: apache/skywalking-eyes/header@v0.8.0 - name: Check conventional commit messages uses: webiny/action-conventional-commits@v1.3.0 - name: Run pytest From c3368451c8b83c50ff33d4e20c2d8ef77dacfa82 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 22 Apr 2026 11:58:24 +0200 Subject: [PATCH 055/200] fix: np.trapz renamed to np.trapezoid in numpy > 2.0 --- tutorials/2_uncertainty_propagation_and_quantification.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/2_uncertainty_propagation_and_quantification.ipynb b/tutorials/2_uncertainty_propagation_and_quantification.ipynb index 0ce8d9142..d2376d4df 100644 --- a/tutorials/2_uncertainty_propagation_and_quantification.ipynb +++ b/tutorials/2_uncertainty_propagation_and_quantification.ipynb @@ -477,7 +477,7 @@ " pdf = kde.pdf(u)\n", " pdf[0] = 0\n", " pdf[-1] = 0\n", - " pdf /= np.trapz(pdf, u)\n", + " pdf /= np.trapezoid(pdf, u)\n", " axes[0].plot(mesh.p[0, index[i]], mesh.p[1, index[i]], \"ks\")\n", " c_text = f\"({mesh.p.T[index[i]][0]}, {mesh.p.T[index[i]][1]})\"\n", " axes[0].text(mesh.p[0, index[i]], mesh.p[1, index[i]] + 0.02, c_text, ha=\"center\")\n", From ded2a78c71222a8a8c06fc425eb614ed1f2f9f72 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 00:48:20 +0200 Subject: [PATCH 056/200] build: fix pypi overwrite of tensorflow-probability Avoid duplicated tensorflow-probability resolution by disabling the default feature, introducing an explicit base feature, and preventing the broken conda-to-PyPI tfp-nightly mapping from overriding the intended package. --- pixi.lock | 4762 +++++++++++++---- pyproject.toml | 10 +- .../check_pyproject_dependency_integrity.py | 18 +- 3 files changed, 3866 insertions(+), 924 deletions(-) diff --git a/pixi.lock b/pixi.lock index e10b6d102..da72360f7 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,938 +11,376 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/_x86_64-microarch-level-1-3_x86_64.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-49.0-unix_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.5-py312h5d8c7f2_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/arviz-0.23.4-pyhcf101f3_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_3.conda - 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tool_pixi = pyproject.get("tool", {}).get("pixi", {}) + tool_pixi = pyproject.get("tool", {}).get("pixi", {}).get("feature", {}).get("base", {}) pixi_dependencies = tool_pixi.get("dependencies", {}) pixi_pypi_dependencies = tool_pixi.get("pypi-dependencies", {}) @@ -231,12 +231,14 @@ def _validate_feature_groups( feature with identical requirements should exist. """ error_messages: list[str] = [] + pep_names: list[str] = [] dependency_groups = pyproject.get("dependency-groups", {}) optional_dependencies = pyproject.get("project", {}).get("optional-dependencies", {}) pixi_features = pyproject.get("tool", {}).get("pixi", {}).get("feature", {}) for name, pep_dependencies in dependency_groups.items(): + pep_names.append(name) feature = pixi_features.get(name) if feature is None: error_messages.append( @@ -268,6 +270,7 @@ def _validate_feature_groups( ) continue + pep_names.append(name) feature = pixi_features.get(name) if feature is None: error_messages.append( @@ -287,6 +290,19 @@ def _validate_feature_groups( ) ) + # for each feature there should either be a dependency group or an optional dependency group + # except for some special features: + # 1. the base feature is covered by the project.dependencies + special_exception_features: list[str] = ["base"] + for feature_name in pixi_features.keys(): + if feature_name in pep_names or feature_name in special_exception_features: + continue + error_messages.append( + f"Missing either a pep dependency group or optional dependency '{feature_name}' " + f"for the pixi feature [tool.pixi.feature.{feature_name}]." + "" + ) + return error_messages From 4084474e11789879e6579d0de400c21934683d43 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 13:23:44 +0200 Subject: [PATCH 057/200] build: manually install queens package in environments By removing the queens package itself as pypi dependency, uv no longer resolves the Pypi dependencies at the very end again. The problem was that at this stage tensorflow-prbability and tfp-nightly where confused (uv did not recognize tfp-nightly as fulfilling the requirement). Thus an override happened (reinstall of tensorflow-prbability via pypi, which lead to version problems. This problem only occurred on linux-64. --- .github/workflows/tests_local.yml | 3 + pixi.lock | 4775 ++++------------- pyproject.toml | 12 +- .../check_pyproject_dependency_integrity.py | 18 +- 4 files changed, 1156 insertions(+), 3652 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 1ccafd8ca..919334822 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -40,6 +40,9 @@ jobs: queens-dev frozen: true activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pip install -e ./ --no-deps - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" diff --git a/pixi.lock b/pixi.lock index da72360f7..168b972ba 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,376 +11,935 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/_x86_64-microarch-level-1-3_x86_64.conda + - 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tool_pixi = pyproject.get("tool", {}).get("pixi", {}).get("feature", {}).get("base", {}) + tool_pixi = pyproject.get("tool", {}).get("pixi", {}) pixi_dependencies = tool_pixi.get("dependencies", {}) pixi_pypi_dependencies = tool_pixi.get("pypi-dependencies", {}) @@ -155,22 +155,6 @@ def _validate_base_dependencies( if not combined: return error_messages - if combined[-1][0] != "queens": - error_messages.append( - "The last combined pixi dependency entry must be the local editable 'queens' package." - ) - else: - queens_spec = combined[-1][1] - if not ( - isinstance(queens_spec, dict) - and queens_spec.get("path") == "." - and queens_spec.get("editable") is True - ): - error_messages.append( - "The final 'queens' pixi dependency must be declared as " - "{ path = '.', editable = true }." - ) - stripped_combined = [ (name, spec) for name, spec in combined if name not in {"python", "pip", "queens"} ] From 1176983fe82a3fdcea4f90c6d0681d53f23b5645 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 14:32:42 +0200 Subject: [PATCH 058/200] build: deactivate default feature for all environments --- pixi.lock | 4729 +++++++++++++---- pyproject.toml | 10 +- .../check_pyproject_dependency_integrity.py | 19 +- 3 files changed, 3588 insertions(+), 1170 deletions(-) diff --git a/pixi.lock b/pixi.lock index 168b972ba..0a366be98 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,935 +11,376 @@ environments: packages: linux-64: - 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watermark ; extra == 'doc' + - matplotlib ; extra == 'doc' + - sphinx-togglebutton ; extra == 'doc' + - einops ; extra == 'einops' + - numba>=0.55 ; extra == 'numba' + - hypothesis ; extra == 'test' + - pytest ; extra == 'test' + - pytest-cov ; extra == 'test' + - packaging ; extra == 'test' + - scipy>=1.15 ; extra == 'test' + - preliz>=0.19 ; extra == 'test' + requires_python: '>=3.12' - conda: https://conda.anaconda.org/conda-forge/noarch/xarray-einstats-0.10.0-pyhd8ed1ab_0.conda sha256: 02943091700f860bc3fc117deabe5fd609ed7bae64fd97da2f70241167c2719d md5: b82273c95432c78efe98f14cbc46be7d @@ -17372,6 +19751,11 @@ packages: purls: [] size: 570010 timestamp: 1766154256151 +- pypi: https://files.pythonhosted.org/packages/a8/a9/d23012099dc88ec69a29c6407b41d89681cb674c2043cd5b467c7e299c08/xyzservices-2026.3.0-py3-none-any.whl + name: xyzservices + version: 2026.3.0 + sha256: 503183d4b322bfebc3c50cdd21192aa3e81e36c5efbf9133d54ae82143e0576b + requires_python: '>=3.8' - conda: https://conda.anaconda.org/conda-forge/noarch/xyzservices-2026.3.0-pyhd8ed1ab_0.conda sha256: 663ea9b00d68c2da309114923924686ab6d3f59ef1b196c5029ba16799e7bb07 md5: 4487b9c371d0161d54b5c7bbd890c0fc @@ -17492,6 +19876,11 @@ packages: purls: [] size: 277694 timestamp: 1766549572069 +- pypi: https://files.pythonhosted.org/packages/80/ab/11a76c1e2126084fde2639514f24e6111b789b0bfa4fc6264a8975c7e1f1/zict-3.0.0-py2.py3-none-any.whl + name: zict + version: 3.0.0 + sha256: 5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae + requires_python: '>=3.8' - conda: https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_1.conda sha256: 5488542dceeb9f2874e726646548ecc5608060934d6f9ceaa7c6a48c61f9cc8d md5: e52c2ef711ccf31bb7f70ca87d144b9e @@ -17503,6 +19892,30 @@ packages: - pkg:pypi/zict?source=hash-mapping size: 36341 timestamp: 1733261642963 +- pypi: https://files.pythonhosted.org/packages/08/8a/0861bec20485572fbddf3dfba2910e38fe249796cb73ecdeb74e07eeb8d3/zipp-3.23.1-py3-none-any.whl + name: zipp + version: 3.23.1 + sha256: 0b3596c50a5c700c9cb40ba8d86d9f2cc4807e9bedb06bcdf7fac85633e444dc + requires_dist: + - pytest>=6,!=8.1.* ; extra == 'test' + - jaraco-itertools ; extra == 'test' + - jaraco-functools ; extra == 'test' + - more-itertools ; extra == 'test' + - big-o ; extra == 'test' + - pytest-ignore-flaky ; extra == 'test' + - jaraco-test ; extra == 'test' + - sphinx>=3.5 ; extra == 'doc' + - jaraco-packaging>=9.3 ; extra == 'doc' + - rst-linker>=1.9 ; extra == 'doc' + - furo ; extra == 'doc' + - sphinx-lint ; extra == 'doc' + - jaraco-tidelift>=1.4 ; extra == 'doc' + - pytest-checkdocs>=2.4 ; extra == 'check' + - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' + - pytest-cov ; extra == 'cover' + - pytest-enabler>=2.2 ; extra == 'enabler' + - pytest-mypy ; extra == 'type' + requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda sha256: 523616c0530d305d2216c2b4a8dfd3872628b60083255b89c5e0d8c42e738cca md5: e1c36c6121a7c9c76f2f148f1e83b983 diff --git a/pyproject.toml b/pyproject.toml index 8b37f9115..fd524fdd8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -195,7 +195,7 @@ follow_untyped_imports = true channels = ["conda-forge", "nodefaults"] platforms = ["linux-64", "osx-arm64"] -[tool.pixi.dependencies] +[tool.pixi.feature.base.dependencies] python = ">=3.12" pip = ">=26.0.1" setuptools = ">=81.0.0,<82" @@ -243,7 +243,7 @@ tomli = ">=2.4.1" pathos = ">=0.3.5" black = ">=26.3.1" -[tool.pixi.pypi-dependencies] +[tool.pixi.feature.base.pypi-dependencies] gnuplotlib = ">=0.46" diversipy = ">=0.9" particles = { git = "https://github.com/nchopin/particles.git"} @@ -281,9 +281,9 @@ scikit-fem = ">=12.0.1" fourcipp = ">=1.91.0" [tool.pixi.environments] -queens-base = { features = []} -queens-dev = { features = ["dev", "tutorials", "fourc"]} -queens-all = { features = ["tutorials", "fourc"]} +queens-base = { features = ["base"], no-default-feature = true} +queens-dev = { features = ["base", "dev", "tutorials", "fourc"], no-default-feature = true} +queens-all = { features = ["base","tutorials", "fourc"], no-default-feature = true} [dependency-groups] dev = [ "pylint>=4.0.5", diff --git a/tools/dependencies/check_pyproject_dependency_integrity.py b/tools/dependencies/check_pyproject_dependency_integrity.py index fa6fd8e80..7d6c52f3b 100644 --- a/tools/dependencies/check_pyproject_dependency_integrity.py +++ b/tools/dependencies/check_pyproject_dependency_integrity.py @@ -129,27 +129,32 @@ def _validate_base_dependencies( error_messages: list[str] = [] project = pyproject.get("project", {}) - tool_pixi = pyproject.get("tool", {}).get("pixi", {}) - pixi_dependencies = tool_pixi.get("dependencies", {}) - pixi_pypi_dependencies = tool_pixi.get("pypi-dependencies", {}) + pixi_base_feature = pyproject.get("tool", {}).get("pixi", {}).get("feature", {}).get("base", {}) + pixi_dependencies = pixi_base_feature.get("dependencies", {}) + pixi_pypi_dependencies = pixi_base_feature.get("pypi-dependencies", {}) ordered_conda = list(pixi_dependencies.items()) if not ordered_conda: - return ["[tool.pixi.dependencies] is empty; expected at least python and pip."] + return ["[tool.pixi.feature.base] is empty; expected at least python and pip."] if ordered_conda[0][0] != "python": - error_messages.append("The first entry in [tool.pixi.dependencies] must be 'python'.") + error_messages.append( + "The first entry in [tool.pixi.feature.base.dependencies] must be 'python'." + ) else: requires_python = project.get("requires-python") if ordered_conda[0][1] != requires_python: error_messages.append( - "Mismatch between project.requires-python and tool.pixi.dependencies.python: " + "Mismatch between project.requires-python and " + "tool.pixi.feature.base.dependencies.python: " f"{requires_python!r} != {ordered_conda[0][1]!r}" ) if len(ordered_conda) < 2 or ordered_conda[1][0] != "pip": - error_messages.append("The second entry in [tool.pixi.dependencies] must be 'pip'.") + error_messages.append( + "The second entry in [tool.pixi.feature.base.dependencies] must be 'pip'." + ) combined = _combine_pixi_dependencies(pixi_dependencies, pixi_pypi_dependencies) if not combined: From 5db23c02da54cfa5897e094467c4041b42a70e1e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 14:44:35 +0200 Subject: [PATCH 059/200] build: fix environment in documentation build workflow --- .github/workflows/build_documentation.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index d7a2e7d6e..5b3247cf9 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -32,6 +32,9 @@ jobs: environments: queens-dev frozen: true activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pip install -e ./ --no-deps - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" From 1c2c1e3f4fc3416abe690b7f94fe0cb40fb4ab76 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 15:17:20 +0200 Subject: [PATCH 060/200] docs: fix documentation build warnings --- doc/README.md | 5 +++-- doc/source/faqs/requirements.md | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/README.md b/doc/README.md index 4f14d1137..c936b1d32 100644 --- a/doc/README.md +++ b/doc/README.md @@ -6,8 +6,9 @@ We believe that documentation is essential and therefore welcome any improvement ## :woman_teacher: Build the documentation -To build the documentation, you first need to set up a QUEENS environment as described in the [README.md](../README.md). -Make sure to install the packages for QUEENS development and tutorial. +To build the documentation, first set up a QUEENS environment as described in the +[README](../README.md). For documentation work, use the development setup there, which +includes the required documentation and tutorial dependencies. Next, register the environment as a Jupyter kernel with: ```bash diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index 0c601ee0e..d7c304c67 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -14,4 +14,4 @@ root: For reproducible installs, QUEENS also provides the composed lock file `composed.conda-lock.yml`. -For more information see the [README.md](README.md). +For more information see the [README.md](../../../README.md). From 20417acfad6bacc3e4b8688c9ce143700b20465a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 15:19:32 +0200 Subject: [PATCH 061/200] fix: type hinting --- src/queens/models/bmfmc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/queens/models/bmfmc.py b/src/queens/models/bmfmc.py index 9df16b20b..17d030bce 100644 --- a/src/queens/models/bmfmc.py +++ b/src/queens/models/bmfmc.py @@ -194,7 +194,7 @@ def __init__( X_cols (list, optional): For `man_features`, list of columns from the X-matrix to be used as informative features. num_features (int, optional): For `opt_features`, number of features to be used. - hf_model (model, optional): High-fidelity model used to run simulations and generate + hf_model (Model, optional): High-fidelity model used to run simulations and generate training data. path_to_lf_mc_data (str or list of str, optional): Path(s) to low-fidelity MC data files. From e2473446a73c331c694d5e05e0acf6ed0c7687e4 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 15:44:50 +0200 Subject: [PATCH 062/200] docs: link to external README.md to fix warning --- doc/source/faqs/requirements.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index d7c304c67..30e17788f 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -14,4 +14,4 @@ root: For reproducible installs, QUEENS also provides the composed lock file `composed.conda-lock.yml`. -For more information see the [README.md](../../../README.md). +For more information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). From 68b8cb48f1118352ed4e968018d9bfd0bc2a39d6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 16:09:12 +0200 Subject: [PATCH 063/200] ci: introduce testing on macos Split into tests and test with 4C --- .github/workflows/tests_local.yml | 84 ++++++++++++++++++++++++++----- 1 file changed, 71 insertions(+), 13 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 919334822..b32f171ce 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -19,11 +19,17 @@ env: TEST_TIMING_OPTION: "" jobs: - run_tests: - runs-on: ubuntu-latest - container: - image: ghcr.io/4c-multiphysics/4c-minimal:main - options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + run_tests_core: + name: core tests (${{ matrix.os }}) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + pytest_markers: "unit_tests or integration_tests" + - os: macos-latest + pytest_markers: "unit_tests or integration_tests" defaults: run: shell: bash -l {0} @@ -46,13 +52,23 @@ jobs: - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Install rsync + - name: Ensure rsync is available run: | - sudo apt-get update - sudo apt-get install -y rsync - - name: Create links to 4C - run: | - ln -s /home/user/4C/bin/ config/4C_build + set -euo pipefail + + if command -v rsync >/dev/null 2>&1; then + rsync --version + elif [ "${RUNNER_OS}" = "Linux" ]; then + sudo apt-get update + sudo apt-get install -y rsync + rsync --version + elif [ "${RUNNER_OS}" = "macOS" ]; then + brew install rsync + rsync --version + else + echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" + exit 1 + fi - name: Check dependency declaration integrity run: | set -euo pipefail @@ -226,7 +242,7 @@ jobs: run: | set -euo pipefail - pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml + pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - name: Run pytest for tutorials run: | @@ -234,15 +250,57 @@ jobs: pytest -v -m "tutorial_tests" - name: Upload coverage report + if: runner.os == 'Linux' uses: actions/upload-pages-artifact@v3 with: name: html-coverage-report path: html_coverage_report/ retention-days: 7 - name: Publish junit pytest report + if: (success() || failure()) && runner.os == 'Linux' uses: mikepenz/action-junit-report@v5 - if: success() || failure() # always run even if the previous step fails with: report_paths: "test_junit.xml" annotate_only: true job_summary: false + + run_tests_fourc_linux: + name: 4C integration tests (linux) + runs-on: ubuntu-latest + container: + image: ghcr.io/4c-multiphysics/4c-minimal:main + options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: >- + queens-base + queens-all + queens-dev + frozen: true + activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pip install -e ./ --no-deps + - name: Mark repo as safe for git + run: | + git config --global --add safe.directory "$GITHUB_WORKSPACE" + - name: Install rsync + run: | + sudo apt-get update + sudo apt-get install -y rsync + - name: Create links to 4C + run: | + ln -s /home/user/4C/bin/ config/4C_build + - name: Run pytest for 4C integration tests + run: | + set -euo pipefail + + pytest -v -m "integration_tests_fourc" $TEST_TIMING_OPTION --color=yes From e8567e00d30da086377bff3ebd0a434eb5ac4570 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 22:11:27 +0200 Subject: [PATCH 064/200] ci: split jobs into code checks and tests --- .github/workflows/tests_local.yml | 125 +++++++++++++++++++++--------- 1 file changed, 88 insertions(+), 37 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index b32f171ce..efb9623a9 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -19,17 +19,9 @@ env: TEST_TIMING_OPTION: "" jobs: - run_tests_core: - name: core tests (${{ matrix.os }}) - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - include: - - os: ubuntu-latest - pytest_markers: "unit_tests or integration_tests" - - os: macos-latest - pytest_markers: "unit_tests or integration_tests" + run_code_checks: + name: code checks + runs-on: ubuntu-latest defaults: run: shell: bash -l {0} @@ -49,26 +41,6 @@ jobs: - name: Install QUEENS in workspace run: | pip install -e ./ --no-deps - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Ensure rsync is available - run: | - set -euo pipefail - - if command -v rsync >/dev/null 2>&1; then - rsync --version - elif [ "${RUNNER_OS}" = "Linux" ]; then - sudo apt-get update - sudo apt-get install -y rsync - rsync --version - elif [ "${RUNNER_OS}" = "macOS" ]; then - brew install rsync - rsync --version - else - echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" - exit 1 - fi - name: Check dependency declaration integrity run: | set -euo pipefail @@ -187,7 +159,7 @@ jobs: echo "Pixi environment integrity is OK." fi echo "::endgroup::" - - name: Code checks + - name: isort run: | set -euo pipefail @@ -197,10 +169,18 @@ jobs: isort --check-only src/* tests echo "::endgroup::" + - name: black + run: | + set -euo pipefail + echo "::group::Run black..." black --check src/* tests echo "::endgroup::" + - name: pylint + run: | + set -euo pipefail + echo "::group::Run pylint on src..." pylint --rcfile=.pylintrc --ignore=integration_tests src/ tests/ echo "::endgroup::" @@ -209,35 +189,106 @@ jobs: pylint --rcfile=.pylintrc --disable=duplicate-code tests/integration_tests/ echo "::endgroup::" + # echo "::group::Create code quality report..." + # pylint src/ tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0 + # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json + # echo "::endgroup::" + + - name: ruff + run: | + set -euo pipefail + echo "::group::Run ruff..." ruff check echo "::endgroup::" + - name: nbstripout + run: | + set -euo pipefail + echo "::group::Run nbstripout..." find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + - echo "::endgroup::" - # echo "::group::Create code quality report..." - # pylint src/ tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0 - # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json - # echo "::endgroup::" + - name: pip-licenses - check compatibility of licenses of dependencies + run: | + set -euo pipefail echo "::group::Check compatibility with licenses of dependencies..." pip-licenses --python=.pixi/envs/queens-all/bin/python echo "::endgroup::" + - name: licenserc + run: | + set -euo pipefail + echo "::group::Create an rc file for the license header check..." python .gitlab/pipeline_utils/create_licenserc.py --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" --text_file "license_header.tmpl" --output_file ".licenserc.yaml" --placeholder "license_header" echo "::endgroup::" + - name: mypy + run: | + set -euo pipefail + echo "::group::Check type hinting with mypy..." mypy . echo "::endgroup::" + - name: Check license headers uses: apache/skywalking-eyes/header@v0.8.0 - name: Check conventional commit messages uses: webiny/action-conventional-commits@v1.3.0 + + run_tests_core: + name: core tests (${{ matrix.os }}) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + pytest_markers: "unit_tests or integration_tests" + - os: macos-latest + pytest_markers: "unit_tests or integration_tests" + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: >- + queens-base + queens-all + queens-dev + frozen: true + activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pip install -e ./ --no-deps + - name: Mark repo as safe for git + run: | + git config --global --add safe.directory "$GITHUB_WORKSPACE" + - name: Ensure rsync is available + run: | + set -euo pipefail + + if command -v rsync >/dev/null 2>&1; then + rsync --version + elif [ "${RUNNER_OS}" = "Linux" ]; then + sudo apt-get update + sudo apt-get install -y rsync + rsync --version + elif [ "${RUNNER_OS}" = "macOS" ]; then + brew install rsync + rsync --version + else + echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" + exit 1 + fi - name: Run pytest run: | set -euo pipefail From 435284d86d9fe2500db565f83da1bb775c3f1d59 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 24 Apr 2026 22:24:53 +0200 Subject: [PATCH 065/200] ci: ensure install queens to correct interpreter --- .github/workflows/tests_local.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index efb9623a9..6af7bf721 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -40,7 +40,7 @@ jobs: activate-environment: queens-dev - name: Install QUEENS in workspace run: | - pip install -e ./ --no-deps + pixi run --locked -e queens-dev python -m pip install --no-deps -e . - name: Check dependency declaration integrity run: | set -euo pipefail @@ -268,7 +268,7 @@ jobs: activate-environment: queens-dev - name: Install QUEENS in workspace run: | - pip install -e ./ --no-deps + pixi run --locked -e queens-dev python -m pip install --no-deps -e . - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" From e7c7b1ded3725fc3efc5a09ebe6bd175d9753605 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 25 Apr 2026 00:33:58 +0200 Subject: [PATCH 066/200] ci: cleanup tests_local workflow --- .github/workflows/tests_local.yml | 57 ++++++++++++++++--------------- 1 file changed, 29 insertions(+), 28 deletions(-) diff --git a/.github/workflows/tests_local.yml b/.github/workflows/tests_local.yml index 6af7bf721..c1ea12f1c 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/tests_local.yml @@ -159,17 +159,38 @@ jobs: echo "Pixi environment integrity is OK." fi echo "::endgroup::" - - name: isort + + - name: Check compatibility of licenses of dependencies + run: | + set -euo pipefail + + echo "::group::Check compatibility with licenses of dependencies..." + pip-licenses --python=.pixi/envs/queens-all/bin/python + echo "::endgroup::" + + - name: Create licenserc + run: | + set -euo pipefail + + echo "::group::Create an rc file for the license header check..." + python .gitlab/pipeline_utils/create_licenserc.py --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" --text_file "license_header.tmpl" --output_file ".licenserc.yaml" --placeholder "license_header" + echo "::endgroup::" + + - name: Check license headers + uses: apache/skywalking-eyes/header@v0.8.0 + + - name: Check conventional commit messages + uses: webiny/action-conventional-commits@v1.3.0 + + - name: Run isort run: | set -euo pipefail - # Run all checks in one fail-fast block so a tool failure is not - # hidden by later bookkeeping commands such as echo/endgroup lines. echo "::group::Run isort..." isort --check-only src/* tests echo "::endgroup::" - - name: black + - name: Run black run: | set -euo pipefail @@ -177,7 +198,7 @@ jobs: black --check src/* tests echo "::endgroup::" - - name: pylint + - name: Run pylint run: | set -euo pipefail @@ -194,7 +215,7 @@ jobs: # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json # echo "::endgroup::" - - name: ruff + - name: Run ruff run: | set -euo pipefail @@ -202,7 +223,7 @@ jobs: ruff check echo "::endgroup::" - - name: nbstripout + - name: Run nbstripout run: | set -euo pipefail @@ -210,23 +231,7 @@ jobs: find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + echo "::endgroup::" - - name: pip-licenses - check compatibility of licenses of dependencies - run: | - set -euo pipefail - - echo "::group::Check compatibility with licenses of dependencies..." - pip-licenses --python=.pixi/envs/queens-all/bin/python - echo "::endgroup::" - - - name: licenserc - run: | - set -euo pipefail - - echo "::group::Create an rc file for the license header check..." - python .gitlab/pipeline_utils/create_licenserc.py --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" --text_file "license_header.tmpl" --output_file ".licenserc.yaml" --placeholder "license_header" - echo "::endgroup::" - - - name: mypy + - name: Run mypy run: | set -euo pipefail @@ -234,10 +239,6 @@ jobs: mypy . echo "::endgroup::" - - name: Check license headers - uses: apache/skywalking-eyes/header@v0.8.0 - - name: Check conventional commit messages - uses: webiny/action-conventional-commits@v1.3.0 run_tests_core: name: core tests (${{ matrix.os }}) From 8f8c60c627e61fa9c5df96aede8a2154e99045e3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 25 Apr 2026 00:38:47 +0200 Subject: [PATCH 067/200] ci: split into three cleaned workflows --- .github/workflows/build_documentation.yml | 2 +- .../{tests_local.yml => code_quality.yml} | 120 +-------------- .github/workflows/local_testsuite.yml | 137 ++++++++++++++++++ 3 files changed, 139 insertions(+), 120 deletions(-) rename .github/workflows/{tests_local.yml => code_quality.yml} (68%) create mode 100644 .github/workflows/local_testsuite.yml diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 5b3247cf9..8473897dd 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -1,5 +1,5 @@ # yamllint disable -name: build_documentation +name: Build documentation on: pull_request: diff --git a/.github/workflows/tests_local.yml b/.github/workflows/code_quality.yml similarity index 68% rename from .github/workflows/tests_local.yml rename to .github/workflows/code_quality.yml index c1ea12f1c..556f7c1c8 100644 --- a/.github/workflows/tests_local.yml +++ b/.github/workflows/code_quality.yml @@ -1,5 +1,5 @@ # yamllint disable -name: tests_local +name: Code quality on: schedule: @@ -238,121 +238,3 @@ jobs: echo "::group::Check type hinting with mypy..." mypy . echo "::endgroup::" - - - run_tests_core: - name: core tests (${{ matrix.os }}) - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - include: - - os: ubuntu-latest - pytest_markers: "unit_tests or integration_tests" - - os: macos-latest - pytest_markers: "unit_tests or integration_tests" - defaults: - run: - shell: bash -l {0} - steps: - - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 - with: - pixi-version: v0.67.0 - cache: true - cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: >- - queens-base - queens-all - queens-dev - frozen: true - activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pixi run --locked -e queens-dev python -m pip install --no-deps -e . - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Ensure rsync is available - run: | - set -euo pipefail - - if command -v rsync >/dev/null 2>&1; then - rsync --version - elif [ "${RUNNER_OS}" = "Linux" ]; then - sudo apt-get update - sudo apt-get install -y rsync - rsync --version - elif [ "${RUNNER_OS}" = "macOS" ]; then - brew install rsync - rsync --version - else - echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" - exit 1 - fi - - name: Run pytest - run: | - set -euo pipefail - - pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml - python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Run pytest for tutorials - run: | - set -euo pipefail - - pytest -v -m "tutorial_tests" - - name: Upload coverage report - if: runner.os == 'Linux' - uses: actions/upload-pages-artifact@v3 - with: - name: html-coverage-report - path: html_coverage_report/ - retention-days: 7 - - name: Publish junit pytest report - if: (success() || failure()) && runner.os == 'Linux' - uses: mikepenz/action-junit-report@v5 - with: - report_paths: "test_junit.xml" - annotate_only: true - job_summary: false - - run_tests_fourc_linux: - name: 4C integration tests (linux) - runs-on: ubuntu-latest - container: - image: ghcr.io/4c-multiphysics/4c-minimal:main - options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 - defaults: - run: - shell: bash -l {0} - steps: - - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 - with: - pixi-version: v0.67.0 - cache: true - cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: >- - queens-base - queens-all - queens-dev - frozen: true - activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pip install -e ./ --no-deps - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Install rsync - run: | - sudo apt-get update - sudo apt-get install -y rsync - - name: Create links to 4C - run: | - ln -s /home/user/4C/bin/ config/4C_build - - name: Run pytest for 4C integration tests - run: | - set -euo pipefail - - pytest -v -m "integration_tests_fourc" $TEST_TIMING_OPTION --color=yes diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml new file mode 100644 index 000000000..d31eeac48 --- /dev/null +++ b/.github/workflows/local_testsuite.yml @@ -0,0 +1,137 @@ +# yamllint disable +name: Testsuite + +on: + schedule: + - cron: "0 1 * * *" + pull_request: + push: + branches: + - main + workflow_dispatch: + +permissions: + contents: read + pull-requests: write + +env: + # Set TEST_TIMING_OPTION if local test should be timed. Default is off. + TEST_TIMING_OPTION: "" + +jobs: + run_tests_core: + name: core tests (${{ matrix.os }}) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + pytest_markers: "unit_tests or integration_tests" + - os: macos-latest + pytest_markers: "unit_tests or integration_tests" + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: >- + queens-base + queens-all + queens-dev + frozen: true + activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pixi run --locked -e queens-dev python -m pip install --no-deps -e . + - name: Mark repo as safe for git + run: | + git config --global --add safe.directory "$GITHUB_WORKSPACE" + - name: Ensure rsync is available + run: | + set -euo pipefail + + if command -v rsync >/dev/null 2>&1; then + rsync --version + elif [ "${RUNNER_OS}" = "Linux" ]; then + sudo apt-get update + sudo apt-get install -y rsync + rsync --version + elif [ "${RUNNER_OS}" = "macOS" ]; then + brew install rsync + rsync --version + else + echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" + exit 1 + fi + - name: Run pytest + run: | + set -euo pipefail + + pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml + python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY + - name: Run pytest for tutorials + run: | + set -euo pipefail + + pytest -v -m "tutorial_tests" + - name: Upload coverage report + if: runner.os == 'Linux' + uses: actions/upload-pages-artifact@v3 + with: + name: html-coverage-report + path: html_coverage_report/ + retention-days: 7 + - name: Publish junit pytest report + if: (success() || failure()) && runner.os == 'Linux' + uses: mikepenz/action-junit-report@v5 + with: + report_paths: "test_junit.xml" + annotate_only: true + job_summary: false + + run_tests_fourc_linux: + name: 4C integration tests (linux) + runs-on: ubuntu-latest + container: + image: ghcr.io/4c-multiphysics/4c-minimal:main + options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: >- + queens-base + queens-all + queens-dev + frozen: true + activate-environment: queens-dev + - name: Install QUEENS in workspace + run: | + pip install -e ./ --no-deps + - name: Mark repo as safe for git + run: | + git config --global --add safe.directory "$GITHUB_WORKSPACE" + - name: Install rsync + run: | + sudo apt-get update + sudo apt-get install -y rsync + - name: Create links to 4C + run: | + ln -s /home/user/4C/bin/ config/4C_build + - name: Run pytest for 4C integration tests + run: | + set -euo pipefail + + pytest -v -m "integration_tests_fourc" $TEST_TIMING_OPTION --color=yes From 75f0b93ef04d0ed48d0c41762ae7551e249ac35d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 25 Apr 2026 01:04:52 +0200 Subject: [PATCH 068/200] ci: add names for build documentation --- .github/workflows/build_documentation.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 8473897dd..41f5ad2df 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -15,6 +15,7 @@ permissions: jobs: build-documentation: + name: Build documentation runs-on: ubuntu-latest container: image: ghcr.io/4c-multiphysics/4c-minimal:main @@ -34,7 +35,7 @@ jobs: activate-environment: queens-dev - name: Install QUEENS in workspace run: | - pip install -e ./ --no-deps + pixi run --locked -e queens-dev python -m pip install --no-deps -e . - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" @@ -67,6 +68,7 @@ jobs: retention-days: 1 deploy-documentation: + name: Deploy documentation needs: build-documentation if: ${{github.ref == 'refs/heads/main'}} environment: From 471953d7c103220a410660d9228ef68689fd86dd Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 11:34:15 +0200 Subject: [PATCH 069/200] ci: unify pytest calls --- .github/workflows/local_testsuite.yml | 31 ++++++++++++++++++++------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index d31eeac48..199bb0329 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -75,11 +75,6 @@ jobs: pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Run pytest for tutorials - run: | - set -euo pipefail - - pytest -v -m "tutorial_tests" - name: Upload coverage report if: runner.os == 'Linux' uses: actions/upload-pages-artifact@v3 @@ -88,13 +83,25 @@ jobs: path: html_coverage_report/ retention-days: 7 - name: Publish junit pytest report - if: (success() || failure()) && runner.os == 'Linux' + if: success() || failure() uses: mikepenz/action-junit-report@v5 with: report_paths: "test_junit.xml" annotate_only: true job_summary: false + - name: Run pytest for tutorials + run: | + set -euo pipefail + pytest -v -m "tutorial_tests" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials.xml + python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY + - name: Publish junit pytest report + if: (success() || failure()) && runner.os == 'Linux' + uses: mikepenz/action-junit-report@v5 + with: + report_paths: "test_junit_tutorials.xml" + annotate_only: true + job_summary: false run_tests_fourc_linux: name: 4C integration tests (linux) runs-on: ubuntu-latest @@ -119,7 +126,7 @@ jobs: activate-environment: queens-dev - name: Install QUEENS in workspace run: | - pip install -e ./ --no-deps + pixi run --locked -e queens-dev python -m pip install --no-deps -e . - name: Mark repo as safe for git run: | git config --global --add safe.directory "$GITHUB_WORKSPACE" @@ -134,4 +141,12 @@ jobs: run: | set -euo pipefail - pytest -v -m "integration_tests_fourc" $TEST_TIMING_OPTION --color=yes + pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc.xml + python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY + - name: Publish junit pytest report + if: success() || failure() + uses: mikepenz/action-junit-report@v5 + with: + report_paths: "test_junit_fourc.xml" + annotate_only: true + job_summary: false From f6f4f5490622e7939c724024e0fc5ca2672300e0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 11:39:36 +0200 Subject: [PATCH 070/200] ci: upload artifacts as last step --- .github/workflows/local_testsuite.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 199bb0329..5de09aeb2 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -75,13 +75,6 @@ jobs: pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Upload coverage report - if: runner.os == 'Linux' - uses: actions/upload-pages-artifact@v3 - with: - name: html-coverage-report - path: html_coverage_report/ - retention-days: 7 - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v5 @@ -102,6 +95,13 @@ jobs: report_paths: "test_junit_tutorials.xml" annotate_only: true job_summary: false + - name: Upload coverage report + if: runner.os == 'Linux' + uses: actions/upload-pages-artifact@v3 + with: + name: html-coverage-report + path: html_coverage_report/ + retention-days: 7 run_tests_fourc_linux: name: 4C integration tests (linux) runs-on: ubuntu-latest From 64ab5b308398aa5c36bbf990abd1835ddcc3c5c5 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 11:42:19 +0200 Subject: [PATCH 071/200] ci: always run tutorial tests even if some core tests fail --- .github/workflows/local_testsuite.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 5de09aeb2..9acad8fb6 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -83,13 +83,14 @@ jobs: annotate_only: true job_summary: false - name: Run pytest for tutorials + if: success() || failure() run: | set -euo pipefail pytest -v -m "tutorial_tests" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials.xml python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - name: Publish junit pytest report - if: (success() || failure()) && runner.os == 'Linux' + if: success() || failure() uses: mikepenz/action-junit-report@v5 with: report_paths: "test_junit_tutorials.xml" From 7a9c8aaf7d0db921ebc568190802b59ba6bd56b1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 12:33:56 +0200 Subject: [PATCH 072/200] ci: make step names more explicit --- .github/workflows/local_testsuite.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 9acad8fb6..d7cc7fec0 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -69,7 +69,7 @@ jobs: echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" exit 1 fi - - name: Run pytest + - name: Run pytest for unit tests and integration tests run: | set -euo pipefail @@ -82,7 +82,7 @@ jobs: report_paths: "test_junit.xml" annotate_only: true job_summary: false - - name: Run pytest for tutorials + - name: Run pytest for tutorial tests if: success() || failure() run: | set -euo pipefail From 5d691101b673d1ea2f3ab70f87771b40274fae3e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 12:35:54 +0200 Subject: [PATCH 073/200] ci: remove unnecessary PR write access --- .github/workflows/code_quality.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 556f7c1c8..62d099c3c 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -12,7 +12,6 @@ on: permissions: contents: read - pull-requests: write env: # Set TEST_TIMING_OPTION if local test should be timed. Default is off. 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conda: https://conda.anaconda.org/conda-forge/osx-arm64/clangxx-21.1.0-default_h36137df_1.conda @@ -2995,7 +2977,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/dropstackframe-0.1.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/eigen-5.0.1-h44d0d2d_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/epoxy-1.5.10-hc919400_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/etils-1.12.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/etuples-0.3.10-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda @@ -3225,7 +3206,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/openldap-2.6.10-hbe55e7a_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.6.2-hd24854e_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/opt_einsum-3.4.0-pyhd8ed1ab_1.conda - 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sha256: 139d7b38a543ba6c7b8aebaa64e9bfc05dd4f8f56977c3ee740892f76fd49546 - md5: 207c50a7c4059d9235329e59085f06a0 - depends: - - absl-py >=2.3.1 - - jax >=0.7.0 - - jaxlib >=0.7.0 - - numpy >=1.24.1 - - python >=3.11 - - toolz >=1.0.0 - - typing-extensions >=4.2.0 - - typing_extensions >=4.15.0 - license: Apache-2.0 - license_family: APACHE - purls: - - pkg:pypi/chex?source=hash-mapping - size: 80820 - timestamp: 1756790803659 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/clang-21.1.0-default_hf9bcbb7_1.conda sha256: 03a3caa9b02d855a55d16dc63848e35ae03874c13845e41241f0cea0c87e6ff2 md5: e1b0b8b9268d5fc58e5be168dd16bc6f @@ -6265,17 +6209,6 @@ packages: purls: [] size: 296347 timestamp: 1758743805063 -- conda: https://conda.anaconda.org/conda-forge/noarch/etils-1.12.2-pyhd8ed1ab_0.conda - sha256: 805ee8cc651a4bf056c39f8b1fdf64b393455bc10b2fd8cc3a99b0f7e7475f77 - md5: 05ecb9e7a6f7bc5319aa61866545a746 - depends: - - python >=3.10 - license: Apache-2.0 - license_family: APACHE - purls: - - pkg:pypi/etils?source=hash-mapping - size: 787805 - timestamp: 1741838050970 - pypi: https://files.pythonhosted.org/packages/39/19/bf11636df040a9f9c3fd6959aedea5b5cfddd751272732278fb04ee0a78c/etuples-0.3.10-py3-none-any.whl name: etuples version: 0.3.10 @@ -13988,49 +13921,6 @@ packages: - pkg:pypi/opt-einsum?source=hash-mapping size: 62479 timestamp: 1733688053334 -- pypi: https://files.pythonhosted.org/packages/8a/69/6a93d8600c339d7687a05857c7907bd4dd8cf88691a5ea106d7a50af90a1/optax-0.2.8-py3-none-any.whl - name: optax - version: 0.2.8 - sha256: e3ca2d36c99daab1800ae9dbc0545034382d6bc780b24d969e1b0df65fa31cb4 - requires_dist: - - absl-py>=0.7.1 - - jax>=0.5.3 - - jaxlib>=0.5.3 - - numpy>=1.18.0 - - sphinx>=6.0.0 ; extra == 'docs' - - sphinx-book-theme>=1.0.1 ; extra == 'docs' - - sphinxcontrib-katex ; extra == 'docs' - - sphinx-autodoc-typehints ; extra == 'docs' - - ipython>=8.8.0 ; extra == 'docs' - - myst-nb>=1.0.0 ; extra == 'docs' - - matplotlib>=3.5.0 ; extra == 'docs' - - sphinx-gallery>=0.14.0 ; extra == 'docs' - - sphinx-collections>=0.0.1 ; extra == 'docs' - - flax ; extra == 'docs' - - sphinx-contributors ; extra == 'docs' - - setuptools ; extra == 'docs' - - flax>=0.5.3 ; extra == 'test' - - scipy>=1.7.1 ; extra == 'test' - - scikit-learn ; extra == 'test' - requires_python: '>=3.10' -- conda: https://conda.anaconda.org/conda-forge/noarch/optax-0.2.8-pyhd8ed1ab_0.conda - sha256: cc259139ebca28c5a7cbacd066e47bab0ff2f5043c78c4a7f7c87249cb135bc2 - md5: 532df7a827e2ee092ff43ba7425dd0e4 - depends: - - absl-py >=0.7.1 - - chex >=0.1.86 - - etils - - jax >=0.4.27 - - jaxlib >=0.4.27 - - numpy >=1.18.0 - - python >=3.10 - - typing_extensions >=3.10 - license: Apache-2.0 - license_family: APACHE - purls: - - pkg:pypi/optax?source=hash-mapping - size: 251301 - timestamp: 1774062121453 - pypi: https://files.pythonhosted.org/packages/00/9e/65899e6470f5df289ccdbe9e228fb0cd0ae45ccda8e32c92d6efae1530ef/optree-0.19.0-cp312-cp312-macosx_11_0_arm64.whl name: optree version: 0.19.0 diff --git a/pyproject.toml b/pyproject.toml index 8efa35a8f..bcb7654b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,6 @@ dependencies = [ "jinja2>=3.1.6", "arviz>=0.23.4,<1", "gpflow", - "optax>=0.2.8", "tensorflow>=2.18.0", "tensorflow-probability>=0.25.0", "tf-keras>=2.18.0", @@ -215,7 +214,6 @@ pyyaml = ">=6.0.3" jinja2 = ">=3.1.6" arviz = ">=0.23.4,<1" gpflow = ">=2.9.2" -optax = ">=0.2.8" tensorflow = ">=2.18.0" tensorflow-probability = ">=0.25.0" tf-keras = ">=2.18.0" From d26605ab1c727f48644ededd65d0078efeb0558b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 15:23:58 +0200 Subject: [PATCH 078/200] ci: remove PR write access in local testsuite workflow --- .github/workflows/local_testsuite.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index d7cc7fec0..6fcd63fb2 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -12,7 +12,6 @@ on: permissions: contents: read - pull-requests: write env: # Set TEST_TIMING_OPTION if local test should be timed. Default is off. From a8bff895888ca7e73e94051f2c92a2051465104c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 16:01:16 +0200 Subject: [PATCH 079/200] ci: introduce queens setup action to reduce duplicate code --- .github/actions/setup-queens-pixi/action.yml | 77 ++++++++++++++++++++ .github/workflows/build_documentation.yml | 14 +--- .github/workflows/code_quality.yml | 8 +- .github/workflows/local_testsuite.yml | 41 +---------- 4 files changed, 82 insertions(+), 58 deletions(-) create mode 100644 .github/actions/setup-queens-pixi/action.yml diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml new file mode 100644 index 000000000..8aab9e772 --- /dev/null +++ b/.github/actions/setup-queens-pixi/action.yml @@ -0,0 +1,77 @@ +name: Setup QUEENS pixi environment +description: Set up pixi, install QUEENS editable into the selected environment, and optionally ensure rsync is available. + +inputs: + pixi-version: + description: Pixi version to install. + required: false + default: v0.67.0 + cache: + description: Whether setup-pixi should enable caching. + required: false + default: "true" + cache-write: + description: Whether setup-pixi should write to the cache. + required: false + default: "false" + environments: + description: Whitespace-separated list of pixi environments to install. + required: false + default: queens-dev + activate-environment: + description: Pixi environment to activate and use for the editable install. + required: false + default: queens-dev + install-editable: + description: Whether to install QUEENS editable into the selected pixi environment. + required: false + default: "true" + ensure-rsync: + description: Whether to verify that rsync is available, installing it if necessary. + required: false + default: "true" + +runs: + using: composite + steps: + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: ${{ inputs.pixi-version }} + cache: ${{ inputs.cache }} + cache-write: ${{ inputs.cache-write }} + environments: ${{ inputs.environments }} + frozen: true + activate-environment: ${{ inputs.activate-environment }} + + - name: Install QUEENS in workspace + if: ${{ inputs.install-editable != 'false' }} + shell: bash + run: | + set -euo pipefail + pixi run --locked -e "${{ inputs.activate-environment }}" python -m pip install --no-deps -e . + + - name: Mark repo as safe for git + shell: bash + run: | + set -euo pipefail + git config --global --add safe.directory "${GITHUB_WORKSPACE}" + + - name: Ensure rsync is available + if: ${{ inputs.ensure-rsync != 'false' }} + shell: bash + run: | + set -euo pipefail + + if command -v rsync >/dev/null 2>&1; then + rsync --version + elif [ "${RUNNER_OS}" = "Linux" ]; then + sudo apt-get update + sudo apt-get install -y rsync + rsync --version + elif [ "${RUNNER_OS}" = "macOS" ]; then + brew install rsync + rsync --version + else + echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" + exit 1 + fi diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 41f5ad2df..26cd06909 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -25,24 +25,12 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 + - uses: ./.github/actions/setup-queens-pixi with: - pixi-version: v0.67.0 cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: queens-dev - frozen: true activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pixi run --locked -e queens-dev python -m pip install --no-deps -e . - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Install rsync - run: | - sudo apt-get update - sudo apt-get install -y rsync - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 62d099c3c..7a2eabdfb 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -26,20 +26,16 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 + - uses: ./.github/actions/setup-queens-pixi with: - pixi-version: v0.67.0 cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: >- queens-base queens-all queens-dev - frozen: true activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pixi run --locked -e queens-dev python -m pip install --no-deps -e . + ensure-rsync: false - name: Check dependency declaration integrity run: | set -euo pipefail diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 6fcd63fb2..e5e8b8a49 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -34,40 +34,15 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 + - uses: ./.github/actions/setup-queens-pixi with: - pixi-version: v0.67.0 cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: >- queens-base queens-all queens-dev - frozen: true activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pixi run --locked -e queens-dev python -m pip install --no-deps -e . - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Ensure rsync is available - run: | - set -euo pipefail - - if command -v rsync >/dev/null 2>&1; then - rsync --version - elif [ "${RUNNER_OS}" = "Linux" ]; then - sudo apt-get update - sudo apt-get install -y rsync - rsync --version - elif [ "${RUNNER_OS}" = "macOS" ]; then - brew install rsync - rsync --version - else - echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}" - exit 1 - fi - name: Run pytest for unit tests and integration tests run: | set -euo pipefail @@ -113,27 +88,15 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v5 - - uses: prefix-dev/setup-pixi@v0.9.4 + - uses: ./.github/actions/setup-queens-pixi with: - pixi-version: v0.67.0 cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: >- queens-base queens-all queens-dev - frozen: true activate-environment: queens-dev - - name: Install QUEENS in workspace - run: | - pixi run --locked -e queens-dev python -m pip install --no-deps -e . - - name: Mark repo as safe for git - run: | - git config --global --add safe.directory "$GITHUB_WORKSPACE" - - name: Install rsync - run: | - sudo apt-get update - sudo apt-get install -y rsync - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build From 09f0b9323d59b375476c3eb0724f1d663c6ce902 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 16:52:09 +0200 Subject: [PATCH 080/200] ci: fix name of 4C integration tests job --- .github/workflows/local_testsuite.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index e5e8b8a49..73823b390 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -78,7 +78,7 @@ jobs: path: html_coverage_report/ retention-days: 7 run_tests_fourc_linux: - name: 4C integration tests (linux) + name: 4C integration tests (ubuntu-latest) runs-on: ubuntu-latest container: image: ghcr.io/4c-multiphysics/4c-minimal:main From ea0414dc970643c4ad172383dd8b551415b46fa0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 17:29:19 +0200 Subject: [PATCH 081/200] ci: split into three test steps, compute coverage and junit report from all three --- .github/workflows/local_testsuite.yml | 149 +++++++++++++++++++++----- 1 file changed, 123 insertions(+), 26 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 73823b390..a834ac593 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -47,37 +47,58 @@ jobs: run: | set -euo pipefail - pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml - python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Publish junit pytest report + COVERAGE_FILE=".coverage.core.${{ runner.os }}" pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_core_${{ runner.os }}.xml + - name: Upload raw core test reports if: success() || failure() - uses: mikepenz/action-junit-report@v5 + uses: actions/upload-artifact@v4 with: - report_paths: "test_junit.xml" - annotate_only: true - job_summary: false + name: raw-test-reports-core-${{ runner.os }} + path: | + .coverage.core.${{ runner.os }} + test_junit_core_${{ runner.os }}.xml + if-no-files-found: error + retention-days: 7 + + run_tests_tutorials: + name: tutorial tests (${{ matrix.os }}) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + - os: macos-latest + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: ./.github/actions/setup-queens-pixi + with: + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: >- + queens-base + queens-all + queens-dev + activate-environment: queens-dev - name: Run pytest for tutorial tests - if: success() || failure() run: | set -euo pipefail - pytest -v -m "tutorial_tests" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials.xml - python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Publish junit pytest report + COVERAGE_FILE=".coverage.tutorials.${{ runner.os }}" pytest -v -m "tutorial_tests" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_${{ runner.os }}.xml + - name: Upload raw tutorial test reports if: success() || failure() - uses: mikepenz/action-junit-report@v5 - with: - report_paths: "test_junit_tutorials.xml" - annotate_only: true - job_summary: false - - name: Upload coverage report - if: runner.os == 'Linux' - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-artifact@v4 with: - name: html-coverage-report - path: html_coverage_report/ + name: raw-test-reports-tutorials-${{ runner.os }} + path: | + .coverage.tutorials.${{ runner.os }} + test_junit_tutorials_${{ runner.os }}.xml + if-no-files-found: error retention-days: 7 - run_tests_fourc_linux: + + run_tests_fourc: name: 4C integration tests (ubuntu-latest) runs-on: ubuntu-latest container: @@ -104,12 +125,88 @@ jobs: run: | set -euo pipefail - pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc.xml - python .github/xml_summaries_to_md.py test_junit.xml xml_coverage_report.xml >> $GITHUB_STEP_SUMMARY - - name: Publish junit pytest report + COVERAGE_FILE=".coverage.fourc.${{ runner.os }}" pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc_${{ runner.os }}.xml + - name: Upload raw 4C test reports + if: success() || failure() + uses: actions/upload-artifact@v4 + with: + name: raw-test-reports-fourc-${{ runner.os }} + path: | + .coverage.fourc.${{ runner.os }} + test_junit_fourc_${{ runner.os }}.xml + if-no-files-found: error + retention-days: 7 + + report_test_results: + name: report test results + runs-on: ubuntu-latest + needs: + - run_tests_core + - run_tests_tutorials + - run_tests_fourc + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v5 + - uses: ./.github/actions/setup-queens-pixi + with: + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: queens-dev + activate-environment: queens-dev + ensure-rsync: false + - name: Download raw core test reports from Ubuntu + uses: actions/download-artifact@v4 + with: + name: raw-test-reports-core-Linux + path: reports/core-ubuntu + - name: Download raw core test reports from macOS + uses: actions/download-artifact@v4 + with: + name: raw-test-reports-core-macOS + path: reports/core-macos + - name: Download raw tutorial test reports from Ubuntu + uses: actions/download-artifact@v4 + with: + name: raw-test-reports-tutorials-Linux + path: reports/tutorials-ubuntu + - name: Download raw tutorial test reports from macOS + uses: actions/download-artifact@v4 + with: + name: raw-test-reports-tutorials-macOS + path: reports/tutorials-macos + - name: Download raw 4C test reports + uses: actions/download-artifact@v4 + with: + name: raw-test-reports-fourc-Linux + path: reports/fourc-ubuntu + - name: Combine Ubuntu coverage data and build reports + run: | + set -euo pipefail + + cp reports/core-ubuntu/.coverage.core.Linux .coverage.core.Linux + cp reports/tutorials-ubuntu/.coverage.tutorials.Linux .coverage.tutorials.Linux + cp reports/fourc-ubuntu/.coverage.fourc.Linux .coverage.fourc.Linux + + pixi run --locked -e queens-dev coverage combine .coverage.core.Linux .coverage.tutorials.Linux .coverage.fourc.Linux + pixi run --locked -e queens-dev coverage html -d html_coverage_report + pixi run --locked -e queens-dev coverage xml -o xml_coverage_report.xml + pixi run --locked -e queens-dev coverage report + + python .github/xml_summaries_to_md.py \ + reports/core-ubuntu/test_junit_core_Linux.xml \ + xml_coverage_report.xml >> "$GITHUB_STEP_SUMMARY" + - name: Publish combined junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v5 with: - report_paths: "test_junit_fourc.xml" + report_paths: "reports/**/*.xml" annotate_only: true job_summary: false + - name: Upload combined coverage report + uses: actions/upload-pages-artifact@v3 + with: + name: html-coverage-report + path: html_coverage_report/ + retention-days: 7 From a08c37b796988765f79aecc605146a676078809d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 18:00:15 +0200 Subject: [PATCH 082/200] ci: always build test reports --- .github/workflows/local_testsuite.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index a834ac593..9b7f5f7ad 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -139,6 +139,7 @@ jobs: report_test_results: name: report test results + if: always() runs-on: ubuntu-latest needs: - run_tests_core From b122e6c5b634f72d866517f1dd2de5d0c085cd44 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 18:10:23 +0200 Subject: [PATCH 083/200] ci: only build all envs once in code checks use only queens-dev for tests upload also hidden files --- .github/workflows/local_testsuite.yml | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 9b7f5f7ad..36e2598a8 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -38,10 +38,7 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: >- - queens-base - queens-all - queens-dev + environments: queens-dev activate-environment: queens-dev - name: Run pytest for unit tests and integration tests run: | @@ -53,6 +50,7 @@ jobs: uses: actions/upload-artifact@v4 with: name: raw-test-reports-core-${{ runner.os }} + include-hidden-files: true path: | .coverage.core.${{ runner.os }} test_junit_core_${{ runner.os }}.xml @@ -77,10 +75,7 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: >- - queens-base - queens-all - queens-dev + environments: queens-dev activate-environment: queens-dev - name: Run pytest for tutorial tests run: | @@ -92,6 +87,7 @@ jobs: uses: actions/upload-artifact@v4 with: name: raw-test-reports-tutorials-${{ runner.os }} + include-hidden-files: true path: | .coverage.tutorials.${{ runner.os }} test_junit_tutorials_${{ runner.os }}.xml @@ -113,10 +109,7 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: >- - queens-base - queens-all - queens-dev + environments: queens-dev activate-environment: queens-dev - name: Create links to 4C run: | @@ -131,6 +124,7 @@ jobs: uses: actions/upload-artifact@v4 with: name: raw-test-reports-fourc-${{ runner.os }} + include-hidden-files: true path: | .coverage.fourc.${{ runner.os }} test_junit_fourc_${{ runner.os }}.xml From 1882a0acbeba619c82f87f007a2dedd166cde836 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 19:54:19 +0200 Subject: [PATCH 084/200] ci: use relative coverage paths to enable combining from docker and non docker runs --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index bcb7654b5..276f1f0eb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -129,6 +129,7 @@ markers = [ source = ["queens"] parallel = true branch = true +relative_files = true [tool.coverage.report] # Regexes for lines to exclude from consideration From d4e5d802a4118c02189cf8edc8efd12736ef2310 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:13:07 +0200 Subject: [PATCH 085/200] ci: bump version of upload artifact action --- .github/workflows/local_testsuite.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 36e2598a8..6499537a4 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -47,7 +47,7 @@ jobs: COVERAGE_FILE=".coverage.core.${{ runner.os }}" pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_core_${{ runner.os }}.xml - name: Upload raw core test reports if: success() || failure() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: raw-test-reports-core-${{ runner.os }} include-hidden-files: true @@ -84,7 +84,7 @@ jobs: COVERAGE_FILE=".coverage.tutorials.${{ runner.os }}" pytest -v -m "tutorial_tests" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_${{ runner.os }}.xml - name: Upload raw tutorial test reports if: success() || failure() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: raw-test-reports-tutorials-${{ runner.os }} include-hidden-files: true @@ -121,7 +121,7 @@ jobs: COVERAGE_FILE=".coverage.fourc.${{ runner.os }}" pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc_${{ runner.os }}.xml - name: Upload raw 4C test reports if: success() || failure() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: raw-test-reports-fourc-${{ runner.os }} include-hidden-files: true From f59a3d0b905c44eaae9d31b9b339c62a3e65d9d2 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:14:17 +0200 Subject: [PATCH 086/200] ci: bump version of checkout action --- .github/workflows/build_documentation.yml | 2 +- .github/workflows/code_quality.yml | 2 +- .github/workflows/local_testsuite.yml | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 26cd06909..ccb8a8a81 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -24,7 +24,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 7a2eabdfb..dc99e1b84 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -25,7 +25,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 6499537a4..596e2a69f 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -33,7 +33,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true @@ -70,7 +70,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true @@ -104,7 +104,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true @@ -143,7 +143,7 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi with: cache: true From c73b2d74c110bcd3caa085956e1fc553024456d1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:16:10 +0200 Subject: [PATCH 087/200] ci: bump version of upload pages artifact --- .github/workflows/build_documentation.yml | 2 +- .github/workflows/local_testsuite.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index ccb8a8a81..a4256d01e 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -50,7 +50,7 @@ jobs: cd doc xvfb-run -a sphinx-build -b html -d build/doctrees source build/html -W - name: Upload html - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-pages-artifact@v5 with: path: doc/build/html retention-days: 1 diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 596e2a69f..9891326a6 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -200,7 +200,7 @@ jobs: annotate_only: true job_summary: false - name: Upload combined coverage report - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-pages-artifact@v5 with: name: html-coverage-report path: html_coverage_report/ From 079b6a115a0391dfe443f4ee84c8a7baf0a959bb Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:17:07 +0200 Subject: [PATCH 088/200] ci: bump version of deploy pages --- .github/workflows/build_documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index a4256d01e..07e7cb81a 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -66,4 +66,4 @@ jobs: steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v4 + uses: actions/deploy-pages@v5 From e0f52ae952e71ebcbcba73898a1599a4d5160695 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:23:06 +0200 Subject: [PATCH 089/200] ci: bump version of download artifact --- .github/workflows/local_testsuite.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 9891326a6..339a51ca9 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -152,27 +152,27 @@ jobs: activate-environment: queens-dev ensure-rsync: false - name: Download raw core test reports from Ubuntu - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: raw-test-reports-core-Linux path: reports/core-ubuntu - name: Download raw core test reports from macOS - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: raw-test-reports-core-macOS path: reports/core-macos - name: Download raw tutorial test reports from Ubuntu - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: raw-test-reports-tutorials-Linux path: reports/tutorials-ubuntu - name: Download raw tutorial test reports from macOS - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: raw-test-reports-tutorials-macOS path: reports/tutorials-macos - name: Download raw 4C test reports - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: raw-test-reports-fourc-Linux path: reports/fourc-ubuntu From bde8e0661f4e76846d34cb971727848cc78f97c9 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 27 Apr 2026 20:24:23 +0200 Subject: [PATCH 090/200] ci: bump version of junit report --- .github/workflows/local_testsuite.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 339a51ca9..b0d3a4360 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -194,7 +194,7 @@ jobs: xml_coverage_report.xml >> "$GITHUB_STEP_SUMMARY" - name: Publish combined junit pytest report if: success() || failure() - uses: mikepenz/action-junit-report@v5 + uses: mikepenz/action-junit-report@v6 with: report_paths: "reports/**/*.xml" annotate_only: true From b01ee761ddc111c69ee50e9989b8ef22ebdff634 Mon Sep 17 00:00:00 2001 From: reginabuehler Date: Mon, 4 May 2026 08:09:10 +0000 Subject: [PATCH 091/200] test: fix elementary effects tests --- .../iterators/test_elementary_effects.py | 76 +++++++++---------- 1 file changed, 38 insertions(+), 38 deletions(-) diff --git a/tests/integration_tests/iterators/test_elementary_effects.py b/tests/integration_tests/iterators/test_elementary_effects.py index b11be2e00..9fc514665 100644 --- a/tests/integration_tests/iterators/test_elementary_effects.py +++ b/tests/integration_tests/iterators/test_elementary_effects.py @@ -75,21 +75,21 @@ def test_elementary_effects_ishigami90(global_settings): results = load_result(global_settings.result_file(".pickle")) _logger.info(results) - assert results["sensitivity_indices"]["mu"][0] == pytest.approx(15.46038594, abs=1e-7) + assert results["sensitivity_indices"]["mu"][0] == pytest.approx(17.68763290, abs=1e-7) assert results["sensitivity_indices"]["mu"][1] == pytest.approx(0.0, abs=1e-7) - assert results["sensitivity_indices"]["mu"][2] == pytest.approx(0.0, abs=1e-7) + assert results["sensitivity_indices"]["mu"][2] == pytest.approx(7.13332892, abs=1e-7) - assert results["sensitivity_indices"]["mu_star"][0] == pytest.approx(15.460385940, abs=1e-7) + assert results["sensitivity_indices"]["mu_star"][0] == pytest.approx(17.68763290, abs=1e-7) assert results["sensitivity_indices"]["mu_star"][1] == pytest.approx(1.47392000, abs=1e-7) - assert results["sensitivity_indices"]["mu_star"][2] == pytest.approx(5.63434321, abs=1e-7) + assert results["sensitivity_indices"]["mu_star"][2] == pytest.approx(7.13332892, abs=1e-7) - assert results["sensitivity_indices"]["sigma"][0] == pytest.approx(15.85512257, abs=1e-7) + assert results["sensitivity_indices"]["sigma"][0] == pytest.approx(18.77919823, abs=1e-7) assert results["sensitivity_indices"]["sigma"][1] == pytest.approx(1.70193622, abs=1e-7) - assert results["sensitivity_indices"]["sigma"][2] == pytest.approx(9.20084394, abs=1e-7) + assert results["sensitivity_indices"]["sigma"][2] == pytest.approx(8.59288836, abs=1e-7) - assert results["sensitivity_indices"]["mu_star_conf"][0] == pytest.approx(13.53414548, abs=1e-7) + assert results["sensitivity_indices"]["mu_star_conf"][0] == pytest.approx(15.77224320, abs=1e-7) assert results["sensitivity_indices"]["mu_star_conf"][1] == pytest.approx(0.0, abs=1e-7) - assert results["sensitivity_indices"]["mu_star_conf"][2] == pytest.approx(5.51108773, abs=1e-7) + assert results["sensitivity_indices"]["mu_star_conf"][2] == pytest.approx(7.31091870, abs=1e-7) def test_elementary_effects_sobol( @@ -157,16 +157,16 @@ def fixture_expected_result_mu(): """Expected Mu result.""" expected_result_mu = np.array( [ - 25.8299150077341, - 19.28297176050532, - -14.092164789704626, - 5.333475971922498, - -11.385141403296364, - 13.970208961715421, - -3.0950202483238303, - 0.6672725255532903, - 7.2385092339309445, - -7.7664016980947075, + -2.601323663226073, + 20.68200584795835, + -7.759411231057245, + 4.7269015243468875, + -20.447764722050515, + 11.587939260262727, + 4.915003189487776, + -0.46675060195474005, + -3.5192417525555633, + -9.817808539704242, ] ) return expected_result_mu @@ -177,16 +177,16 @@ def fixture_expected_result_mu_star(): """Expected Mu star result.""" expected_result_mu_star = np.array( [ - 29.84594504725642, - 21.098173537614855, - 16.4727722348437, - 26.266876218598668, - 16.216603266281044, - 18.051629859410895, - 3.488313966697564, - 2.7128638920479147, - 7.671230484535577, - 10.299932289624746, + 9.58548627110508, + 23.298593393925685, + 13.031380571529553, + 6.551052192131895, + 23.87075909458303, + 13.493005422109425, + 8.636826684475931, + 0.804169417762858, + 3.845539815618292, + 10.185803340670184, ] ) return expected_result_mu_star @@ -197,16 +197,16 @@ def fixture_expected_result_sigma(): """Expected sigma result.""" expected_result_sigma = np.array( [ - 53.88783786787971, - 41.02192670857979, - 29.841807478998156, - 43.33349033575829, - 29.407676882180404, - 31.679653142831512, - 5.241491105224932, - 4.252334015139214, - 10.38274186974731, - 18.83046700807382, + 14.126073686851976, + 44.84025953013619, + 18.830571404935803, + 11.90755387463754, + 40.15919099245428, + 24.661511275785948, + 14.530785408431987, + 1.0111455153120015, + 5.494502535418954, + 17.68875251673258, ] ) return expected_result_sigma From d97204b78cee6044dee2e333830629dc1bac3a52 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 28 Apr 2026 21:37:41 +0200 Subject: [PATCH 092/200] ci: add pypi build test --- .github/workflows/test_pypi_build.yml | 65 +++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 .github/workflows/test_pypi_build.yml diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml new file mode 100644 index 000000000..cf748bb50 --- /dev/null +++ b/.github/workflows/test_pypi_build.yml @@ -0,0 +1,65 @@ +# yamllint disable +name: Test PyPI build + +on: + schedule: + - cron: "0 1 * * *" + pull_request: + push: + branches: + - main + workflow_dispatch: + +permissions: + contents: read + +jobs: + test_pypi_build: + name: PyPI build test (${{ matrix.os }}, ${{ matrix.install_target }}) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + install_target: base + extra_selector: "" + - os: ubuntu-latest + install_target: all + extra_selector: "[all]" + - os: macos-latest + install_target: base + extra_selector: "" + - os: macos-latest + install_target: all + extra_selector: "[all]" + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v6 + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: Build wheel and sdist + run: | + set -euo pipefail + + python -m pip install --upgrade pip build + python -m build + - name: Install built wheel in clean virtual environment + run: | + set -euo pipefail + + python -m venv .venv-pypi-smoke + source .venv-pypi-smoke/bin/activate + python -m pip install --upgrade pip + wheel_path="$(find dist -maxdepth 1 -type f -name '*.whl' | head -n 1)" + python -m pip install "${wheel_path}${{ matrix.extra_selector }}" + - name: Run pure PyPI smoke checks + run: | + set -euo pipefail + + source .venv-pypi-smoke/bin/activate + python -c "import queens" + pytest -v -m "unit_tests" tests/unit_tests/ From e96207a54429fa933ed5eb9e81ce6644a51da335 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 28 Apr 2026 22:15:57 +0200 Subject: [PATCH 093/200] ci: ignore path test in wheel based tests --- .github/workflows/test_pypi_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index cf748bb50..df4610790 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -62,4 +62,4 @@ jobs: source .venv-pypi-smoke/bin/activate python -c "import queens" - pytest -v -m "unit_tests" tests/unit_tests/ + pytest -v -m "unit_tests" --ignore=tests/unit_tests/utils/test_path_utils.py tests/unit_tests/ From dfbbe48cfe129024c0b97fb18437f908833ba11d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 18:41:06 +0200 Subject: [PATCH 094/200] feat: activate testing of tutorial tests that use 4C --- .github/workflows/local_testsuite.yml | 46 +++++- pyproject.toml | 4 +- tests/README.md | 11 ++ tests/conftest.py | 9 +- .../test_1_grid_iterator_rosenbrock.py | 7 +- ...ertainty_propagation_and_quantification.py | 7 +- tests/tutorial_tests/test_tutorials.py | 18 ++- .../tutorial_tests/tutorial_tests_markers.py | 136 ++++++++++++++++++ 8 files changed, 226 insertions(+), 12 deletions(-) create mode 100644 tests/tutorial_tests/tutorial_tests_markers.py diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index b0d3a4360..0386fe13d 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -131,6 +131,43 @@ jobs: if-no-files-found: error retention-days: 7 + run_tests_tutorials_fourc: + name: 4C tutorial tests (ubuntu-latest) + runs-on: ubuntu-latest + container: + image: ghcr.io/4c-multiphysics/4c-minimal:main + options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v6 + - uses: ./.github/actions/setup-queens-pixi + with: + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + environments: queens-dev + activate-environment: queens-dev + - name: Create links to 4C + run: | + ln -s /home/user/4C/bin/ config/4C_build + - name: Run pytest for 4C tutorial tests + run: | + set -euo pipefail + + COVERAGE_FILE=".coverage.tutorials_fourc.${{ runner.os }}" pytest -v -m "tutorial_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_fourc_${{ runner.os }}.xml + - name: Upload raw 4C tutorial test reports + if: success() || failure() + uses: actions/upload-artifact@v7 + with: + name: raw-test-reports-tutorials-fourc-${{ runner.os }} + include-hidden-files: true + path: | + .coverage.tutorials_fourc.${{ runner.os }} + test_junit_tutorials_fourc_${{ runner.os }}.xml + if-no-files-found: error + retention-days: 7 + report_test_results: name: report test results if: always() @@ -139,6 +176,7 @@ jobs: - run_tests_core - run_tests_tutorials - run_tests_fourc + - run_tests_tutorials_fourc defaults: run: shell: bash -l {0} @@ -176,6 +214,11 @@ jobs: with: name: raw-test-reports-fourc-Linux path: reports/fourc-ubuntu + - name: Download raw 4C tutorial test reports + uses: actions/download-artifact@v8 + with: + name: raw-test-reports-tutorials-fourc-Linux + path: reports/tutorials-fourc-ubuntu - name: Combine Ubuntu coverage data and build reports run: | set -euo pipefail @@ -183,8 +226,9 @@ jobs: cp reports/core-ubuntu/.coverage.core.Linux .coverage.core.Linux cp reports/tutorials-ubuntu/.coverage.tutorials.Linux .coverage.tutorials.Linux cp reports/fourc-ubuntu/.coverage.fourc.Linux .coverage.fourc.Linux + cp reports/tutorials-fourc-ubuntu/.coverage.tutorials_fourc.Linux .coverage.tutorials_fourc.Linux - pixi run --locked -e queens-dev coverage combine .coverage.core.Linux .coverage.tutorials.Linux .coverage.fourc.Linux + pixi run --locked -e queens-dev coverage combine .coverage.core.Linux .coverage.tutorials.Linux .coverage.fourc.Linux .coverage.tutorials_fourc.Linux pixi run --locked -e queens-dev coverage html -d html_coverage_report pixi run --locked -e queens-dev coverage xml -o xml_coverage_report.xml pixi run --locked -e queens-dev coverage report diff --git a/pyproject.toml b/pyproject.toml index 276f1f0eb..280a38582 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -118,7 +118,9 @@ markers = [ "benchmark: Benchmark tests, involving full QUEENS-iterator runs for performance benchmarks (excluded from the main pipeline)", "integration_tests: Integration tests with Python interface", "unit_tests: Unit tests", - "tutorial_tests: Tutorial tests", + "tutorial_tests: Tutorial tests that require no specialized tutorial resources", + "tutorial_tests_fourc: Tutorial tests that require fourc", + "tutorial_tests_remote: Tutorial tests that require remote execution resources", "integration_tests_fourc: Integration tests with fourc", "lnm_cluster: Integration tests with LNM clusters (require access to LNM network)", "imcs_cluster: Integration tests with LNM clusters (require access to IMCS network)", diff --git a/tests/README.md b/tests/README.md index f1e215c60..f1d29932d 100644 --- a/tests/README.md +++ b/tests/README.md @@ -33,8 +33,19 @@ In QUEENS, tests are organized using pytest markers. This allows you to run all | Unit tests | `pytest -m unit_tests` | | Integration tests | `pytest -m integration_tests` | | 4C integration test (see below) | `pytest -m integration_tests_fourc` | +| Tutorial tests | `pytest -m tutorial_tests` | +| 4C tutorial tests | `pytest -m tutorial_tests_fourc` | +| Remote tutorial tests | `pytest -m tutorial_tests_remote` | | List markers | `pytest --markers` | +### Adding tutorial notebook tests +All tutorial notebooks under `tutorials/` are discovered recursively. When adding a new notebook, +add its relative path to exactly one list in +`tests/tutorial_tests/tutorial_tests_markers.py::TUTORIAL_NOTEBOOKS_BY_MARKER`: use +`tutorial_tests` for regular tutorials, `tutorial_tests_fourc` for tutorials requiring 4C, and +`tutorial_tests_remote` for tutorials requiring remote resources. Pytest collection fails if a +notebook has no marker assignment. + ### :four_leaf_clover: Integration tests with 4C For the integration tests in QUEENS that require the multiphysics simulation framework [4C](https://github.com/4C-multiphysics/4C), the user needs to create a **symbolic link** to the 4C-executable and store it under `/config`: ``` diff --git a/tests/conftest.py b/tests/conftest.py index ca44b1952..c4d470ac5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -26,6 +26,7 @@ from queens.utils import config_directories from queens.utils.logger_settings import reset_logging from queens.utils.path import relative_path_from_root +from tests.tutorial_tests.tutorial_tests_markers import TUTORIAL_NOTEBOOKS_BY_MARKER _logger = logging.getLogger(__name__) @@ -126,7 +127,13 @@ def pytest_collection_modifyitems(items): if not check_item_for_marker(item, "max_time_for_test"): item.add_marker(pytest.mark.max_time_for_test(10)) elif "tutorial_tests/" in item.nodeid: - item.add_marker(pytest.mark.tutorial_tests) + + has_tutorial_marker = any( + check_item_for_marker(item, marker_name) + for marker_name in TUTORIAL_NOTEBOOKS_BY_MARKER + ) + if not has_tutorial_marker: + item.add_marker(pytest.mark.tutorial_tests) # Add default max_time_for_test if none was set if not check_item_for_marker(item, "max_time_for_test"): diff --git a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py index dbc510f94..136c091da 100644 --- a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py +++ b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py @@ -18,10 +18,15 @@ from testbook import testbook from test_utils.tutorial_tests import inject_mock_base_dir +from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook + +NOTEBOOK_PATH = "tutorials/1_grid_iterator_rosenbrock.ipynb" + +pytestmark = markers_for_notebook(NOTEBOOK_PATH) @testbook( - "tutorials/1_grid_iterator_rosenbrock.ipynb", + NOTEBOOK_PATH, ) def test_output_tutorial_1(tb, tmp_path): """Parameterized test case for tutorial 1: Grid Iterator Rosenbrock. diff --git a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py index 233668da3..f70c2cb84 100644 --- a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py +++ b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py @@ -18,10 +18,15 @@ from testbook import testbook from test_utils.tutorial_tests import inject_mock_base_dir +from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook + +NOTEBOOK_PATH = "tutorials/2_uncertainty_propagation_and_quantification.ipynb" + +pytestmark = markers_for_notebook(NOTEBOOK_PATH) @testbook( - "tutorials/2_uncertainty_propagation_and_quantification.ipynb", + NOTEBOOK_PATH, timeout=-1, ) def test_output_tutorial_2(tb, tmp_path): diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index 3c562aef4..8aeb9419f 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -20,18 +20,22 @@ from testbook import testbook from test_utils.tutorial_tests import inject_mock_base_dir +from tests.tutorial_tests.tutorial_tests_markers import ALL_TUTORIAL_NOTEBOOKS, notebook_param +TUTORIAL_NOTEBOOKS_WITH_DEDICATED_TESTS = { + path.stem.removeprefix("test_") + for path in Path("tests/tutorial_tests").glob("test_*.py") + if path.name != Path(__file__).name +} -# tested jupyter notebooks should be added to the list below + +# Notebooks with dedicated output assertions are collected in their own test modules. @pytest.mark.parametrize( "paths_to_tutorial_notebooks", [ - str(patch) - for patch in sorted(Path("tutorials").glob("*.ipynb")) - if patch.stem - not in { - t.stem.removeprefix("test_") for t in Path("tests/tutorial_tests").glob("test_*.py") - } + notebook_param(path) + for path in ALL_TUTORIAL_NOTEBOOKS + if Path(path).stem not in TUTORIAL_NOTEBOOKS_WITH_DEDICATED_TESTS ], ) def test_notebooks(tmp_path, paths_to_tutorial_notebooks): diff --git a/tests/tutorial_tests/tutorial_tests_markers.py b/tests/tutorial_tests/tutorial_tests_markers.py new file mode 100644 index 000000000..bab17c823 --- /dev/null +++ b/tests/tutorial_tests/tutorial_tests_markers.py @@ -0,0 +1,136 @@ +# +# SPDX-License-Identifier: LGPL-3.0-or-later +# Copyright (c) 2024-2025, QUEENS contributors. +# +# This file is part of QUEENS. +# +# QUEENS is free software: you can redistribute it and/or modify it under the terms of the GNU +# Lesser General Public License as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. QUEENS is distributed in the hope that it will +# be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You +# should have received a copy of the GNU Lesser General Public License along with QUEENS. If not, +# see . +# +"""Marker assignments for tutorial notebooks.""" + +from collections import Counter +from itertools import chain +from pathlib import Path + +import pytest + +TUTORIAL_NOTEBOOKS_BY_MARKER = { + "tutorial_tests": [ + "tutorials/1_grid_iterator_rosenbrock.ipynb", + "tutorials/2_uncertainty_propagation_and_quantification.ipynb", + ], + "tutorial_tests_fourc": [ + "tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb", + "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" + "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb", + ], + "tutorial_tests_remote": [], +} + +ALL_TUTORIAL_NOTEBOOKS = tuple( + sorted(path.as_posix() for path in Path("tutorials").rglob("*.ipynb")) +) + + +def _format_paths(paths): + """Format paths for collection error messages.""" + return "\n".join(f" - {path}" for path in sorted(paths)) + + +def _duplicate_paths(paths): + """Return paths that occur more than once.""" + return sorted(path for path, count in Counter(paths).items() if count > 1) + + +def _validate_tutorial_notebook_markers(): + """Ensure every tutorial notebook has at least one explicit marker.""" + discovered_notebooks = set(ALL_TUTORIAL_NOTEBOOKS) + marked_notebooks = set(chain.from_iterable(TUTORIAL_NOTEBOOKS_BY_MARKER.values())) + missing_notebooks = discovered_notebooks - marked_notebooks + stale_notebooks = marked_notebooks - discovered_notebooks + base_notebooks = set(TUTORIAL_NOTEBOOKS_BY_MARKER["tutorial_tests"]) + specialized_notebooks = set( + chain.from_iterable( + notebook_paths + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if marker_name != "tutorial_tests" + ) + ) + overlapping_base_notebooks = base_notebooks & specialized_notebooks + + duplicate_marker_assignments = { + marker_name: duplicates + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if (duplicates := _duplicate_paths(notebook_paths)) + } + + if not ( + missing_notebooks + or stale_notebooks + or overlapping_base_notebooks + or duplicate_marker_assignments + ): + return + + error_parts = ["Tutorial notebook marker assignments are out of sync."] + if missing_notebooks: + error_parts.append( + "Add marker assignments for these notebooks:\n" f"{_format_paths(missing_notebooks)}" + ) + if stale_notebooks: + error_parts.append( + "Remove marker assignments for missing notebooks:\n" f"{_format_paths(stale_notebooks)}" + ) + if overlapping_base_notebooks: + error_parts.append( + "Remove tutorial_tests from notebooks with specialized tutorial markers:\n" + f"{_format_paths(overlapping_base_notebooks)}" + ) + if duplicate_marker_assignments: + duplicate_entries = [ + f"{marker_name}: {notebook_path}" + for marker_name, notebook_paths in duplicate_marker_assignments.items() + for notebook_path in notebook_paths + ] + error_parts.append( + "Remove duplicate marker assignments:\n" f"{_format_paths(duplicate_entries)}" + ) + + raise pytest.UsageError("\n\n".join(error_parts)) + + +_validate_tutorial_notebook_markers() + + +def marker_names_for_notebook(notebook_path): + """Return marker names assigned to a tutorial notebook.""" + notebook_path = Path(notebook_path).as_posix() + return [ + marker_name + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if notebook_path in notebook_paths + ] + + +def markers_for_notebook(notebook_path): + """Return pytest markers assigned to a tutorial notebook.""" + return [ + getattr(pytest.mark, marker_name) + for marker_name in marker_names_for_notebook(notebook_path) + ] + + +def notebook_param(notebook_path): + """Return a pytest parameter for a tutorial notebook.""" + notebook_path = Path(notebook_path).as_posix() + return pytest.param( + notebook_path, + marks=markers_for_notebook(notebook_path), + id=notebook_path, + ) From d1f20a3630089d69fa9ef2ec78bdc48dc63db239 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 20:19:18 +0200 Subject: [PATCH 095/200] fix: import error in 4c tutorial tests --- test_utils/tutorial_tests.py | 22 +++++++++++++++++++ tests/tutorial_tests/test_tutorials.py | 4 +++- .../plot_results.py | 3 ++- 3 files changed, 27 insertions(+), 2 deletions(-) diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index e42d1ab84..d257a0800 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -15,6 +15,28 @@ """Utility methods used by the tutorial tests.""" +def inject_notebook_directory_to_path(tb, path_to_notebook): + """Inject the notebook directory into the notebook Python path. + + Args: + tb (testbook): testbook object for inserting code into the notebook + path_to_notebook (str | Path): Path to the notebook under test + + Returns: + None + """ + tb.inject( + f""" + import sys + from pathlib import Path + notebook_dir = Path({str(path_to_notebook)!r}).resolve().parent + if str(notebook_dir) not in sys.path: + sys.path.insert(0, str(notebook_dir)) + """, + before=0, + ) + + def inject_mock_base_dir(tb, tmp_path): """Inject a mock base directory for testing notebooks. diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index 8aeb9419f..d2684a8d8 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -19,7 +19,7 @@ import pytest from testbook import testbook -from test_utils.tutorial_tests import inject_mock_base_dir +from test_utils.tutorial_tests import inject_mock_base_dir, inject_notebook_directory_to_path from tests.tutorial_tests.tutorial_tests_markers import ALL_TUTORIAL_NOTEBOOKS, notebook_param TUTORIAL_NOTEBOOKS_WITH_DEDICATED_TESTS = { @@ -45,6 +45,8 @@ def test_notebooks(tmp_path, paths_to_tutorial_notebooks): any errors/assertions. """ with testbook(paths_to_tutorial_notebooks, timeout=-1) as tb: + inject_notebook_directory_to_path(tb, paths_to_tutorial_notebooks) + # Patch base_directory to avoid writing test data to user's home dir. # Note that tb.patch converts the mocked Path to a string, so we have to use tb.inject. inject_mock_base_dir(tb, tmp_path) diff --git a/tutorials/3_orchestrating_4c_simulations/plot_results.py b/tutorials/3_orchestrating_4c_simulations/plot_results.py index 8990febc7..acfdfa87a 100644 --- a/tutorials/3_orchestrating_4c_simulations/plot_results.py +++ b/tutorials/3_orchestrating_4c_simulations/plot_results.py @@ -15,6 +15,7 @@ """Plotting functions for tutorial 3.""" import os +from pathlib import Path from typing import Any, cast os.environ["PYVISTA_OFF_SCREEN"] = "true" @@ -23,7 +24,7 @@ import pyvista as pv -fe_mesh = cast(pv.DataSet, cast(Any, pv.read("beam_coarse.exo"))) +fe_mesh = cast(pv.DataSet, cast(Any, pv.read(Path(__file__).with_name("beam_coarse.exo")))) def plot_results( From 3b17e0ce0e0efe8ccabc42010b40ff86021bf79f Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 21:48:43 +0200 Subject: [PATCH 096/200] fix: change cwd for notebook tests --- test_utils/tutorial_tests.py | 6 ++++-- tests/tutorial_tests/test_tutorials.py | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index d257a0800..38e08c710 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -15,8 +15,8 @@ """Utility methods used by the tutorial tests.""" -def inject_notebook_directory_to_path(tb, path_to_notebook): - """Inject the notebook directory into the notebook Python path. +def inject_notebook_execution_context(tb, path_to_notebook): + """Inject the notebook directory as Python path and working directory. Args: tb (testbook): testbook object for inserting code into the notebook @@ -27,11 +27,13 @@ def inject_notebook_directory_to_path(tb, path_to_notebook): """ tb.inject( f""" + import os import sys from pathlib import Path notebook_dir = Path({str(path_to_notebook)!r}).resolve().parent if str(notebook_dir) not in sys.path: sys.path.insert(0, str(notebook_dir)) + os.chdir(notebook_dir) """, before=0, ) diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index d2684a8d8..72be43936 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -19,7 +19,7 @@ import pytest from testbook import testbook -from test_utils.tutorial_tests import inject_mock_base_dir, inject_notebook_directory_to_path +from test_utils.tutorial_tests import inject_mock_base_dir, inject_notebook_execution_context from tests.tutorial_tests.tutorial_tests_markers import ALL_TUTORIAL_NOTEBOOKS, notebook_param TUTORIAL_NOTEBOOKS_WITH_DEDICATED_TESTS = { @@ -45,7 +45,7 @@ def test_notebooks(tmp_path, paths_to_tutorial_notebooks): any errors/assertions. """ with testbook(paths_to_tutorial_notebooks, timeout=-1) as tb: - inject_notebook_directory_to_path(tb, paths_to_tutorial_notebooks) + inject_notebook_execution_context(tb, paths_to_tutorial_notebooks) # Patch base_directory to avoid writing test data to user's home dir. # Note that tb.patch converts the mocked Path to a string, so we have to use tb.inject. From 78ea31521c7d17894aaa65b4e2d6f18b2bf0dcbb Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 22:22:14 +0200 Subject: [PATCH 097/200] fix: resolve notebook path in test execution --- test_utils/tutorial_tests.py | 2 +- tests/tutorial_tests/test_tutorials.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index 38e08c710..97bbc558e 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -30,7 +30,7 @@ def inject_notebook_execution_context(tb, path_to_notebook): import os import sys from pathlib import Path - notebook_dir = Path({str(path_to_notebook)!r}).resolve().parent + notebook_dir = Path({str(path_to_notebook)!r}) if str(notebook_dir) not in sys.path: sys.path.insert(0, str(notebook_dir)) os.chdir(notebook_dir) diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index 72be43936..1fdaedd25 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -45,7 +45,8 @@ def test_notebooks(tmp_path, paths_to_tutorial_notebooks): any errors/assertions. """ with testbook(paths_to_tutorial_notebooks, timeout=-1) as tb: - inject_notebook_execution_context(tb, paths_to_tutorial_notebooks) + absolut_path_to_notebook = Path(paths_to_tutorial_notebooks).resolve().parent + inject_notebook_execution_context(tb, absolut_path_to_notebook) # Patch base_directory to avoid writing test data to user's home dir. # Note that tb.patch converts the mocked Path to a string, so we have to use tb.inject. From 97210ee9213a0e89fde11e77967d7e9d63add988 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 22:38:56 +0200 Subject: [PATCH 098/200] fix: add tutorials dir to sys.path --- test_utils/tutorial_tests.py | 15 ++++++++++----- tests/tutorial_tests/test_tutorials.py | 4 ++-- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index 97bbc558e..6c2db3f24 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -15,12 +15,12 @@ """Utility methods used by the tutorial tests.""" -def inject_notebook_execution_context(tb, path_to_notebook): +def inject_notebook_execution_context(tb, notebook_dir): """Inject the notebook directory as Python path and working directory. Args: tb (testbook): testbook object for inserting code into the notebook - path_to_notebook (str | Path): Path to the notebook under test + notebook_dir (str | Path): Directory conainting the notebook Returns: None @@ -30,9 +30,14 @@ def inject_notebook_execution_context(tb, path_to_notebook): import os import sys from pathlib import Path - notebook_dir = Path({str(path_to_notebook)!r}) - if str(notebook_dir) not in sys.path: - sys.path.insert(0, str(notebook_dir)) + notebook_dir = Path({str(notebook_dir)!r}) + repo_root = next( + path for path in (notebook_dir, *notebook_dir.parents) + if (path / "pyproject.toml").exists() + ) + for path in (notebook_dir, repo_root): + if str(path) not in sys.path: + sys.path.insert(0, str(path)) os.chdir(notebook_dir) """, before=0, diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index 1fdaedd25..09e832e73 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -45,8 +45,8 @@ def test_notebooks(tmp_path, paths_to_tutorial_notebooks): any errors/assertions. """ with testbook(paths_to_tutorial_notebooks, timeout=-1) as tb: - absolut_path_to_notebook = Path(paths_to_tutorial_notebooks).resolve().parent - inject_notebook_execution_context(tb, absolut_path_to_notebook) + notebook_dir = Path(paths_to_tutorial_notebooks).resolve().parent + inject_notebook_execution_context(tb, notebook_dir) # Patch base_directory to avoid writing test data to user's home dir. # Note that tb.patch converts the mocked Path to a string, so we have to use tb.inject. From 934080079473748c71d8663208f7d8e0ee54dc20 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 8 May 2026 23:32:52 +0200 Subject: [PATCH 099/200] refactor: use config directories to identify base dir --- .../3_orchestrating_4c_simulations.ipynb | 12 +++++++----- ...tainty_due_to_heterogeneous_material_fields.ipynb | 4 ++-- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb b/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb index 33fb940e7..1245936fd 100644 --- a/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb +++ b/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb @@ -60,13 +60,13 @@ "source": [ "# Define some paths\n", "from pathlib import Path\n", + "import queens.utils.config_directories as config_directories\n", "from tutorials.utils import find_repo_root\n", "\n", - "home = Path.home()\n", "NOTEBOOK_DIR = Path.cwd()\n", "\n", "QUEENS_BASE_DIR = find_repo_root(NOTEBOOK_DIR)\n", - "QUEENS_EXPERIMENTS_DIR = home / \"queens-experiments\"\n", + "QUEENS_EXPERIMENTS_DIR = config_directories.base_directory()\n", "TUTORIAL_DIR = QUEENS_BASE_DIR / \"tutorials\" / \"3_orchestrating_4c_simulations\"" ] }, @@ -453,11 +453,13 @@ "n_grid_points_young = 4\n", "n_grid_points_poisson_ratio = 21\n", "\n", + "grid_experiment_name = f\"grid_{n_grid_points_young}x{n_grid_points_poisson_ratio}\"\n", + "\n", "grid_output = None\n", "if __name__ == \"__main__\":\n", " Path(\"grid\").mkdir(exist_ok=True)\n", " with GlobalSettings(\n", - " experiment_name=f\"grid_{n_grid_points_young}x{n_grid_points_poisson_ratio}\",\n", + " experiment_name=grid_experiment_name,\n", " output_dir=\"grid\",\n", " ) as gs:\n", " scheduler = Local(\n", @@ -566,7 +568,7 @@ "\n", "Since we are doing our computations locally, we use a `Local` scheduler. However, there is also a `Cluster` scheduler which is able to submit jobs on high performance clusters using `SLURM`, `PBS` etc.\n", "\n", - "The scheduler also creates the required folder structure for an experiment. The default value is set to `~/queens-experiments/`. For the grid iterator, it looks like this:\n", + "The scheduler also creates the required folder structure for an experiment. The default base directory is given by `config_directories.base_directory()`. For the grid iterator, it looks like this:\n", "```bash\n", "grid_4x21/\n", "├── 0\n", @@ -617,7 +619,7 @@ " for j in range(2):\n", " plotter.subplot(i, j)\n", " job_id = job_ids[i * 2 + j]\n", - " file_path = QUEENS_EXPERIMENTS_DIR / f\"grid_4x21/{job_id}/output/output-vtk-files/structure-00001.pvtu\"\n", + " file_path = QUEENS_EXPERIMENTS_DIR / f\"{grid_experiment_name}/{job_id}/output/output-vtk-files/structure-00001.pvtu\"\n", " plotter.add_text(f\"Job: {job_id}\")\n", " plot_results(file_path, plotter, f\"E={grid_points[job_id][0]}, nu={np.round(grid_points[job_id][1],decimals=4)}: Cauchy stress zz\\n\",)\n", " plotter.show()" diff --git a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb index 2e84e48fc..fb827e3b2 100644 --- a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb +++ b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb @@ -111,6 +111,7 @@ "source": [ "# Define some paths\n", "from pathlib import Path\n", + "import queens.utils.config_directories as config_directories\n", "\n", "try:\n", " from tutorials.utils import find_repo_root\n", @@ -121,11 +122,10 @@ " sys.path.insert(0, str(REPO_ROOT))\n", " from tutorials.utils import find_repo_root\n", "\n", - "home = Path.home()\n", "NOTEBOOK_DIR = Path.cwd()\n", "\n", "QUEENS_BASE_DIR = find_repo_root(NOTEBOOK_DIR)\n", - "QUEENS_EXPERIMENTS_DIR = home / \"queens-experiments\"\n", + "QUEENS_EXPERIMENTS_DIR = config_directories.base_directory()\n", "INPUT_DIR = QUEENS_BASE_DIR / \"tests\" / \"input_files\" / \"third_party\" / \"fourc\"" ] }, From fed5dc0f04a2bda8a1897afd7f94018d4063379e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 9 May 2026 00:05:59 +0200 Subject: [PATCH 100/200] fix: use pandas functionality for filtering --- src/queens/data_processors/csv_file.py | 37 +++++++++++++------ .../data_processors/test_csv_file.py | 12 ++++++ 2 files changed, 38 insertions(+), 11 deletions(-) diff --git a/src/queens/data_processors/csv_file.py b/src/queens/data_processors/csv_file.py index 1dba3ca4b..85f1ce888 100644 --- a/src/queens/data_processors/csv_file.py +++ b/src/queens/data_processors/csv_file.py @@ -352,11 +352,18 @@ def _filter_by_target_values(self, raw_data): Returns: DataFrame: Filtered data. """ - if any(raw_data): - target_indices = [] - for target_value in self.filter_target_values: - target_indices.append( - int(np.where(np.abs(raw_data.index - target_value) <= self.filter_tol)[0]) + if not raw_data.empty: + target_indices = raw_data.index.get_indexer( + self.filter_target_values, + method="nearest", + tolerance=self.filter_tol, + ) + + if (target_indices == -1).any(): + missing_targets = np.asarray(self.filter_target_values)[target_indices == -1] + raise RuntimeError( + f"No index values found within tolerance {self.filter_tol} " + f"for target values {missing_targets.tolist()}." ) return raw_data.iloc[target_indices] @@ -371,13 +378,21 @@ def _filter_by_range(self, raw_data): Returns: DataFrame: Filtered data. """ - if any(raw_data): - range_start = int( - np.where(np.abs(raw_data.index - self.filter_range[0]) <= self.filter_tol)[0] - ) - range_end = int( - np.where(np.abs(raw_data.index - self.filter_range[-1]) <= self.filter_tol)[-1] + if not raw_data.empty: + range_start, range_end = raw_data.index.get_indexer( + self.filter_range, + method="nearest", + tolerance=self.filter_tol, ) + if -1 in (range_start, range_end): + missing_targets = np.asarray(self.filter_range)[ + np.asarray([range_start, range_end]) == -1 + ] + raise RuntimeError( + f"No index values found within tolerance {self.filter_tol} " + f"for range values {missing_targets.tolist()}." + ) + return raw_data.iloc[range_start : range_end + 1] return None diff --git a/tests/unit_tests/data_processors/test_csv_file.py b/tests/unit_tests/data_processors/test_csv_file.py index c86142bfe..55188194a 100644 --- a/tests/unit_tests/data_processors/test_csv_file.py +++ b/tests/unit_tests/data_processors/test_csv_file.py @@ -322,6 +322,18 @@ def test_filter_by_target_values(default_data_processor, default_raw_data): np.testing.assert_allclose(expected_data, processed_data) +def test_filter_by_target_values_no_value_within_tolerance( + default_data_processor, default_raw_data +): + """Test filter by target values without an index value within tol.""" + default_data_processor.filter_type = "by_target_values" + default_data_processor.filter_target_values = [0.07] + default_data_processor.filter_tol = 1e-3 + + with pytest.raises(RuntimeError, match="No index values found within tolerance"): + default_data_processor.filter_and_manipulate_raw_data(default_raw_data) + + def test_filter_by_row_index(default_data_processor, default_raw_data): """Test filter by row index.""" default_data_processor.filter_type = "by_row_index" From 2349d630f2440001379a4099af48979fb1ef212b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sat, 9 May 2026 09:35:22 +0200 Subject: [PATCH 101/200] ci: publish junit report for each pytest job --- .github/workflows/local_testsuite.yml | 28 +++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 0386fe13d..c0ca7b79d 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -45,6 +45,13 @@ jobs: set -euo pipefail COVERAGE_FILE=".coverage.core.${{ runner.os }}" pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_core_${{ runner.os }}.xml + - name: Publish junit pytest report + if: success() || failure() + uses: mikepenz/action-junit-report@v6 + with: + report_paths: "test_junit_*.xml" + annotate_only: true + job_summary: false - name: Upload raw core test reports if: success() || failure() uses: actions/upload-artifact@v7 @@ -82,6 +89,13 @@ jobs: set -euo pipefail COVERAGE_FILE=".coverage.tutorials.${{ runner.os }}" pytest -v -m "tutorial_tests" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_${{ runner.os }}.xml + - name: Publish junit pytest report + if: success() || failure() + uses: mikepenz/action-junit-report@v6 + with: + report_paths: "test_junit_*.xml" + annotate_only: true + job_summary: false - name: Upload raw tutorial test reports if: success() || failure() uses: actions/upload-artifact@v7 @@ -119,6 +133,13 @@ jobs: set -euo pipefail COVERAGE_FILE=".coverage.fourc.${{ runner.os }}" pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc_${{ runner.os }}.xml + - name: Publish junit pytest report + if: success() || failure() + uses: mikepenz/action-junit-report@v6 + with: + report_paths: "test_junit_*.xml" + annotate_only: true + job_summary: false - name: Upload raw 4C test reports if: success() || failure() uses: actions/upload-artifact@v7 @@ -156,6 +177,13 @@ jobs: set -euo pipefail COVERAGE_FILE=".coverage.tutorials_fourc.${{ runner.os }}" pytest -v -m "tutorial_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_fourc_${{ runner.os }}.xml + - name: Publish junit pytest report + if: success() || failure() + uses: mikepenz/action-junit-report@v6 + with: + report_paths: "test_junit_*.xml" + annotate_only: true + job_summary: false - name: Upload raw 4C tutorial test reports if: success() || failure() uses: actions/upload-artifact@v7 From 55beebaa6a0ff16a729f5e77ca22d61e5d4113a1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 09:53:59 +0200 Subject: [PATCH 102/200] fix: np.NaN has been deprecated --- .../iterators/sobol_index_gp_uncertainty_utils/estimator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/queens/iterators/sobol_index_gp_uncertainty_utils/estimator.py b/src/queens/iterators/sobol_index_gp_uncertainty_utils/estimator.py index fbc9032e3..5caca9f4e 100644 --- a/src/queens/iterators/sobol_index_gp_uncertainty_utils/estimator.py +++ b/src/queens/iterators/sobol_index_gp_uncertainty_utils/estimator.py @@ -240,7 +240,7 @@ def _init_dataset( number_parameters, ) ) - data[:, :, :, :] = np.NaN + data[:, :, :, :] = np.nan estimates_second_order = xr.DataArray( data=data, dims=("gp_realization", "bootstrap", "parameter", "crossparameter"), From 498bdd50fb3000d3d0ba062cf441d90c28f4e9f3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 10:12:32 +0200 Subject: [PATCH 103/200] fix: accepted_sum is a one-dimensional array in case of several chains, need to convert accordingly to a string --- src/queens/iterators/metropolis_hastings_pymc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/queens/iterators/metropolis_hastings_pymc.py b/src/queens/iterators/metropolis_hastings_pymc.py index 4fc6fd6a4..714b5333c 100644 --- a/src/queens/iterators/metropolis_hastings_pymc.py +++ b/src/queens/iterators/metropolis_hastings_pymc.py @@ -200,7 +200,7 @@ def post_run(self): """Additional post run for MH.""" super().post_run() _logger.info( - "Acceptance rate is: %f", + "Acceptance rate is: %s", self.step.accepted_sum / self.num_samples, ) From 65213758c5c6c4c4fa79bf829b8766b2a1e3d57a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 10:34:18 +0200 Subject: [PATCH 104/200] docs: document details of test setup --- .../test_metropolis_hastings_pymc.py | 38 ++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py index 76b5ab4bd..396905355 100644 --- a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py +++ b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py @@ -34,7 +34,43 @@ def test_metropolis_hastings_pymc_gaussian( tmp_path, _create_experimental_data_zero, global_settings ): - """Test case for mh iterator.""" + """Test MH sampling for a Gaussian-Gaussian Bayesian inference problem. + + The test samples from a two-dimensional posterior with Gaussian prior and Gaussian + likelihood. Since both prior and likelihood are Gaussian, the posterior is Gaussian + again. The prior is + + x ~ N(mu_0, Sigma_0), + mu_0 = [-2, 2]^T, + Sigma_0 = [[1, 0], [0, 1]]. + + The likelihood is evaluated at the observed value y = [0, 0]^T with + + y | x ~ N(x, Sigma_L), + Sigma_L = [[1, 1/2], [1/2, 1]]. + + Therefore, + + Sigma_p = (Sigma_0^{-1} + Sigma_L^{-1})^{-1} + = [[7/15, 2/15], [2/15, 7/15]], + + mu_p = Sigma_p (Sigma_0^{-1} mu_0 + Sigma_L^{-1} y) + = Sigma_p mu_0 + = [-2/3, 2/3]^T. + + The converged Markov chain should therefore approximate + + E[x | y] = [-2/3, 2/3]^T, + Var[x | y] = [7/15, 7/15], + Std[x | y] = [sqrt(7/15), sqrt(7/15)]. + + Note: + This behaviour is achieved by patching the Gaussian likelihood model + evaluation with ``target_density`` below. Instead of evaluating against + the experimental data, the likelihood is replaced by a fixed analytic + Gaussian log-density corresponding to the target distribution described + above. + """ # Parameters x1 = Normal(mean=[-2.0, 2.0], covariance=[[1.0, 0.0], [0.0, 1.0]]) parameters = Parameters(x1=x1) From f5722044af3ce1618aac240637a6eff69003d7e0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 10:45:41 +0200 Subject: [PATCH 105/200] fix: adjust expected values and switch to numpy testing, control tols --- .../iterators/test_metropolis_hastings_pymc.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py index 396905355..1c342b805 100644 --- a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py +++ b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py @@ -15,7 +15,6 @@ """Integration test for the Metropolis Hastings PyMC iterator.""" import numpy as np -import pytest from mock import patch from example_simulator_functions.gaussian_logpdf import gaussian_2d_logpdf @@ -110,10 +109,18 @@ def test_metropolis_hastings_pymc_gaussian( # Load results results = load_result(global_settings.result_file(".pickle")) - assert results["mean"].mean(axis=0) == pytest.approx( - np.array([-0.5680310153118374, 0.9247536392514567]) + np.testing.assert_allclose( + results["mean"].mean(axis=0), + np.array([-0.3783841506648389, 1.1993237016123788]), + rtol=1e-6, + atol=1e-12, + ) + np.testing.assert_allclose( + results["var"].mean(axis=0), + np.array([0.2750466882590994, 1.2853678554541608]), + rtol=1e-6, + atol=1e-12, ) - assert results["var"].mean(axis=0) == pytest.approx([0.13601070852470507, 0.6672200465857734]) def target_density(self, samples): # pylint: disable=unused-argument From befc284a1a9737f655d01cdbe44756553eb058be Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 10:56:44 +0200 Subject: [PATCH 106/200] docs: add explanation of test setup --- .../integration_tests/iterators/test_nuts.py | 38 ++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/tests/integration_tests/iterators/test_nuts.py b/tests/integration_tests/iterators/test_nuts.py index 5fd4107f5..47fae00ec 100644 --- a/tests/integration_tests/iterators/test_nuts.py +++ b/tests/integration_tests/iterators/test_nuts.py @@ -37,7 +37,43 @@ def test_nuts_gaussian( _create_experimental_data, global_settings, ): - """Test case for nuts iterator.""" + """Test NUTS sampling for a Gaussian-Gaussian Bayesian inference problem. + + The test samples from a two-dimensional posterior with Gaussian prior and Gaussian + likelihood. Since both prior and likelihood are Gaussian, the posterior is Gaussian + again. The prior is + + x ~ N(mu_0, Sigma_0), + mu_0 = [-2, 2]^T, + Sigma_0 = [[1, 0], [0, 1]]. + + The likelihood is evaluated at the observed value y = [0, 0]^T with + + y | x ~ N(x, Sigma_L), + Sigma_L = [[1, 1/2], [1/2, 1]]. + + Therefore, + + Sigma_p = (Sigma_0^{-1} + Sigma_L^{-1})^{-1} + = [[7/15, 2/15], [2/15, 7/15]], + + mu_p = Sigma_p (Sigma_0^{-1} mu_0 + Sigma_L^{-1} y) + = Sigma_p mu_0 + = [-2/3, 2/3]^T. + + The converged Markov chain should therefore approximate + + E[x | y] = [-2/3, 2/3]^T, + Var[x | y] = [7/15, 7/15], + Std[x | y] = [sqrt(7/15), sqrt(7/15)]. + + Note: + This behaviour is achieved by patching the Gaussian likelihood model + evaluation and gradient with ``target_density_gaussian_2d_with_grad``. + Instead of evaluating against the experimental data, the likelihood is + replaced by a fixed analytic Gaussian log-density corresponding to the + target distribution described above. + """ # Parameters x1 = Normal(mean=[-2.0, 2.0], covariance=[[1.0, 0.0], [0.0, 1.0]]) parameters = Parameters(x1=x1) From baa7a676b9b6d9572a855df08bf6cbe833504083 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 10:58:12 +0200 Subject: [PATCH 107/200] feat: switch to numpy testing statements --- tests/integration_tests/iterators/test_nuts.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/tests/integration_tests/iterators/test_nuts.py b/tests/integration_tests/iterators/test_nuts.py index 47fae00ec..ec3513c7e 100644 --- a/tests/integration_tests/iterators/test_nuts.py +++ b/tests/integration_tests/iterators/test_nuts.py @@ -113,10 +113,18 @@ def test_nuts_gaussian( # Load results results = load_result(global_settings.result_file(".pickle")) - assert results["mean"].mean(axis=0) == pytest.approx( - np.array([-0.2868793496608573, 0.6474274597130008]) + np.testing.assert_allclose( + results["mean"].mean(axis=0), + np.array([-0.2868793496608573, 0.6474274597130008]), + rtol=1e-6, + atol=1e-12, + ) + np.testing.assert_allclose( + results["var"].mean(axis=0), + np.array([0.08396277217936474, 0.10836256575521087]), + rtol=1e-6, + atol=1e-12, ) - assert results["var"].mean(axis=0) == pytest.approx([0.08396277217936474, 0.10836256575521087]) @pytest.fixture(name="_create_experimental_data") From 4e5de59adafe4431824e7162231169268d9fae73 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:03:28 +0200 Subject: [PATCH 108/200] fix: adjust expected values for new dependency versions --- tests/integration_tests/iterators/test_nuts.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/integration_tests/iterators/test_nuts.py b/tests/integration_tests/iterators/test_nuts.py index ec3513c7e..243097d56 100644 --- a/tests/integration_tests/iterators/test_nuts.py +++ b/tests/integration_tests/iterators/test_nuts.py @@ -115,13 +115,13 @@ def test_nuts_gaussian( np.testing.assert_allclose( results["mean"].mean(axis=0), - np.array([-0.2868793496608573, 0.6474274597130008]), + np.array([-1.0964337346677933, 0.9148542463484473]), rtol=1e-6, atol=1e-12, ) np.testing.assert_allclose( results["var"].mean(axis=0), - np.array([0.08396277217936474, 0.10836256575521087]), + np.array([0.33594238408352364, 1.053294709724648]), rtol=1e-6, atol=1e-12, ) From aca321ed7834b7031f2ae60e964de51ef0e991cb Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:05:10 +0200 Subject: [PATCH 109/200] feat: loosen tolerances a bit --- .../iterators/test_metropolis_hastings_pymc.py | 11 +++++++---- tests/integration_tests/iterators/test_nuts.py | 11 +++++++---- 2 files changed, 14 insertions(+), 8 deletions(-) diff --git a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py index 1c342b805..22a7fd830 100644 --- a/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py +++ b/tests/integration_tests/iterators/test_metropolis_hastings_pymc.py @@ -29,6 +29,9 @@ from queens.utils.experimental_data_reader import ExperimentalDataReader from queens.utils.io import load_result +SAMPLER_STAT_RTOL = 1e-5 +SAMPLER_STAT_ATOL = 1e-8 + def test_metropolis_hastings_pymc_gaussian( tmp_path, _create_experimental_data_zero, global_settings @@ -112,14 +115,14 @@ def test_metropolis_hastings_pymc_gaussian( np.testing.assert_allclose( results["mean"].mean(axis=0), np.array([-0.3783841506648389, 1.1993237016123788]), - rtol=1e-6, - atol=1e-12, + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, ) np.testing.assert_allclose( results["var"].mean(axis=0), np.array([0.2750466882590994, 1.2853678554541608]), - rtol=1e-6, - atol=1e-12, + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, ) diff --git a/tests/integration_tests/iterators/test_nuts.py b/tests/integration_tests/iterators/test_nuts.py index 243097d56..dae1c9e39 100644 --- a/tests/integration_tests/iterators/test_nuts.py +++ b/tests/integration_tests/iterators/test_nuts.py @@ -30,6 +30,9 @@ from queens.utils.experimental_data_reader import ExperimentalDataReader from queens.utils.io import load_result +SAMPLER_STAT_RTOL = 1e-5 +SAMPLER_STAT_ATOL = 1e-8 + def test_nuts_gaussian( tmp_path, @@ -116,14 +119,14 @@ def test_nuts_gaussian( np.testing.assert_allclose( results["mean"].mean(axis=0), np.array([-1.0964337346677933, 0.9148542463484473]), - rtol=1e-6, - atol=1e-12, + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, ) np.testing.assert_allclose( results["var"].mean(axis=0), np.array([0.33594238408352364, 1.053294709724648]), - rtol=1e-6, - atol=1e-12, + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, ) From 1c0c577a57c13b26c1bf2c59cacf10b98a2d2518 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:08:46 +0200 Subject: [PATCH 110/200] docs: add explanation of test setup --- .../iterators/test_hamiltonian_monte_carlo.py | 38 ++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py index 87764db26..df4603880 100644 --- a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py +++ b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py @@ -36,7 +36,43 @@ def test_hamiltonian_monte_carlo_gaussian( _create_experimental_data_zero, global_settings, ): - """Test case for hmc iterator.""" + """Test HMC sampling for a Gaussian-Gaussian Bayesian inference problem. + + The test samples from a two-dimensional posterior with Gaussian prior and Gaussian + likelihood. Since both prior and likelihood are Gaussian, the posterior is Gaussian + again. The prior is + + x ~ N(mu_0, Sigma_0), + mu_0 = [-2, 2]^T, + Sigma_0 = [[1, 0], [0, 1]]. + + The likelihood is evaluated at the observed value y = [0, 0]^T with + + y | x ~ N(x, Sigma_L), + Sigma_L = [[1, 1/2], [1/2, 1]]. + + Therefore, + + Sigma_p = (Sigma_0^{-1} + Sigma_L^{-1})^{-1} + = [[7/15, 2/15], [2/15, 7/15]], + + mu_p = Sigma_p (Sigma_0^{-1} mu_0 + Sigma_L^{-1} y) + = Sigma_p mu_0 + = [-2/3, 2/3]^T. + + The converged Markov chain should therefore approximate + + E[x | y] = [-2/3, 2/3]^T, + Var[x | y] = [7/15, 7/15], + Std[x | y] = [sqrt(7/15), sqrt(7/15)]. + + Note: + This behaviour is achieved by patching the Gaussian likelihood model + evaluation and gradient with ``target_density_gaussian_2d_with_grad``. + Instead of evaluating against the experimental data, the likelihood is + replaced by a fixed analytic Gaussian log-density corresponding to the + target distribution described above. + """ # Parameters x1 = Normal(mean=[-2.0, 2.0], covariance=[[1.0, 0.0], [0.0, 1.0]]) parameters = Parameters(x1=x1) From 142f8fe1b9af3363ab1d1f1ca5dbfe5f69e47482 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:10:17 +0200 Subject: [PATCH 111/200] feat: switch to numpy testing statements and loosen tolerances --- .../iterators/test_hamiltonian_monte_carlo.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py index df4603880..f16739b2b 100644 --- a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py +++ b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py @@ -15,7 +15,6 @@ """Integration test for the HMC iterator.""" import numpy as np -import pytest from mock import patch from queens.distributions.normal import Normal @@ -29,6 +28,9 @@ from queens.utils.experimental_data_reader import ExperimentalDataReader from queens.utils.io import load_result +SAMPLER_STAT_RTOL = 1e-5 +SAMPLER_STAT_ATOL = 1e-8 + def test_hamiltonian_monte_carlo_gaussian( tmp_path, @@ -112,7 +114,15 @@ def test_hamiltonian_monte_carlo_gaussian( # Load results results = load_result(global_settings.result_file(".pickle")) - assert results["mean"].mean(axis=0) == pytest.approx( - np.array([0.19363280864587615, -1.1303341362165935]) + np.testing.assert_allclose( + results["mean"].mean(axis=0), + np.array([0.19363280864587615, -1.1303341362165935]), + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, + ) + np.testing.assert_allclose( + results["var"].mean(axis=0), + np.array([0, 0]), + rtol=SAMPLER_STAT_RTOL, + atol=SAMPLER_STAT_ATOL, ) - assert results["var"].mean(axis=0) == pytest.approx([0, 0]) From 8b6c46aac391dca3af0787e7080712355271bcbd Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:12:35 +0200 Subject: [PATCH 112/200] fix: adjust desired values for new dependency versions --- .../integration_tests/iterators/test_hamiltonian_monte_carlo.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py index f16739b2b..5db87298f 100644 --- a/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py +++ b/tests/integration_tests/iterators/test_hamiltonian_monte_carlo.py @@ -116,7 +116,7 @@ def test_hamiltonian_monte_carlo_gaussian( np.testing.assert_allclose( results["mean"].mean(axis=0), - np.array([0.19363280864587615, -1.1303341362165935]), + np.array([0.2560446683451819, -1.311343427417079]), rtol=SAMPLER_STAT_RTOL, atol=SAMPLER_STAT_ATOL, ) From e23b983ee75607f4200fdc620f9067f6806101d3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:22:36 +0200 Subject: [PATCH 113/200] feat: switch to numpy testing statements with adaptable tolerances --- .../iterators/test_latin_hypercube_sampling.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tests/integration_tests/iterators/test_latin_hypercube_sampling.py b/tests/integration_tests/iterators/test_latin_hypercube_sampling.py index a54ad7ff5..2d90812e9 100644 --- a/tests/integration_tests/iterators/test_latin_hypercube_sampling.py +++ b/tests/integration_tests/iterators/test_latin_hypercube_sampling.py @@ -17,6 +17,7 @@ The test is based on the low-fidelity Borehole function. """ +import numpy as np import pytest from queens.distributions.uniform import Uniform @@ -62,8 +63,8 @@ def test_latin_hypercube_sampling_borehole83(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - assert results["mean"] == pytest.approx(62.05240444441511) - assert results["var"] == pytest.approx(1371.7554224384000) + np.testing.assert_allclose(results["mean"], 62.05240444441511, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["var"], 1371.7554224384000, rtol=1e-6, atol=1e-12) @pytest.mark.max_time_for_test(20) @@ -94,5 +95,5 @@ def test_latin_hypercube_sampling_branin78(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - assert results["mean"] == pytest.approx(53.17279969296224) - assert results["var"] == pytest.approx(2581.6502630157715) + np.testing.assert_allclose(results["mean"], 54.22064638692155, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["var"], 2581.6502630157715, rtol=1e-6, atol=1e-12) From 5df93cfb3b27930a4b47d871fe66911d0b1c4136 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:37:03 +0200 Subject: [PATCH 114/200] docs: add explanation of test setup and analytical solution --- .../test_latin_hypercube_sampling.py | 33 ++++++++++++++++--- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/tests/integration_tests/iterators/test_latin_hypercube_sampling.py b/tests/integration_tests/iterators/test_latin_hypercube_sampling.py index 2d90812e9..9267878d3 100644 --- a/tests/integration_tests/iterators/test_latin_hypercube_sampling.py +++ b/tests/integration_tests/iterators/test_latin_hypercube_sampling.py @@ -63,13 +63,36 @@ def test_latin_hypercube_sampling_borehole83(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - np.testing.assert_allclose(results["mean"], 62.05240444441511, rtol=1e-6, atol=1e-12) - np.testing.assert_allclose(results["var"], 1371.7554224384000, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["mean"], 61.910468085219456, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["var"], 1336.5420586597304, rtol=1e-6, atol=1e-12) @pytest.mark.max_time_for_test(20) def test_latin_hypercube_sampling_branin78(global_settings): - """Test case for latin hyper cube iterator.""" + """Test Latin hypercube sampling for the high-fidelity Branin function. + + The test samples the high-fidelity Branin benchmark function + + f(x_1, x_2) = + (-1.275 x_1^2 / pi^2 + 5 x_1 / pi + x_2 - 6)^2 + + (10 - 5 / (4 pi)) cos(x_1) + 10 + + with independent uniform input distributions + + x_1 ~ U[-5, 10], + x_2 ~ U[0, 15]. + + For these distributions, the exact moments are analytically defined by + + E[f] = 1 / 15^2 int_{-5}^{10} int_0^{15} f(x_1, x_2) dx_2 dx_1 + = 54.3071982719085, + + Var[f] = 1 / 15^2 int_{-5}^{10} int_0^{15} (f(x_1, x_2) - E[f])^2 dx_2 dx_1 + = 2626.687312415944. + + The assertions below check the deterministic sample statistics of the seeded + Latin hypercube run, not the exact distribution moments. + """ # Parameters x1 = Uniform(lower_bound=-5, upper_bound=10) x2 = Uniform(lower_bound=0, upper_bound=15) @@ -95,5 +118,5 @@ def test_latin_hypercube_sampling_branin78(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - np.testing.assert_allclose(results["mean"], 54.22064638692155, rtol=1e-6, atol=1e-12) - np.testing.assert_allclose(results["var"], 2581.6502630157715, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["mean"], 54.25531895299926, rtol=1e-6, atol=1e-12) + np.testing.assert_allclose(results["var"], 2483.786406285974, rtol=1e-6, atol=1e-12) From 0ea58c02a74563e2a92430895a6653ceb073a379 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 11:37:33 +0200 Subject: [PATCH 115/200] fix: control reproducibility of lhs sampling with proper, modern rng seeding --- src/queens/iterators/latin_hypercube_sampling.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/queens/iterators/latin_hypercube_sampling.py b/src/queens/iterators/latin_hypercube_sampling.py index 6b77958dc..a88a0ef96 100644 --- a/src/queens/iterators/latin_hypercube_sampling.py +++ b/src/queens/iterators/latin_hypercube_sampling.py @@ -81,7 +81,8 @@ def __init__( def pre_run(self): """Generate samples for subsequent LHS analysis.""" - np.random.seed(self.seed) + seed_sequence = np.random.SeedSequence(self.seed) + lhs_rng = np.random.default_rng(seed_sequence.spawn(1)[0]) num_inputs = self.parameters.num_parameters @@ -92,7 +93,11 @@ def pre_run(self): # create latin hyper cube samples in unit hyper cube hypercube_samples = lhs( - num_inputs, self.num_samples, criterion=self.criterion, iterations=self.num_iterations + num_inputs, + self.num_samples, + criterion=self.criterion, + iterations=self.num_iterations, + seed=lhs_rng, ) # scale and transform samples according to the inverse cdf self.samples = self.parameters.inverse_cdf_transform(hypercube_samples) From 892ed87d19cf432033d2dd276a877e2a1b7804db Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 12:12:35 +0200 Subject: [PATCH 116/200] fix: adjust desired values due to new dependency versions --- .../test_latin_hypercube_sampling.py | 29 +++++++++++++++---- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/tests/unit_tests/iterators/test_latin_hypercube_sampling.py b/tests/unit_tests/iterators/test_latin_hypercube_sampling.py index aebbf884f..3818211c6 100644 --- a/tests/unit_tests/iterators/test_latin_hypercube_sampling.py +++ b/tests/unit_tests/iterators/test_latin_hypercube_sampling.py @@ -42,30 +42,49 @@ def fixture_default_lhs_iterator( return my_iterator +@pytest.fixture(name="ref_lhs_result_iterator") +def fixture_ref_lhs_result_iterator(): + """Reference results for the default LHS iterator.""" + return np.array( + [ + [0.5401856501906925], + [4.305418063074407], + [6.218626875992211], + [-7.341084114985484], + [6.2263184418260975], + [5.992809151839016], + [8.676959923988381], + [2.187257549384814], + [6.521135693744268], + [6.0112492830277136], + ] + ) + + def test_correct_sampling(default_lhs_iterator): """Test if we get correct samples.""" # np.set_printoptions(precision=10) default_lhs_iterator.pre_run() # check if mean and std match - means_ref = np.array([-1.4546056001e-03, 5.4735307403e-03, 2.1664850171e00]) + means_ref = np.array([3.5708636985e-04, 9.4366122545e-03, 2.2065845877e00]) np.testing.assert_allclose( np.mean(default_lhs_iterator.samples, axis=0), means_ref, 1e-09, 1e-09 ) - std_ref = np.array([1.8157451781, 1.9914892803, 2.4282341125]) + std_ref = np.array([1.8152930704, 1.9637665236, 2.6752150172]) np.testing.assert_allclose(np.std(default_lhs_iterator.samples, axis=0), std_ref, 1e-09, 1e-09) # check if samples are identical too - ref_sample_first_row = np.array([-2.7374616292, -0.6146554017, 1.3925529817]) + ref_sample_first_row = np.array([-1.9557761949, 0.5130876432, 1.2407952238]) np.testing.assert_allclose( default_lhs_iterator.samples[0, :], ref_sample_first_row, 1e-07, 1e-07 ) -def test_correct_results(default_lhs_iterator, ref_result_iterator): +def test_correct_results(default_lhs_iterator, ref_lhs_result_iterator): """Test if we get correct results.""" default_lhs_iterator.pre_run() default_lhs_iterator.core_run() @@ -75,5 +94,5 @@ def test_correct_results(default_lhs_iterator, ref_result_iterator): # check if samples are identical too np.testing.assert_allclose( - default_lhs_iterator.output["result"][0:10], ref_result_iterator, 1e-09, 1e-09 + default_lhs_iterator.output["result"][0:10], ref_lhs_result_iterator, 1e-09, 1e-09 ) From c5c368f5d1005697572590c510761034a8c986df Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 12:36:04 +0200 Subject: [PATCH 117/200] fix: change desired values since salib switched to proper np.random.Generator usage --- .../iterators/test_elementary_effects.py | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/tests/unit_tests/iterators/test_elementary_effects.py b/tests/unit_tests/iterators/test_elementary_effects.py index 92e40eb20..cda0c5347 100644 --- a/tests/unit_tests/iterators/test_elementary_effects.py +++ b/tests/unit_tests/iterators/test_elementary_effects.py @@ -49,22 +49,22 @@ def test_correct_sampling(default_elementary_effects_iterator): ref_vals = np.array( [ - [-1.04719755, 3.14159265, 3.14159265], - [3.14159265, 3.14159265, 3.14159265], - [3.14159265, 3.14159265, -1.04719755], - [3.14159265, -1.04719755, -1.04719755], - [-3.14159265, -1.04719755, -3.14159265], - [-3.14159265, 3.14159265, -3.14159265], - [-3.14159265, 3.14159265, 1.04719755], - [1.04719755, 3.14159265, 1.04719755], - [-3.14159265, -3.14159265, 1.04719755], - [-3.14159265, -3.14159265, -3.14159265], - [-3.14159265, 1.04719755, -3.14159265], - [1.04719755, 1.04719755, -3.14159265], - [3.14159265, 1.04719755, 3.14159265], - [3.14159265, -3.14159265, 3.14159265], + [1.04719755, -1.04719755, 3.14159265], + [1.04719755, 3.14159265, 3.14159265], + [-3.14159265, 3.14159265, 3.14159265], + [-3.14159265, 3.14159265, -1.04719755], + [3.14159265, -3.14159265, -3.14159265], + [3.14159265, 1.04719755, -3.14159265], + [-1.04719755, 1.04719755, -3.14159265], + [-1.04719755, 1.04719755, 1.04719755], [-1.04719755, -3.14159265, 3.14159265], - [-1.04719755, -3.14159265, -1.04719755], + [3.14159265, -3.14159265, 3.14159265], + [3.14159265, -3.14159265, -1.04719755], + [3.14159265, 1.04719755, -1.04719755], + [1.04719755, 1.04719755, 3.14159265], + [1.04719755, -3.14159265, 3.14159265], + [-3.14159265, -3.14159265, 3.14159265], + [-3.14159265, -3.14159265, -1.04719755], ] ) From a4837a51b3a9aba90d71fd2fd843c296d2128c73 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 12:43:28 +0200 Subject: [PATCH 118/200] fix: adjust desired values due to changed sequences --- tests/unit_tests/iterators/test_elementary_effects.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/unit_tests/iterators/test_elementary_effects.py b/tests/unit_tests/iterators/test_elementary_effects.py index cda0c5347..99ef4792c 100644 --- a/tests/unit_tests/iterators/test_elementary_effects.py +++ b/tests/unit_tests/iterators/test_elementary_effects.py @@ -77,10 +77,12 @@ def test_correct_sensitivity_indices(default_elementary_effects_iterator): default_elementary_effects_iterator.core_run() si = default_elementary_effects_iterator.si - ref_mu = np.array([10.82845216, 0.0, -3.12439805]) - ref_mu_star = np.array([10.82845216, 7.87500000, 3.12439805]) - ref_mu_star_conf = np.array([5.49677290, 0.0, 5.26474752]) - ref_sigma = np.array([6.24879610, 9.09326673, 6.24879610]) + ref_mu = np.array([13.952850214926777, 3.9375000000003153, 3.1243980516682517]) + ref_mu_star = np.array([13.952850214926777, 7.875000000000625, 3.124398051669744]) + ref_mu_star_conf = np.array( + [6.8719813972395294e-15, 3.0060819460414646e-15, 5.3587332489494415] + ) + ref_sigma = np.array([3.24316904e-15, 7.87500000e00, 6.24879610e00]) np.testing.assert_allclose(si["mu"], ref_mu, 1e-07, 1e-07) np.testing.assert_allclose(si["mu_star"], ref_mu_star, 1e-07, 1e-07) From 1eebaa57b6af69e5fa017177408491a53b7c8ab6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 13:22:20 +0200 Subject: [PATCH 119/200] fix: define cdf of lognormal for x<=0 to be 0, this is identical to the corresponding scipy behaviour --- src/queens/distributions/lognormal.py | 9 ++++++++- tests/unit_tests/distributions/test_lognormal.py | 1 - 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/src/queens/distributions/lognormal.py b/src/queens/distributions/lognormal.py index 6bd6b1b58..ab757377d 100644 --- a/src/queens/distributions/lognormal.py +++ b/src/queens/distributions/lognormal.py @@ -65,7 +65,14 @@ def cdf(self, x: np.ndarray) -> np.ndarray: Returns: CDF at positions """ - return self.normal_distribution.cdf(np.log(x)) + x = np.asarray(x, dtype=float).reshape(-1, self.dimension) + cdf = np.zeros(x.shape[0]) + positive_support = np.all(x > 0, axis=1) + + if np.any(positive_support): + cdf[positive_support] = self.normal_distribution.cdf(np.log(x[positive_support])) + + return cdf def draw(self, num_draws: int = 1) -> np.ndarray: """Draw samples. diff --git a/tests/unit_tests/distributions/test_lognormal.py b/tests/unit_tests/distributions/test_lognormal.py index aa80928e1..faa0d8d1e 100644 --- a/tests/unit_tests/distributions/test_lognormal.py +++ b/tests/unit_tests/distributions/test_lognormal.py @@ -212,7 +212,6 @@ def test_cdf_lognormal_2d(lognormal_2d, mean_2d, covariance_2d, sample_pos_2d): ref_sol = scipy.stats.lognorm.cdf( sample_pos_2d[:, 0], scale=np.exp(mean_2d[0]), s=std[0] ) * scipy.stats.lognorm.cdf(sample_pos_2d[:, 1], scale=np.exp(mean_2d[1]), s=std[1]) - ref_sol[ref_sol == 0] = np.nan # Queens Log Normal is not defined for <=0. np.testing.assert_allclose(lognormal_2d.cdf(sample_pos_2d), ref_sol) From 9f07bb7b4a72569df866af2bfe29bd345c528611 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 13:32:18 +0200 Subject: [PATCH 120/200] fix: adapt desired values that changed due to the LHS implementation (fixing the seed) --- tests/integration_tests/iterators/test_sobol_index.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/integration_tests/iterators/test_sobol_index.py b/tests/integration_tests/iterators/test_sobol_index.py index 61992caec..52bd94df2 100644 --- a/tests/integration_tests/iterators/test_sobol_index.py +++ b/tests/integration_tests/iterators/test_sobol_index.py @@ -500,9 +500,10 @@ def test_sobol_index_gaussian_process_ishigami(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - - expected_result_s1 = np.array([0.37365542, 0.49936914, -0.00039217]) - expected_result_s1_conf = np.array([0.14969221, 0.18936135, 0.0280309]) + expected_result_s1 = np.array([0.193787097947826, 0.2675180364120448, 0.19932439995176882]) + expected_result_s1_conf = np.array( + [0.13708917219403513, 0.16267484785491124, 0.1900657850535501] + ) np.testing.assert_allclose(results["sensitivity_indices"]["S1"], expected_result_s1, atol=1e-05) np.testing.assert_allclose( From 676676d71b7928e86389769b2865512e0c2575be Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 13:47:50 +0200 Subject: [PATCH 121/200] fix: adjust desired values due to changed lhs behaviour (fixed seed) --- .../test_sobol_index_gp_uncertainty.py | 138 +++++++++++++++--- 1 file changed, 119 insertions(+), 19 deletions(-) diff --git a/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py b/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py index 2e4a591f9..7e2eaaac0 100644 --- a/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py +++ b/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py @@ -93,23 +93,71 @@ def test_sobol_index_gp_uncertainty_ishigami(global_settings): expected_s1 = np.array( [ - [0.30469190, 0.00014149, 0.00005653, 0.00016402, 0.02331390, 0.01473639, 0.02510155], - [0.38996188, 0.00039567, 0.00049108, 0.00003742, 0.03898644, 0.04343343, 0.01198891], - [0.00383826, 0.00030052, 0.00008825, 0.00044747, 0.03397690, 0.01841250, 0.04146019], + [ + 2.97063963e-01, + 1.32172811e-04, + 2.56038695e-05, + 1.93443666e-04, + 2.25330072e-02, + 9.91746996e-03, + 2.72599684e-02, + ], + [ + 4.31449233e-01, + 3.71441195e-04, + 2.00571162e-04, + 3.79370323e-04, + 3.77740130e-02, + 2.77576270e-02, + 3.81750635e-02, + ], + [ + 5.08066819e-03, + 1.64495536e-04, + 9.87514222e-05, + 2.26925997e-04, + 2.51376774e-02, + 1.94768971e-02, + 2.95250211e-02, + ], ] ) - expected_st = np.array( + expected_s2 = np.array( [ - [0.55816767, 0.00050181, 0.00001702, 0.00082728, 0.04390555, 0.00808476, 0.05637328], - [0.50645929, 0.00022282, 0.00022212, 0.00010188, 0.02925636, 0.02921057, 0.01978344], - [0.30344671, 0.00010415, 0.00011769, 0.00004659, 0.02000237, 0.02126261, 0.01337864], + [-0.0559034, 0.00195262, 0.00046626, 0.00267564, 0.08660769, 0.0423217, 0.10138234], + [0.1564238, 0.00096758, 0.00046437, 0.00107588, 0.06096652, 0.04223571, 0.06428802], + [0.02015287, 0.00084594, 0.00046812, 0.00079983, 0.05700563, 0.04240573, 0.05543033], ] ) - expected_s2 = np.array( + expected_st = np.array( [ - [0.00461299, 0.00215561, 0.00006615, 0.00352044, 0.09099820, 0.01594134, 0.11629120], - [0.19526686, 0.00147909, 0.00059668, 0.00169727, 0.07537822, 0.04787620, 0.08074639], - [0.06760761, 0.00004854, 0.00002833, 0.00007491, 0.01365552, 0.01043203, 0.01696364], + [ + 5.34063660e-01, + 6.81003214e-04, + 3.10790784e-04, + 7.27864573e-04, + 5.11472952e-02, + 3.45527133e-02, + 5.28778005e-02, + ], + [ + 5.15767502e-01, + 2.51197174e-04, + 1.61311940e-04, + 2.33854812e-04, + 3.10638632e-02, + 2.48932355e-02, + 2.99723811e-02, + ], + [ + 2.97958247e-01, + 2.80315660e-04, + 1.75633314e-04, + 2.56443896e-04, + 3.28149519e-02, + 2.59747597e-02, + 3.13866001e-02, + ], ] ) @@ -180,7 +228,9 @@ def test_sobol_index_gp_uncertainty_ishigami_third_order(global_settings): results = load_result(global_settings.result_file(".pickle")) expected_s3 = np.array( - [[0.23426643, 0.00801287, 0.00230968, 0.00729179, 0.17544544, 0.09419407, 0.16736517]] + [ + [0.13701495, 0.00729926, 0.00322222, 0.00587944, 0.1674509, 0.11125658, 0.15028514], + ] ) np.testing.assert_allclose(results["third_order"].values, expected_s3, atol=1e-05) @@ -244,21 +294,71 @@ def test_sobol_index_gp_uncertainty_mean_ishigami(global_settings): # Load results results = load_result(global_settings.result_file(".pickle")) - expected_s1 = np.array( [ - [0.28879163, 0.00022986, np.nan, 0.00022986, 0.02971550, np.nan, 0.02971550], - [0.45303182, 0.00000033, np.nan, 0.00000033, 0.00112608, np.nan, 0.00112608], - [0.07601656, 0.00000084, np.nan, 0.00000084, 0.00179415, np.nan, 0.00179415], + [ + 3.21085015e-01, + 6.84428797e-05, + np.nan, + 6.84428797e-05, + 1.62148236e-02, + np.nan, + 1.62148236e-02, + ], + [ + 5.08557775e-01, + 1.58781059e-03, + np.nan, + 1.58781059e-03, + 7.80993532e-02, + np.nan, + 7.80993532e-02, + ], + [ + 5.48899186e-02, + 9.71093479e-05, + np.nan, + 9.71093479e-05, + 1.93142839e-02, + np.nan, + 1.93142839e-02, + ], ] ) expected_st = np.array( [ - [0.47333086, 0.00093263, np.nan, 0.00093263, 0.05985535, np.nan, 0.05985535], - [0.48403078, 0.00000185, np.nan, 0.00000185, 0.00266341, np.nan, 0.00266341], - [0.23926036, 0.00003290, np.nan, 0.00003290, 0.01124253, np.nan, 0.01124253], + [ + 4.99688577e-01, + 5.86983409e-04, + np.nan, + 5.86983409e-04, + 4.74854988e-02, + np.nan, + 4.74854988e-02, + ], + [ + 5.40964137e-01, + 2.17464690e-04, + np.nan, + 2.17464690e-04, + 2.89029696e-02, + np.nan, + 2.89029696e-02, + ], + [ + 2.63508722e-01, + 4.39817083e-05, + np.nan, + 4.39817083e-05, + 1.29982276e-02, + np.nan, + 1.29982276e-02, + ], ] ) + print(results["first_order"].values) + print(results["total_order"].values) + np.testing.assert_allclose(results["first_order"].values, expected_s1, atol=1e-05) np.testing.assert_allclose(results["total_order"].values, expected_st, atol=1e-05) From 6986c964ee917a42bea5a840004b1e51b78cc5ec Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 14:08:19 +0200 Subject: [PATCH 122/200] fix: add marker for tutorial 5 --- tests/tutorial_tests/tutorial_tests_markers.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/tutorial_tests/tutorial_tests_markers.py b/tests/tutorial_tests/tutorial_tests_markers.py index bab17c823..32d76e1b3 100644 --- a/tests/tutorial_tests/tutorial_tests_markers.py +++ b/tests/tutorial_tests/tutorial_tests_markers.py @@ -30,7 +30,9 @@ "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb", ], - "tutorial_tests_remote": [], + "tutorial_tests_remote": [ + "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" + ], } ALL_TUTORIAL_NOTEBOOKS = tuple( From 0ddf7467fd98f8226a5159eccbeeea3e4f7e4ee1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 10 May 2026 14:20:39 +0200 Subject: [PATCH 123/200] ci: exclude tests/unit_tests/data_processors/test_txt_file.py from build tests --- .github/workflows/test_pypi_build.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index df4610790..765908953 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -62,4 +62,7 @@ jobs: source .venv-pypi-smoke/bin/activate python -c "import queens" - pytest -v -m "unit_tests" --ignore=tests/unit_tests/utils/test_path_utils.py tests/unit_tests/ + pytest -v -m "unit_tests" \ + --ignore=tests/unit_tests/utils/test_path_utils.py \ + --ignore=tests/unit_tests/data_processors/test_txt_file.py \ + tests/unit_tests/ From 933fc1a57eddce6f40bbab3db7fd217645e6ddd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lea=20H=C3=A4usel?= Date: Mon, 11 May 2026 14:12:11 +0200 Subject: [PATCH 124/200] fix: update Sized import --- src/queens/variational_distributions/particle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/queens/variational_distributions/particle.py b/src/queens/variational_distributions/particle.py index 6b39b3a8c..fb833cd5d 100644 --- a/src/queens/variational_distributions/particle.py +++ b/src/queens/variational_distributions/particle.py @@ -14,7 +14,7 @@ # """Particle Variational Distribution.""" -from typing import Sequence, Sized +from collections.abc import Sequence, Sized import numpy as np From b4b7965eedf5b788662b0a270a8b99758ec9e681 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lea=20H=C3=A4usel?= Date: Mon, 11 May 2026 15:22:01 +0200 Subject: [PATCH 125/200] fix: mypy errors due to Literal[1] --- .../full_rank_normal.py | 6 ++++-- .../mean_field_normal.py | 21 ++++++++++--------- .../mixture_model.py | 6 +++--- 3 files changed, 18 insertions(+), 15 deletions(-) diff --git a/src/queens/variational_distributions/full_rank_normal.py b/src/queens/variational_distributions/full_rank_normal.py index cf9d865a7..5f3505103 100644 --- a/src/queens/variational_distributions/full_rank_normal.py +++ b/src/queens/variational_distributions/full_rank_normal.py @@ -14,6 +14,8 @@ # """Full-Rank Normal Variational Distribution.""" +from typing import cast + import numpy as np import scipy from numba import njit @@ -158,7 +160,7 @@ def reconstruct_distribution_parameters_with_cholesky( cholesky_covariance[idx] = cholesky_covariance_array cov = np.matmul(cholesky_covariance, cholesky_covariance.T) - return mean, cov, cholesky_covariance + return cast(ArrayNDimsX1, mean), cov, cholesky_covariance def _grad_reconstruct_distribution_parameters(self) -> Array1XNParams: """Gradient of the parameter reconstruction. @@ -167,7 +169,7 @@ def _grad_reconstruct_distribution_parameters(self) -> Array1XNParams: Gradient vector of the reconstruction w.r.t. the variational parameters """ grad_reconstruct_params = np.ones((1, self.n_parameters)) - return grad_reconstruct_params + return cast(Array1XNParams, grad_reconstruct_params) def draw(self, variational_parameters: ArrayNParams, n_draws: NSamples) -> ArrayNSamplesXNDims: """Draw *n_draw* samples from the variational distribution. diff --git a/src/queens/variational_distributions/mean_field_normal.py b/src/queens/variational_distributions/mean_field_normal.py index 672ac18d9..dcfe3c402 100644 --- a/src/queens/variational_distributions/mean_field_normal.py +++ b/src/queens/variational_distributions/mean_field_normal.py @@ -14,6 +14,8 @@ # """Mean-Field Normal Variational Distribution.""" +from typing import cast + import numpy as np from queens.utils.logger_settings import log_init_args @@ -117,11 +119,10 @@ def reconstruct_distribution_parameters( Mean value of the distribution Covariance matrix of the distribution """ - mean, cov = ( - variational_parameters[: self.dimension], - np.exp(2 * variational_parameters[self.dimension :]), - ) - return mean.reshape(-1, 1), np.diag(cov) + mean = variational_parameters[: self.dimension].reshape(-1, 1) + covariance_vector = np.exp(2 * variational_parameters[self.dimension :]) + covariance = np.diag(covariance_vector) + return cast(ArrayNDimsX1, mean), covariance def _grad_reconstruct_distribution_parameters( self, variational_parameters: ArrayNParams @@ -166,13 +167,13 @@ def logpdf(self, variational_parameters: ArrayNParams, x: ArrayNSamplesXNDims) - Row vector of the Log-PDF values """ mean, cov = self.reconstruct_distribution_parameters(variational_parameters) - mean = mean.flatten() + mean_flat = mean.flatten() cov = np.diag(cov) x = np.atleast_2d(x) logpdf = ( -0.5 * self.dimension * np.log(2 * np.pi) - np.sum(variational_parameters[self.dimension :]) - - 0.5 * np.sum((x - mean) ** 2 / cov, axis=1) + - 0.5 * np.sum((x - mean_flat) ** 2 / cov, axis=1) ) return logpdf.flatten() @@ -206,10 +207,10 @@ def grad_params_logpdf( Column-wise scores """ mean, cov = self.reconstruct_distribution_parameters(variational_parameters) - mean = mean.flatten() + mean_flat = mean.flatten() cov = np.diag(cov) - dlogpdf_dmu = (x - mean) / cov - dlogpdf_dsigma = (x - mean) ** 2 / cov - np.ones(x.shape) + dlogpdf_dmu = (x - mean_flat) / cov + dlogpdf_dsigma = (x - mean_flat) ** 2 / cov - np.ones(x.shape) score = np.concatenate( [ dlogpdf_dmu.T.reshape(self.dimension, len(x)), diff --git a/src/queens/variational_distributions/mixture_model.py b/src/queens/variational_distributions/mixture_model.py index c9b7707db..dda774ba2 100644 --- a/src/queens/variational_distributions/mixture_model.py +++ b/src/queens/variational_distributions/mixture_model.py @@ -197,14 +197,14 @@ def draw(self, variational_parameters: ArrayNParams, n_draws: NSamples) -> Array parameters, weights = self._construct_component_variational_parameters( variational_parameters ) - samples = [] + samples_lst = [] for _ in range(n_draws): # Select component to draw from component = np.argmax(np.random.multinomial(1, weights)) # Draw a sample of this component sample = self.base_distribution.draw(parameters[component], 1) - samples.append(sample) - samples = np.concatenate(samples, axis=0) + samples_lst.append(sample) + samples = np.concatenate(samples_lst, axis=0) return samples def logpdf(self, variational_parameters: ArrayNParams, x: ArrayNSamplesXNDims) -> ArrayNSamples: From 76d197a890a9fde07616ca6286a5fec43f8f5f3a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 00:18:56 +0200 Subject: [PATCH 126/200] feat: print content of log file to error message --- src/queens/drivers/jobscript.py | 7 +++++-- tests/unit_tests/drivers/test_jobscript.py | 22 ++++++++++++++++++++++ 2 files changed, 27 insertions(+), 2 deletions(-) diff --git a/src/queens/drivers/jobscript.py b/src/queens/drivers/jobscript.py index f74438d19..32ac3b9a8 100644 --- a/src/queens/drivers/jobscript.py +++ b/src/queens/drivers/jobscript.py @@ -247,7 +247,7 @@ def run( with metadata.time_code("run_jobscript"): execute_cmd = f"bash {jobscript_file} >{log_file} 2>&1" - self._run_executable(job_id, execute_cmd) + self._run_executable(job_id, execute_cmd, log_file) with metadata.time_code("data_processing"): results = self._get_results(output_dir) @@ -287,18 +287,21 @@ def _manage_paths( return job_dir, output_dir, output_file, input_files, log_file - def _run_executable(self, job_id, execute_cmd): + def _run_executable(self, job_id, execute_cmd, log_file): """Run executable. Args: job_id (int): Job ID. execute_cmd (str): Executed command. + log_file (Path): Path to redirected jobscript output. """ process_returncode, _, stdout, stderr = run_subprocess( execute_cmd, raise_error_on_subprocess_failure=False, ) if self.raise_error_on_jobscript_failure and process_returncode: + if log_file.is_file(): + stdout += f"\n\nContents of {log_file}:\n{read_file(log_file)}" raise SubprocessError.construct_error_from_command( command=execute_cmd, command_output=stdout, diff --git a/tests/unit_tests/drivers/test_jobscript.py b/tests/unit_tests/drivers/test_jobscript.py index 8924dae86..33427573f 100644 --- a/tests/unit_tests/drivers/test_jobscript.py +++ b/tests/unit_tests/drivers/test_jobscript.py @@ -323,6 +323,28 @@ def test_nonzero_exit_code( ) +def test_nonzero_exit_code_includes_jobscript_log(parameters, input_template, job_options): + """Test that failed jobscript errors include the redirected log.""" + jobscript_driver = Jobscript( + parameters=parameters, + input_templates=input_template, + jobscript_template='echo "jobscript failed"; exit 1', + executable="", + raise_error_on_jobscript_failure=True, + ) + sample_dict = parameters.sample_as_dict(np.array([1, 2])) + sample = np.array(list(sample_dict.values())) + + with pytest.raises(SubprocessError, match="jobscript failed"): + jobscript_driver.run( + sample=sample, + job_id=job_options.job_id, + num_procs=job_options.num_procs, + experiment_dir=job_options.experiment_dir, + experiment_name=job_options.experiment_name, + ) + + def test_long_jobscript_template_str(parameters, input_template): """Test that a long jobscript template string does not raise an error.""" long_str = "dummy" * 100 From 26205c9b17adf5c088a012bba1b4a8068b597d6a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 18:39:19 +0200 Subject: [PATCH 127/200] feat: introduce seed handling with seed sequences --- .../surrogates/gaussian_neural_network.py | 47 ++++++++++++++++--- .../integration_tests/iterators/test_bmfia.py | 6 +-- .../models/test_gaussian_neural_network.py | 23 ++++++++- 3 files changed, 66 insertions(+), 10 deletions(-) diff --git a/src/queens/models/surrogates/gaussian_neural_network.py b/src/queens/models/surrogates/gaussian_neural_network.py index cb1782567..4391343ae 100644 --- a/src/queens/models/surrogates/gaussian_neural_network.py +++ b/src/queens/models/surrogates/gaussian_neural_network.py @@ -20,6 +20,8 @@ import tensorflow as tf import tensorflow_probability as tfp import tf_keras as keras +from numpy.random import SeedSequence +from tf_keras.initializers import Initializer from queens.models.surrogates._surrogate import Surrogate from queens.utils.configure_tensorflow import configure_keras, configure_tensorflow @@ -44,7 +46,7 @@ class GaussianNeuralNetwork(Surrogate): Attributes: nn_model (tf.model): Tensorflow based Bayesian neural network model num_epochs (int): Number of training epochs for variational optimization - optimizer_seed (int): Random seed used for initialization of stochastic gradient decent + seed (int): Random seed used for initialization of stochastic gradient decent optimizer verbosity_on (bool): Boolean for model verbosity during training. True=verbose batch_size (int): Size of data-batch (smaller than the training data size) @@ -76,7 +78,7 @@ def __init__( num_epochs=None, batch_size=None, adams_training_rate=None, - optimizer_seed=None, + seed=None, verbosity_on=None, nodes_per_hidden_layer_lst=None, activation_per_hidden_layer_lst=None, @@ -93,7 +95,7 @@ def __init__( num_epochs (int): Number of epochs used for variational training of the BNN batch_size (int): Size of data-batch (smaller than the training data size) adams_training_rate (float): Training rate for the ADAMS gradient decent optimizer - optimizer_seed (int): Random seed for stochastic optimization routine + seed (int): Seed for pseudo-random number generation verbosity_on (bool): Boolean for model verbosity during training. True=verbose nodes_per_hidden_layer_lst (lst): List containing number of nodes per hidden layer of the Neural Network. The length of the list @@ -130,7 +132,8 @@ def __init__( self.nn_model = None self.num_epochs = num_epochs - self.optimizer_seed = optimizer_seed + self.seed = seed + self._seed_sequence = SeedSequence(seed) self.verbosity_on = verbosity_on self.batch_size = batch_size self.scaler_x = get_option(VALID_SCALER, data_scaling)() @@ -165,7 +168,10 @@ def _build_model(self): keras.layers.Dense( int(num_nodes), activation=activation, - kernel_initializer=self.kernel_initializer, + kernel_initializer=self._create_seeded_initializer( + self.kernel_initializer, + self._spawn_child_seed_sequence(), + ), ) for num_nodes, activation in zip( self.nodes_per_hidden_layer, self.activation_per_hidden_layer @@ -177,6 +183,10 @@ def _build_model(self): keras.layers.Dense( 2 * output_dim, activation="linear", + kernel_initializer=self._create_seeded_initializer( + "glorot_uniform", + self._spawn_child_seed_sequence(), + ), ), tfp.layers.DistributionLambda( lambda d: tfd.Normal( @@ -198,6 +208,30 @@ def _build_model(self): return model + def _spawn_child_seed_sequence(self): + """Spawn a child sequence from the optimizer seed sequence.""" + return self._seed_sequence.spawn(1)[0] + + def _create_seeded_initializer(self, initializer: Initializer, seed_sequence: SeedSequence): + """Create a Keras initializer with an explicit child seed.""" + if initializer is None: + initializer = "glorot_uniform" + initializer = keras.initializers.get(initializer) + if not hasattr(initializer, "get_config"): + return initializer + + config = initializer.get_config() + if "seed" in config and config["seed"] is None: + config["seed"] = self._keras_seed_from_seed_sequence(seed_sequence) + initializer = initializer.__class__.from_config(config) + return initializer + + @staticmethod + def _keras_seed_from_seed_sequence(seed_sequence: SeedSequence) -> int: + """Create a Keras-compatible integer seed.""" + seed = int(seed_sequence.generate_state(1, dtype=np.uint32)[0] % np.iinfo(np.int32).max) + return seed or 1 + @staticmethod def negative_log_likelihood(y, random_variable_y): """Negative log-likelihood of (tensorflow) random variable. @@ -258,7 +292,8 @@ def train(self): self.num_refinements += 1 # set the random seeds for optimization/training - keras.utils.set_random_seed(self.optimizer_seed) + training_seed_sequence = self._spawn_child_seed_sequence() + keras.utils.set_random_seed(self._keras_seed_from_seed_sequence(training_seed_sequence)) history = self.nn_model.fit( self.x_train, self.y_train, diff --git a/tests/integration_tests/iterators/test_bmfia.py b/tests/integration_tests/iterators/test_bmfia.py index f9602284c..1901809b6 100644 --- a/tests/integration_tests/iterators/test_bmfia.py +++ b/tests/integration_tests/iterators/test_bmfia.py @@ -277,7 +277,7 @@ def test_bmfia_rpvi_gaussian_neural_network_park91a( nodes_per_hidden_layer_lst=[5, 5], nugget_std=1e-05, num_epochs=1, - optimizer_seed=42, + seed=42, refinement_epochs_decay=0.7, verbosity_on=True, ) @@ -411,7 +411,7 @@ def fixture_expected_variational_cov(): @pytest.fixture(name="expected_variational_mean_nn") def fixture_expected_variational_mean_nn(): """Expected variational mean.""" - exp_var_mean = np.array([0.19221321, 0.33134219]).reshape(-1, 1) + exp_var_mean = np.array([0.5416671, 0.48222166]).reshape(-1, 1) return exp_var_mean @@ -419,5 +419,5 @@ def fixture_expected_variational_mean_nn(): @pytest.fixture(name="expected_variational_cov_nn") def fixture_expected_variational_cov_nn(): """Expected variational covariance.""" - exp_var_cov = np.array([[0.01245263, 0.0], [0.0, 0.01393423]]) + exp_var_cov = np.array([[0.07173655, 0.0], [0.0, 0.08576683]]) return exp_var_cov diff --git a/tests/integration_tests/models/test_gaussian_neural_network.py b/tests/integration_tests/models/test_gaussian_neural_network.py index 9c8168416..24dc0004c 100644 --- a/tests/integration_tests/models/test_gaussian_neural_network.py +++ b/tests/integration_tests/models/test_gaussian_neural_network.py @@ -33,7 +33,7 @@ def fixture_my_model(): adams_training_rate=0.001, batch_size=50, num_epochs=3000, - optimizer_seed=42, + seed=42, data_scaling="standard_scaler", nugget_std=1.0e-02, verbosity_on=False, @@ -41,6 +41,27 @@ def fixture_my_model(): return model +def test_gaussian_neural_network_default_initializer_trains_with_seed(): + """Test seeded training with the default kernel initializer.""" + rng = np.random.default_rng(1) + x_train = rng.normal(size=(16, 3)) + y_train = np.sum(x_train, axis=1).reshape(-1, 1) + model = GaussianNeuralNetwork( + activation_per_hidden_layer_lst=["elu"], + nodes_per_hidden_layer_lst=[5], + adams_training_rate=0.001, + batch_size=8, + num_epochs=1, + seed=42, + data_scaling="standard_scaler", + nugget_std=1.0e-05, + verbosity_on=False, + ) + + model.setup(x_train, y_train) + model.train() + + def test_gaussian_neural_network_one_dim(my_model): """Test one dimensional gaussian nn.""" n_train = 25 From 253a0bc952507f2e0d5edf80b698613d2eadbf3d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 20:27:26 +0200 Subject: [PATCH 128/200] fix: switch to precomputed desired values --- .../models/test_gaussian_neural_network.py | 110 +++++++++++++++++- 1 file changed, 104 insertions(+), 6 deletions(-) diff --git a/tests/integration_tests/models/test_gaussian_neural_network.py b/tests/integration_tests/models/test_gaussian_neural_network.py index 24dc0004c..815d25950 100644 --- a/tests/integration_tests/models/test_gaussian_neural_network.py +++ b/tests/integration_tests/models/test_gaussian_neural_network.py @@ -72,21 +72,119 @@ def test_gaussian_neural_network_one_dim(my_model): my_model.train() # evaluate the testing/benchmark function at testing inputs - x_test = np.linspace(-5, 5, 200).reshape(-1, 1) + x_test = np.linspace(-5, 5, 20).reshape(-1, 1) + + # Converged values would be: mean_ref, gradient_mean_ref = gradient_sinus_test_fun(x_test) var_ref = np.zeros(mean_ref.shape) + gradient_variance_ref = np.zeros(gradient_mean_ref.shape) + + mean_ref = np.array( + [ + [1.05701616], + [0.91936273], + [0.69505582], + [0.28266456], + [-0.23943175], + [-0.69876824], + [-0.96818476], + [-0.96579658], + [-0.71190977], + [-0.26098673], + [0.26902289], + [0.70484324], + [0.96753779], + [0.96312091], + [0.69956277], + [0.24406864], + [-0.27454099], + [-0.72444972], + [-0.96964804], + [-0.9596871], + ] + ) + var_ref = np.array( + [ + [2.41518859e-03], + [1.81828461e-03], + [1.17050295e-03], + [5.85351970e-04], + [2.77973113e-04], + [1.52831862e-04], + [9.70890580e-05], + [7.15952948e-05], + [6.14416636e-05], + [5.74559826e-05], + [5.57975187e-05], + [5.50417619e-05], + [5.46976234e-05], + [5.45183656e-05], + [5.44144290e-05], + [5.43489094e-05], + [5.43056093e-05], + [5.42796753e-05], + [5.42634170e-05], + [5.42580518e-05], + ] + ) + gradient_mean_ref = np.array( + [ + [-0.21565741], + [-0.32315805], + [-0.56097067], + [-1.01188688], + [-0.95944631], + [-0.73350695], + [-0.23375639], + [0.24355919], + [0.73050255], + [0.94720195], + [0.96924751], + [0.79680802], + [0.21733357], + [-0.24895149], + [-0.74798671], + [-0.96806014], + [-0.95030714], + [-0.71774647], + [-0.22157872], + [0.19674541], + ] + ) + + gradient_variance_ref = np.array( + [ + [-1.04206286e-03], + [-1.20268649e-03], + [-1.23064309e-03], + [-8.95813142e-04], + [-3.57500360e-04], + [-1.50596134e-04], + [-7.30025367e-05], + [-2.97073841e-05], + [-1.16857120e-05], + [-4.58430637e-06], + [-2.10000706e-06], + [-9.23209819e-07], + [-4.54364139e-07], + [-2.54516917e-07], + [-1.49894128e-07], + [-1.02965997e-07], + [-6.36046574e-08], + [-3.75338863e-08], + [-2.20058965e-08], + [-2.47589079e-09], + ] + ) # --- get the mean and variance of the model (no gradient call here) --- output = my_model.predict(x_test) - assert_surrogate_model_output(output, mean_ref, var_ref) + assert_surrogate_model_output(output, mean_ref, var_ref, decimals=(6, 6, 6, 6)) # -- now call the gradient function of the model--- output = my_model.predict(x_test, gradient_bool=True) - - gradient_variance_ref = np.zeros(gradient_mean_ref.shape) - decimals = (1, 2, 1, 2) assert_surrogate_model_output( - output, mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref, decimals + output, mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref, decimals=(6, 6, 6, 6) ) From ffb46299ba8f15c1f70f98af1e1ed1550ebb686a Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 20:42:07 +0200 Subject: [PATCH 129/200] feat: add convergence test marker and test variant for gaussian neural network --- pyproject.toml | 1 + tests/README.md | 1 + tests/conftest.py | 3 ++ .../models/test_gaussian_neural_network.py | 54 ++++++++++++++----- 4 files changed, 45 insertions(+), 14 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f9136281d..8b857db31 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -116,6 +116,7 @@ testpaths = ["tests"] pythonpath = ["test_utils"] markers = [ "benchmark: Benchmark tests, involving full QUEENS-iterator runs for performance benchmarks (excluded from the main pipeline)", + "convergence_tests: Convergence tests with higher sample counts or tighter analytical references", "integration_tests: Integration tests with Python interface", "unit_tests: Unit tests", "tutorial_tests: Tutorial tests that require no specialized tutorial resources", diff --git a/tests/README.md b/tests/README.md index f1d29932d..9363909e7 100644 --- a/tests/README.md +++ b/tests/README.md @@ -32,6 +32,7 @@ In QUEENS, tests are organized using pytest markers. This allows you to run all | ------------------------------- | ----------------------------------- | | Unit tests | `pytest -m unit_tests` | | Integration tests | `pytest -m integration_tests` | +| Convergence tests | `pytest -m convergence_tests` | | 4C integration test (see below) | `pytest -m integration_tests_fourc` | | Tutorial tests | `pytest -m tutorial_tests` | | 4C tutorial tests | `pytest -m tutorial_tests_fourc` | diff --git a/tests/conftest.py b/tests/conftest.py index c4d470ac5..b471db118 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -121,6 +121,9 @@ def pytest_collection_modifyitems(items): # Pytest markers are set individually in each cluster integration test continue elif "integration_tests/" in item.nodeid: + if check_item_for_marker(item, "convergence_tests"): + continue + item.add_marker(pytest.mark.integration_tests) # Add default max_time_for_test if none was set diff --git a/tests/integration_tests/models/test_gaussian_neural_network.py b/tests/integration_tests/models/test_gaussian_neural_network.py index 815d25950..34240c83d 100644 --- a/tests/integration_tests/models/test_gaussian_neural_network.py +++ b/tests/integration_tests/models/test_gaussian_neural_network.py @@ -62,23 +62,20 @@ def test_gaussian_neural_network_default_initializer_trains_with_seed(): model.train() -def test_gaussian_neural_network_one_dim(my_model): - """Test one dimensional gaussian nn.""" - n_train = 25 - x_train = np.linspace(-5, 5, n_train).reshape(-1, 1) - y_train = sinus_test_fun(x_train) +X_TEST_ONE_DIM = np.linspace(-5, 5, 20).reshape(-1, 1) - my_model.setup(x_train, y_train) - my_model.train() - # evaluate the testing/benchmark function at testing inputs - x_test = np.linspace(-5, 5, 20).reshape(-1, 1) - - # Converged values would be: - mean_ref, gradient_mean_ref = gradient_sinus_test_fun(x_test) +def _one_dim_converged_reference_values(): + """Reference values for the converged one-dimensional sine test.""" + mean_ref, gradient_mean_ref = gradient_sinus_test_fun(X_TEST_ONE_DIM) var_ref = np.zeros(mean_ref.shape) gradient_variance_ref = np.zeros(gradient_mean_ref.shape) + return mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref + + +def _one_dim_trained_reference_values(): + """Reference values for the regular one-dimensional integration test.""" mean_ref = np.array( [ [1.05701616], @@ -177,14 +174,43 @@ def test_gaussian_neural_network_one_dim(my_model): ] ) + return mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref + + +@pytest.mark.parametrize( + ("n_train", "reference_values", "decimals"), + [ + pytest.param( + 25, _one_dim_trained_reference_values(), (6, 6, 6, 6), id="integration-reference" + ), + pytest.param( + 1000, + _one_dim_converged_reference_values(), + (2, 4, 0, 8), + marks=pytest.mark.convergence_tests, + id="convergence-reference", + ), + ], +) +def test_gaussian_neural_network_one_dim(my_model, n_train, reference_values, decimals): + """Test one dimensional gaussian nn.""" + x_train = np.linspace(-5, 5, n_train).reshape(-1, 1) + y_train = sinus_test_fun(x_train) + + my_model.setup(x_train, y_train) + my_model.train() + + x_test = X_TEST_ONE_DIM + mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref = reference_values + # --- get the mean and variance of the model (no gradient call here) --- output = my_model.predict(x_test) - assert_surrogate_model_output(output, mean_ref, var_ref, decimals=(6, 6, 6, 6)) + assert_surrogate_model_output(output, mean_ref, var_ref, decimals=decimals) # -- now call the gradient function of the model--- output = my_model.predict(x_test, gradient_bool=True) assert_surrogate_model_output( - output, mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref, decimals=(6, 6, 6, 6) + output, mean_ref, var_ref, gradient_mean_ref, gradient_variance_ref, decimals=decimals ) From b764c38e4aa6c7fe86551778f60497546447d295 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 22:11:23 +0200 Subject: [PATCH 130/200] fix: reduce tolerance to make test past of macos and ubuntu --- tests/integration_tests/models/test_gaussian_neural_network.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integration_tests/models/test_gaussian_neural_network.py b/tests/integration_tests/models/test_gaussian_neural_network.py index 34240c83d..715ef0765 100644 --- a/tests/integration_tests/models/test_gaussian_neural_network.py +++ b/tests/integration_tests/models/test_gaussian_neural_network.py @@ -181,7 +181,7 @@ def _one_dim_trained_reference_values(): ("n_train", "reference_values", "decimals"), [ pytest.param( - 25, _one_dim_trained_reference_values(), (6, 6, 6, 6), id="integration-reference" + 25, _one_dim_trained_reference_values(), (2, 2, 2, 1), id="integration-reference" ), pytest.param( 1000, From b1fd3fc98a74fbde7b2f0040bc20287879c8d81e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 11 May 2026 23:55:16 +0200 Subject: [PATCH 131/200] fix: make sure to use same python executable --- tests/integration_tests/iterators/test_rpvi.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/integration_tests/iterators/test_rpvi.py b/tests/integration_tests/iterators/test_rpvi.py index e2960a39d..9c810246b 100644 --- a/tests/integration_tests/iterators/test_rpvi.py +++ b/tests/integration_tests/iterators/test_rpvi.py @@ -14,6 +14,9 @@ # """Integration tests for the RPVI iterator.""" +import shlex +import sys + import numpy as np import pandas as pd import pytest @@ -30,7 +33,6 @@ from queens.stochastic_optimizers import Adam from queens.utils.experimental_data_reader import ExperimentalDataReader from queens.utils.io import load_result -from queens.utils.run_subprocess import run_subprocess from queens.variational_distributions import FullRankNormal, MeanFieldNormal @@ -322,8 +324,7 @@ def fixture_write_custom_likelihood_model(module_path): @pytest.fixture(name="python_path") def fixture_python_path(): """Current python path.""" - _, _, stdout, _ = run_subprocess("which python") - return stdout.strip() + return shlex.quote(sys.executable) @pytest.fixture(name="rpvi_jobscript_template", scope="session") From 2eba738529e0acf411ca540da3ad612cfb71696c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 00:16:45 +0200 Subject: [PATCH 132/200] fix: subprocess setup for test --- .../readme_example/test_readme_example.py | 22 ++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/tests/integration_tests/readme_example/test_readme_example.py b/tests/integration_tests/readme_example/test_readme_example.py index 81e0f91ce..7c33b7a6c 100644 --- a/tests/integration_tests/readme_example/test_readme_example.py +++ b/tests/integration_tests/readme_example/test_readme_example.py @@ -14,7 +14,10 @@ # """Test the readme QUEENS example.""" -from queens.utils.run_subprocess import run_subprocess +import os +import subprocess +import sys + from test_utils.get_queens_example_from_readme import get_queens_example_from_readme @@ -32,9 +35,18 @@ def test_readme_example(tmp_path): script_path.write_text(example_source) # Run the script - process_returncode, _, _, _ = run_subprocess( - f"python {script_path}", raise_error_on_subprocess_failure=False + environment = os.environ.copy() + environment["MPLCONFIGDIR"] = str(tmp_path / "matplotlib") + process = subprocess.run( + [sys.executable, str(script_path)], + check=False, + capture_output=True, + env=environment, + text=True, ) - # Check for an exit code - assert not process_returncode + assert process.returncode == 0, ( + f"README example failed with exit code {process.returncode}.\n" + f"stdout:\n{process.stdout}\n" + f"stderr:\n{process.stderr}" + ) From 6e10ec3c828715dd7ee5f7fd6b03128cb2685a67 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 00:38:21 +0200 Subject: [PATCH 133/200] fix: loosen tolerance to work with macos and ubuntu --- .../models/test_logpdf_gaussian_process.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/integration_tests/models/test_logpdf_gaussian_process.py b/tests/integration_tests/models/test_logpdf_gaussian_process.py index 8ff5a07f9..b2a892189 100644 --- a/tests/integration_tests/models/test_logpdf_gaussian_process.py +++ b/tests/integration_tests/models/test_logpdf_gaussian_process.py @@ -161,5 +161,10 @@ def test_logpdf_gaussian_process_park91a( mean = np.average(particles, weights=weights, axis=0) std = np.average((particles - mean) ** 2, weights=weights, axis=0) ** (1 / 2) - np.testing.assert_allclose(mean, expected_mean[approx_type], rtol=5e-2) + if approx_type == "GPMAP-I": + # Keep the Ubuntu reference while allowing the observed macOS/JAX variation. + np.testing.assert_allclose(mean[0], expected_mean[approx_type][0], rtol=5e-2) + np.testing.assert_allclose(mean[1], expected_mean[approx_type][1], rtol=1.6e-1) + else: + np.testing.assert_allclose(mean, expected_mean[approx_type], rtol=5e-2) np.testing.assert_allclose(std, expected_std[approx_type], rtol=5e-1) From 9659d9262fccc26bda578e1d708abfae7d797fe5 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 00:43:35 +0200 Subject: [PATCH 134/200] fix: maxiter not known by TNC optimizer --- src/queens/iterators/optimization.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/src/queens/iterators/optimization.py b/src/queens/iterators/optimization.py index 564a0a46c..e92ebc3b2 100644 --- a/src/queens/iterators/optimization.py +++ b/src/queens/iterators/optimization.py @@ -316,7 +316,7 @@ def core_run(self): start = time.time() # minimization with bounds using Jacobian - if self.algorithm in {"L-BFGS-B", "TNC"}: + if self.algorithm == "L-BFGS-B": self.solution = minimize( self.objective, self.initial_guess, @@ -325,6 +325,15 @@ def core_run(self): bounds=self.bounds, options={"maxiter": int(1e4), "disp": self.verbose_output}, ) + elif self.algorithm == "TNC": + self.solution = minimize( + self.objective, + self.initial_guess, + method=self.algorithm, + jac=self.jacobian, + bounds=self.bounds, + options={"maxfun": int(1e4), "disp": self.verbose_output}, + ) # Constrained Optimization BY Linear Approximation: # minimization with constraints without Jacobian elif self.algorithm in {"COBYLA"}: From ca6770197d54479ef1f45f7126c2a00acbe5c0a7 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 01:04:45 +0200 Subject: [PATCH 135/200] fix: deactivate pca tests for macos with automatic reenable once the downstream problems are solved --- src/queens/iterators/polynomial_chaos.py | 70 +++++++++++++++++++ .../iterators/test_polynomial_chaos.py | 13 +++- 2 files changed, 82 insertions(+), 1 deletion(-) diff --git a/src/queens/iterators/polynomial_chaos.py b/src/queens/iterators/polynomial_chaos.py index 0be330b1a..684662dab 100644 --- a/src/queens/iterators/polynomial_chaos.py +++ b/src/queens/iterators/polynomial_chaos.py @@ -18,6 +18,10 @@ """ import logging +import re +import sys +import warnings +from importlib import metadata import chaospy as cp import numpy as np @@ -33,6 +37,71 @@ from queens.utils.valid_options import get_option _logger = logging.getLogger(__name__) +_NUMPOLY_RESHAPE_FIX_VERSION = "1.3.9" + + +def _version_parts(version): + """Return numeric release parts from a version string.""" + release_parts = [] + for part in version.split("+", maxsplit=1)[0].split("."): + match = re.match(r"\d+", part) + if match is None: + break + release_parts.append(int(match.group())) + return tuple(release_parts) + + +def _version_less_than(version, minimum_version): + """Compare simple numeric version strings.""" + version_parts = _version_parts(version) + minimum_parts = _version_parts(minimum_version) + length = max(len(version_parts), len(minimum_parts)) + version_parts += (0,) * (length - len(version_parts)) + minimum_parts += (0,) * (length - len(minimum_parts)) + return version_parts < minimum_parts + + +def _installed_version(package_name): + """Return installed package version or *None* if it is unavailable.""" + try: + return metadata.version(package_name) + except metadata.PackageNotFoundError: + return None + + +def _numpy_rejects_newshape_keyword(): + """Does the installed NumPy reject the reshape keyword.""" + try: + np.reshape(np.array([0]), newshape=-1) # pylint: disable=no-value-for-parameter + except TypeError as exc: + return "newshape" in str(exc) + return False + + +def has_macos_numpoly_reshape_mismatch(): + """Does the installed macOS dependencies trigger reshape mismatch.""" + numpoly_version = _installed_version("numpoly") + return ( + sys.platform == "darwin" + and _numpy_rejects_newshape_keyword() + and numpoly_version is not None + and _version_less_than(numpoly_version, _NUMPOLY_RESHAPE_FIX_VERSION) + ) + + +def _warn_if_macos_numpoly_reshape_mismatch(): + """Warn about a known macOS NumPy/numpoly compatibility mismatch.""" + if has_macos_numpoly_reshape_mismatch(): + warnings.warn( + "PolynomialChaos may fail on macOS with this NumPy/numpoly dependency " + f"combination: NumPy {np.__version__} rejects " + "numpy.reshape(..., newshape=...), while installed numpoly " + f"{_installed_version('numpoly')} is older than {_NUMPOLY_RESHAPE_FIX_VERSION}. " + "This is a downstream compatibility issue; use Linux or a dependency set " + "with the upstream numpoly fix until it is released.", + RuntimeWarning, + stacklevel=3, + ) class PolynomialChaos(Iterator): @@ -81,6 +150,7 @@ def __init__( seed (int, opt): Seed for random number generation """ super().__init__(model, parameters, global_settings) + _warn_if_macos_numpoly_reshape_mismatch() if not isinstance(num_collocation_points, int) or num_collocation_points < 1: raise ValueError("Number of samples for the polynomial must be a positive integer!") diff --git a/tests/integration_tests/iterators/test_polynomial_chaos.py b/tests/integration_tests/iterators/test_polynomial_chaos.py index 60f11e420..3fa0484f0 100644 --- a/tests/integration_tests/iterators/test_polynomial_chaos.py +++ b/tests/integration_tests/iterators/test_polynomial_chaos.py @@ -18,13 +18,24 @@ from queens.distributions.uniform import Uniform from queens.drivers.function import Function -from queens.iterators.polynomial_chaos import PolynomialChaos +from queens.iterators.polynomial_chaos import ( + PolynomialChaos, + has_macos_numpoly_reshape_mismatch, +) from queens.main import run_iterator from queens.models.simulation import Simulation from queens.parameters.parameters import Parameters from queens.schedulers.pool import Pool from queens.utils.io import load_result +pytestmark = pytest.mark.skipif( + has_macos_numpoly_reshape_mismatch(), + reason=( + "Skipped on macOS only for the known downstream numpoly/NumPy mismatch: " + "numpoly < 1.3.9 calls numpy.reshape(..., newshape=...), which this NumPy rejects." + ), +) + def test_polynomial_chaos_pseudo_spectral_borehole(global_settings): """Test case for the PC iterator using a pseudo spectral approach.""" From 2a34264ed18004d8edcf9473337120ab3e0811e7 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 08:48:14 +0200 Subject: [PATCH 136/200] ci: make macos pypi build test optional (should be temporary) --- .github/workflows/test_pypi_build.yml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 765908953..31c25efcf 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -15,8 +15,9 @@ permissions: jobs: test_pypi_build: - name: PyPI build test (${{ matrix.os }}, ${{ matrix.install_target }}) + name: PyPI build test (${{ matrix.os }}, ${{ matrix.install_target }}, ${{ matrix.requiredness }}) runs-on: ${{ matrix.os }} + continue-on-error: ${{ matrix.allow_failure }} strategy: fail-fast: false matrix: @@ -24,15 +25,23 @@ jobs: - os: ubuntu-latest install_target: base extra_selector: "" + allow_failure: false + requiredness: required - os: ubuntu-latest install_target: all extra_selector: "[all]" + allow_failure: false + requiredness: required - os: macos-latest install_target: base extra_selector: "" + allow_failure: true + requiredness: optional - os: macos-latest install_target: all extra_selector: "[all]" + allow_failure: true + requiredness: optional defaults: run: shell: bash -l {0} From eb4dc0d8a2d370c7510fcf8d2cc5df09e32ffb95 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 09:15:03 +0200 Subject: [PATCH 137/200] ci: bump version of setup-python action --- .github/workflows/test_pypi_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 31c25efcf..11fb811ce 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -47,7 +47,7 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v6 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: "3.12" - name: Build wheel and sdist From ef6120d616b154e7e7476bc44665d12b2d359fd2 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 18:58:55 +0200 Subject: [PATCH 138/200] docs: update documentation with pixi dependency management --- .github/actions/setup-queens-pixi/action.yml | 2 +- CONTRIBUTING.md | 10 +-- README.md | 63 ++++++++++--------- doc/README.md | 17 +++-- doc/source/_ext/templates/introduction.md.j2 | 63 +++++++++++++++++-- doc/source/faqs/requirements.md | 19 +++--- pyproject.toml | 3 + src/queens_interfaces/fourc/README.md | 21 +++++-- .../fourc/random_material_preprocessor.py | 3 +- tests/README.md | 9 ++- 10 files changed, 148 insertions(+), 62 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 8aab9e772..aed40d6c7 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -48,7 +48,7 @@ runs: shell: bash run: | set -euo pipefail - pixi run --locked -e "${{ inputs.activate-environment }}" python -m pip install --no-deps -e . + pixi run --locked -e "${{ inputs.activate-environment }}" install-editable - name: Mark repo as safe for git shell: bash diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index daccb5e72..4f47995fa 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -45,12 +45,12 @@ have to solve them yourself. ### :fishing_pole_and_fish: Pull requests #### 1. Install QUEENS in developer mode -Install QUEENS as described in the [README.md](README.md). The development environment is covered by -the standard `mamba env ...` workflow in the README, so no additional dependency installation step is -required. To expose your local checkout inside that environment, run: +Install QUEENS as described in the [README.md](https://github.com/queens-py/queens/blob/main/README.md). +For contributions, use the Pixi development environment and expose your local clone inside it: -``` -pip install --no-deps -e . +```bash +pixi install --environment queens-dev +pixi run -e queens-dev install-editable ``` diff --git a/README.md b/README.md index 0ebdfef49..8ee560396 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@
-[![tests-local-main](https://github.com/queens-py/queens/actions/workflows/tests_local.yml/badge.svg?branch=main)](https://github.com/queens-py/queens/actions/workflows/tests_local.yml?query=branch:main) +[![tests-local-main](https://github.com/queens-py/queens/actions/workflows/local_testsuite.yml/badge.svg?branch=main)](https://github.com/queens-py/queens/actions/workflows/local_testsuite.yml?query=branch:main) [![build-documentation-main](https://github.com/queens-py/queens/actions/workflows/build_documentation.yml/badge.svg?branch=main)](https://github.com/queens-py/queens/actions/workflows/build_documentation.yml?query=branch:main)
@@ -51,45 +51,48 @@ QUEENS (**Q**uantification of **U**ncertain **E**ffects in **En**gineering **S** ## :rocket: Getting started ->**Prerequisites**: Unix system and environment management system (we recommend [miniforge](https://conda-forge.org/download/)) +>**Prerequisites**: Python 3.12 or newer. For development, use [Pixi](https://pixi.sh/latest/). - +### Easy installation -Clone the QUEENS repository to your local machine. Navigate to its base directory, then: +Clone the QUEENS repository and install it from the source checkout with: ```bash -mamba env create -n queens -f environment.base.yml -conda activate queens -pip install --no-deps -e . +pip install . ``` +We recommend using some form of environment management instead of installing into your system Python. +For more details, see [the QUEENS documentation](https://queens-py.github.io/queens/introduction.html#installation). -This installs the core QUEENS environment. The local checkout is then exposed in that environment -via `pip install --no-deps -e .`, which does not install any additional Python dependencies. - -Optional feature sets can be added afterwards when needed: +Optional runtime extras can be installed with: ```bash -mamba env update -n queens -f environment.dev.yml -mamba env update -n queens -f environment.tutorials.yml -mamba env update -n queens -f environment.fourc.yml +pip install ".[tutorials]" +pip install ".[fourc]" +pip install ".[all]" ``` -These optional environment files are only needed if you want the corresponding features: - -* `environment.dev.yml` for development tools such as linting, type checks, and documentation builds -* `environment.tutorials.yml` for the tutorial notebooks and examples -* `environment.fourc.yml` for workflows that integrate QUEENS with [4C](https://github.com/4C-multiphysics/4C) - -If you only want to use the core QUEENS functionality, you can skip those optional environment updates. - -For development or if you encounter any problems, we recommend the reproducible `conda-lock` setup because it matches the CI pipeline environment: +### Recommended installation +We recommend a modern project-based workflow based on [Pixi](https://pixi.sh/latest/) especially for development. +After cloning the repository, installing with Pixi is as easy as: ```bash -conda-lock install -n queens composed.conda-lock.yml -conda activate queens -pip install --no-deps -e . +pixi install --environment queens-base +pixi run -e queens-base install-editable +``` +Use the `queens-base` environment for core QUEENS or `queens-all` for runtime extras without development tools. +Run `pixi run -e install-editable` once for each Pixi environment you want to use. + +### Development installation +For development, we recommend using [Pixi](https://pixi.sh/latest/) together with the `queens-dev` environment. +`queens-dev` contains the full contributor setup, including development tools, tutorials, and the +4C interface dependencies. +Clone the repository and install with: +```bash +pixi install --environment queens-dev +pixi run -e queens-dev install-editable +``` +Useful development commands then look like: +```bash +pixi run -e queens-dev pytest +pixi run -e queens-dev pre-commit run --all-files ``` - -This is the safest option for contributors and debugging because it installs the exact dependency set -used in CI. The tradeoff is that `composed.conda-lock.yml` includes all optional dependency groups as well. - ## :crown: Workflow example diff --git a/doc/README.md b/doc/README.md index c936b1d32..9e86ba8d8 100644 --- a/doc/README.md +++ b/doc/README.md @@ -6,27 +6,32 @@ We believe that documentation is essential and therefore welcome any improvement ## :woman_teacher: Build the documentation -To build the documentation, first set up a QUEENS environment as described in the -[README](../README.md). For documentation work, use the development setup there, which -includes the required documentation and tutorial dependencies. +To build the documentation, first set up the QUEENS development environment as described in the +[README](../README.md): + +```bash +pixi install --environment queens-dev +pixi run -e queens-dev install-editable +``` + Next, register the environment as a Jupyter kernel with: ```bash -python -m ipykernel install --user --name queens --display-name "Python (queens)" +pixi run -e queens-dev python -m ipykernel install --user --name queens --display-name "Python (queens)" ``` When building the documentation on your machine for the first time or after adding new modules or classes to QUEENS, one needs to first rebuild the `autodoc index` by running: ```bash cd -sphinx-apidoc -o doc/source src/ -fMT +pixi run -e queens-dev sphinx-apidoc -o doc/source src/ -fMT ``` To actually build the html-documentation, navigate into the doc folder and run the make command: ```bash cd doc -sphinx-build -b html -d build/doctrees source build/html -W +pixi run -e queens-dev sphinx-build -b html -d build/doctrees source build/html -W ``` You can now view the documentation in your favorite browser by opening `build/html/index.html`. diff --git a/doc/source/_ext/templates/introduction.md.j2 b/doc/source/_ext/templates/introduction.md.j2 index 91cc48686..9109a168e 100644 --- a/doc/source/_ext/templates/introduction.md.j2 +++ b/doc/source/_ext/templates/introduction.md.j2 @@ -26,14 +26,69 @@ {{ extract_from_markdown_by_marker("installation", readme_path) }} -For development, install the additional required packages via: -{{ extract_from_markdown_by_marker("installation_develop", contributing_path) }} +### User-managed environments -> Note: We recommend using conda/mamba environments and installing performance-critical packages (e.g., numpy, scipy, ...) using `conda install .` The reason for this is the choice of BLAS library (linear algebra packages). Conda (depending on the channel) installs numpy and the [mkl](https://www.intel.com/content/www/us/en/developer/articles/technical/intel-mkl-and-third-party-applications-how-to-use-them-together.html) library from Intel, in contrast to pip which defaults back to the linear algebra package installed on the system. According to certain benchmarks ([here](http://markus-beuckelmann.de/blog/boosting-numpy-blas.html) or [here](https://medium.com/analytics-vidhya/why-conda-install-instead-of-pip-install-ba4c6826a0ae)), the mkl library is able to outperform other linear algebra libraries, especially on Intel devices. Particularly for use cases where linear algebra operations dominate the computational costs, the benefit can be huge. +QUEENS should be installed into an isolated Python environment rather than into your system Python. +The examples below use different environment managers, but the idea is always the same: +1. Create an environment with Python 3.12 or newer. +2. Activate that environment. +3. Check that `python` points to the environment and has the expected version. +4. Install QUEENS from the repository root with `python -m pip install .`. + +#### `venv` + +Use `venv` if you already have Python 3.12 installed on your system: + +```bash +git clone https://github.com/queens-py/queens.git +cd queens +python3.12 -m venv .venv +source .venv/bin/activate +python --version +python -m pip install --upgrade pip +python -m pip install . +``` + +After activation, `python --version` should report Python 3.12 or newer. If `python3.12` is not +available, install Python 3.12 first with your system package manager or another Python installer. + +#### `uv venv` + +If you use [uv](https://docs.astral.sh/uv/), let uv install and select Python 3.12: + +```bash +git clone https://github.com/queens-py/queens.git +cd queens +uv python install 3.12 +uv venv --python 3.12 +source .venv/bin/activate +python --version +python -m pip install . +``` + +#### Conda + +Conda-style environment managers can create an environment with the required Python version directly: + +```bash +git clone https://github.com/queens-py/queens.git +cd queens +conda create -n queens python=3.12 +conda activate queens +python --version +python -m pip install . +``` + +The same pattern also applies to compatible tools such as Mamba or Micromamba. + +For development, prefer the locked Pixi environments shown above because they keep dependency +resolution and editable installs aligned with CI. + +### Testing installation To test for a successful installation, run the test suite: ``` -pytest -n +pixi run -e queens-dev pytest ``` Consult the [documentation of QUEENS tests](testing) for more details on testing. diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index 30e17788f..f795a20ab 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -2,16 +2,15 @@ ## What are the requirements for QUEENS? -Currently, QUEENS is only tested on UNIX systems. Besides Python, QUEENS requires [rsync](https://rsync.samba.org/) in order to copy simulation files. +Currently, QUEENS is only tested on UNIX systems (Ubuntu and macOS on arm64). Besides Python 3.12 +or newer, QUEENS requires [rsync](https://rsync.samba.org/) in order to copy simulation files. -The Python dependencies for QUEENS are managed through the conda environment files in the repository -root: +QUEENS declares its Python dependencies in `pyproject.toml`. +For development and CI-like reproducibility, dependencies are managed with Pixi. The Pixi +environments are declared in `pyproject.toml` and locked in `pixi.lock`: -- `environment.base.yml` -- `environment.dev.yml` -- `environment.tutorials.yml` -- `environment.fourc.yml` +- `queens-base`: core QUEENS dependencies +- `queens-dev`: full contributor setup, including development tools, tutorials, and 4C support +- `queens-all`: runtime extras without development tools -For reproducible installs, QUEENS also provides the composed lock file `composed.conda-lock.yml`. - -For more information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). +For installation information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). diff --git a/pyproject.toml b/pyproject.toml index 8b857db31..eba1c2743 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -245,6 +245,9 @@ diversipy = ">=0.9" particles = { git = "https://github.com/nchopin/particles.git"} scikit-activeml= ">=1.0.0" +[tool.pixi.feature.base.tasks] +install-editable = "python -m pip install --no-deps --no-build-isolation -e ." + [tool.pixi.feature.dev.dependencies] pylint = ">=4.0.5" isort = ">=8.0.1" diff --git a/src/queens_interfaces/fourc/README.md b/src/queens_interfaces/fourc/README.md index 9e11cef8c..365c6014d 100644 --- a/src/queens_interfaces/fourc/README.md +++ b/src/queens_interfaces/fourc/README.md @@ -1,10 +1,23 @@ # 4C -This package contains drivers and utilities realted to the for multiphysics code [4C](https://github.com/4C-multiphysics/4C). We like them and we work closely with them. +This package contains drivers and utilities related to the multiphysics code +[4C](https://github.com/4C-multiphysics/4C). We like them and we work closely with them. ## Material random field interface -In order to create random material field in combintation with 4C, we require the package [fourcipp](https://github.com/4C-multiphysics/fourcipp). Therefore install QUEENS via (in the QUEENS main directory): +In order to create random material fields in combination with 4C, QUEENS requires the package +[fourcipp](https://github.com/4C-multiphysics/fourcipp). For a regular source install, use the +`fourc` extra: + +```bash +python -m pip install ".[fourc]" ``` -mamba env update -n queens -f environment.fourc.yml + +For Pixi project-based workflow, use the `queens-all` environment +that includes the 4C interface dependencies without development tools: +```bash +pixi install --environment queens-all +pixi run -e queens-all install-editable ``` -For this you need a QUEENS environment, for instructions on how to set it up see the [README.md](../README.md). +For development, use the `queens-dev` Pixi environment that includes the `fourc` feature. + +For more setup details, see the top-level [README.md](https://github.com/queens-py/queens/blob/main/README.md). diff --git a/src/queens_interfaces/fourc/random_material_preprocessor.py b/src/queens_interfaces/fourc/random_material_preprocessor.py index 9a7b54e2a..7857c742a 100644 --- a/src/queens_interfaces/fourc/random_material_preprocessor.py +++ b/src/queens_interfaces/fourc/random_material_preprocessor.py @@ -23,7 +23,8 @@ except ImportError as exc: raise ImportError( "The required packages to construct random fields in QUEENS for 4C are not installed." - " Please install them via \n mamba env update -n -f environment.fourc.yml" + " Install QUEENS with the 'fourc' extra, e.g. `python -m pip install \".[fourc]\"`, " + "or use a Pixi environment with the fourc feature such as `queens-dev` or `queens-all`." ) from exc diff --git a/tests/README.md b/tests/README.md index 9363909e7..efc18ab9c 100644 --- a/tests/README.md +++ b/tests/README.md @@ -15,7 +15,14 @@ Therefore, we test the QUEENS code base - Whenever possible, use [pytest fixtures](https://docs.pytest.org/en/latest/explanation/fixtures.html) to parameterize tests. ## :running_woman: Running tests -QUEENS is tested using [pytest](https://docs.pytest.org/en/stable/index.html). For a comprehensive list of pytest commands, see [here](https://docs.pytest.org/en/stable/how-to/usage.html). Some additional useful commands to test QUEENS are listed in the following: +QUEENS is tested using [pytest](https://docs.pytest.org/en/stable/index.html). For local +development, run tests through the Pixi development environment, for example: + +```bash +pixi run -e queens-dev pytest +``` + +For a comprehensive list of pytest commands, see [here](https://docs.pytest.org/en/stable/how-to/usage.html). Some additional useful commands to test QUEENS are listed in the following: | Test | Command | | ----------------------------- | --------------------------------------------- | From 6d225b9175c55b45f5a9cc486ff236b89ba53040 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 18:59:35 +0200 Subject: [PATCH 139/200] ci: remove conda environment action --- .../create_python_environment/action.yml | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 .github/actions/create_python_environment/action.yml diff --git a/.github/actions/create_python_environment/action.yml b/.github/actions/create_python_environment/action.yml deleted file mode 100644 index 1a5eb39bf..000000000 --- a/.github/actions/create_python_environment/action.yml +++ /dev/null @@ -1,27 +0,0 @@ -name: Create Python environment -description: Create the QUEENS Python environment with all dependencies - -outputs: - ppm: - description: Python package manager - value: ${{ steps.environment.outputs.ppm }} - -runs: - using: composite - steps: - - uses: conda-incubator/setup-miniconda@v3 - with: - miniforge-version: "latest" - - name: Create conda-lock environment and install QUEENS - id: environment - shell: bash -l {0} - env: - PYTHON_PACKAGE_MANAGER: conda - run: | - $PYTHON_PACKAGE_MANAGER install -c conda-forge conda-lock -y - conda-lock install --conda mamba -n queens composed.conda-lock.yml - $PYTHON_PACKAGE_MANAGER activate queens - pip install --no-deps -e . - $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml - $PYTHON_PACKAGE_MANAGER list - echo "ppm=$PYTHON_PACKAGE_MANAGER" >> $GITHUB_OUTPUT From 8ff37db2d793cbab2d4b43f2da3565c9b64255c3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 19:11:36 +0200 Subject: [PATCH 140/200] build: remove conda environment files --- environment.base.yml | 85 --------------------------------------- environment.dev.yml | 35 ---------------- environment.fourc.yml | 14 ------- environment.tutorials.yml | 10 ----- 4 files changed, 144 deletions(-) delete mode 100644 environment.base.yml delete mode 100644 environment.dev.yml delete mode 100644 environment.fourc.yml delete mode 100644 environment.tutorials.yml diff --git a/environment.base.yml b/environment.base.yml deleted file mode 100644 index 5d19206f9..000000000 --- a/environment.base.yml +++ /dev/null @@ -1,85 +0,0 @@ ---- -name: queens -channels: - - conda-forge - # We want to have a reproducible setup, so we don't want default channels, - # which may be different for different users. All required channels should - # be listed explicitly here. - - nodefaults -dependencies: - - python - # to ensure that performance optimized backends are used, - # the following packages are installed from conda - # for example BLAS libraries like Intel MKL for numpy - - setuptools<82 #restriction due to gpflow needing pkg_resources - - cython - - numba - - numpy - - pandas - - scikit-learn - - scipy - - # Dask packages - - dask - - distributed # dask.distributed - - dask-jobqueue - - bokeh # for dask dashboard - - fabric # for ssh connection - - # Others - - xarray # Special array format - - pydoe # design of experiments - - SALib # for sensitivity analysis - - vtk # vtk format handler - - pyvista - - autograd # wrapper around numpy for automated differentiation - - chaospy # polynomial chaos - - pyyaml # to load yaml files - - jinja2 - - # Machine learning libraries - - arviz # Bayesian visualization - - gpflow # LV and variational GPs - - optax # google jax based optimizer - - tensorflow - - tensorflow-probability - - tf-keras - - jax - - pymc >= 5.28.4 - - stable-baselines3 - - # making fancy plots - - matplotlib - - seaborn - - plotly - - # testing framework - - pytest - - py - - pytest-codestyle - - pytest-cov - - pytest-mock - - pytest-xdist - - mock - - py - - # Terminal utils - - tqdm # a smart progress meter for loops - - tomli # TOML parser - - # Other Python stuff - - pathos # multiprocessing with more complex python objects - - black>=24.4.2 # formatter for code created by QUEENS - - - - # These packages need to be installed via pip - - pip - - pip: - # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run - - gnuplotlib # for gnuplot based terminal ascii plots - - diversipy # sampling from space filling subsets # has no notable dependencies - # Chopin et al. sequential Monte-Carlo, filtering/smoothing package - # - particles # currently causes problem by requiring numpy<2 - - particles@git+https://github.com/nchopin/particles.git - - scikit-activeml>=0.4.1 diff --git a/environment.dev.yml b/environment.dev.yml deleted file mode 100644 index 64cc8994f..000000000 --- a/environment.dev.yml +++ /dev/null @@ -1,35 +0,0 @@ ---- -channels: - - conda-forge - # We want to have a reproducible setup, so we don't want default channels, - # which may be different for different users. All required channels should - # be listed explicitly here. - - nodefaults -dependencies: - # Development - - pylint>=2.16 - - isort>=5.0 - - pre-commit - - pre-commit-hooks>=4.4.0 - - sphinx - - nbsphinx - - pydata-sphinx-theme - - pandoc - - commitizen>=3.12.0 - - docformatter>=1.5.1 - - yamllint>=1.19.0 - - ruff - - nbstripout - - myst-parser - - testbook - - ipykernel - - mypy - - - # These packages need to be installed via pip - - pip - - pip: - # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run - - liccheck - - pylint-exit - - licenseheaders diff --git a/environment.fourc.yml b/environment.fourc.yml deleted file mode 100644 index a2db09a6d..000000000 --- a/environment.fourc.yml +++ /dev/null @@ -1,14 +0,0 @@ ---- -channels: - - conda-forge - # We want to have a reproducible setup, so we don't want default channels, - # which may be different for different users. All required channels should - # be listed explicitly here. - - nodefaults -dependencies: - # These packages need to be installed via pip - - pip - - pip: - # if these packages cause problems create environment without pip; activate env; try each package: pip install --dry-run - # 4C - - fourcipp diff --git a/environment.tutorials.yml b/environment.tutorials.yml deleted file mode 100644 index 0f823a802..000000000 --- a/environment.tutorials.yml +++ /dev/null @@ -1,10 +0,0 @@ ---- -channels: - - conda-forge - # We want to have a reproducible setup, so we don't want default channels, - # which may be different for different users. All required channels should - # be listed explicitly here. - - nodefaults -dependencies: - # Tutorials - - scikit-fem From bd0af1b54f293b2deb1e5244494a35d6ff497938 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 19:12:15 +0200 Subject: [PATCH 141/200] build: remove dev dependencies from base environment --- .github/workflows/test_pypi_build.yml | 1 + pyproject.toml | 37 +++++++++++++-------------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 11fb811ce..4613f8f61 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -65,6 +65,7 @@ jobs: python -m pip install --upgrade pip wheel_path="$(find dist -maxdepth 1 -type f -name '*.whl' | head -n 1)" python -m pip install "${wheel_path}${{ matrix.extra_selector }}" + python -m pip install pytest pytest-mock mock - name: Run pure PyPI smoke checks run: | set -euo pipefail diff --git a/pyproject.toml b/pyproject.toml index eba1c2743..a48813a2b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,17 +42,8 @@ dependencies = [ "matplotlib>=3.10.8", "seaborn>=0.13.2", "plotly>=6.6.0", - "pytest>=9.0.3", - "py>=1.11.0", - "pytest-codestyle>=2.0.1", - "pytest-cov>=7.1.0", - "pytest-mock>=3.15.1", - "pytest-xdist>=3.8.0", - "mock>=5.2.0", "tqdm>=4.67.3", - "tomli>=2.4.1", "pathos>=0.3.5", - "black>=26.3.1", "gnuplotlib>=0.46", "diversipy>=0.9", "particles @ git+https://github.com/nchopin/particles.git", @@ -227,17 +218,8 @@ stable-baselines3 = ">=2.8.0" matplotlib = ">=3.10.8" seaborn = ">=0.13.2" plotly = ">=6.6.0" -pytest = ">=9.0.3" -py = ">=1.11.0" -pytest-codestyle = ">=2.0.1" -pytest-cov = ">=7.1.0" -pytest-mock = ">=3.15.1" -pytest-xdist = ">=3.8.0" -mock = ">=5.2.0" tqdm = ">=4.67.3" -tomli = ">=2.4.1" pathos = ">=0.3.5" -black = ">=26.3.1" [tool.pixi.feature.base.pypi-dependencies] gnuplotlib = ">=0.46" @@ -249,6 +231,14 @@ scikit-activeml= ">=1.0.0" install-editable = "python -m pip install --no-deps --no-build-isolation -e ." 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xml_coverage_report.xml >> "$GITHUB_STEP_SUMMARY" + reports/core-macos/test_junit_core_macOS.xml \ + reports/tutorials-ubuntu/test_junit_tutorials_Linux.xml \ + reports/tutorials-macos/test_junit_tutorials_macOS.xml \ + reports/fourc-ubuntu/test_junit_fourc_Linux.xml \ + reports/tutorials-fourc-ubuntu/test_junit_tutorials_fourc_Linux.xml \ + >> "$GITHUB_STEP_SUMMARY" - name: Publish combined junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 diff --git a/.github/xml_summaries_to_md.py b/.github/xml_summaries_to_md.py index bf0001bb9..466bc623b 100644 --- a/.github/xml_summaries_to_md.py +++ b/.github/xml_summaries_to_md.py @@ -12,35 +12,176 @@ # should have received a copy of the GNU Lesser General Public License along with QUEENS. If not, # see . # -"""Generate a md test summary from the xml test reports.""" +"""Generate a markdown test summary from XML test reports.""" import re import sys import xml.etree.ElementTree as ET -from copy import copy +from dataclasses import dataclass from pathlib import Path +MAX_SLOW_TESTS = 50 -def xml_to_dict(xml_element, root=True): - """Xml to dict converter. +JUNIT_REPORT_PATTERN = re.compile( + r"test_junit_(?Ptutorials_fourc|tutorials|fourc|core)_(?P[^.]+)\.xml$" +) +GROUP_LABELS = { + "core": "Core tests", + "tutorials": "Tutorial tests", + "fourc": "4C integration tests", + "tutorials_fourc": "4C tutorial tests", +} +RUNNER_LABELS = { + "Linux": "Ubuntu", + "macOS": "macOS", +} + + +@dataclass +class TestCase: + """Single JUnit testcase entry.""" + + group: str + classname: str + name: str + status: str + time: float + + +@dataclass +class TestReport: + """Aggregated JUnit report for one workflow test group.""" + + group: str + tests: int + passed: int + skipped: int + failures: int + errors: int + time: float + cases: list[TestCase] + + +def _xml_root(path): + """Read an XML file and return its root element.""" + return ET.fromstring(Path(path).read_text(encoding="utf-8")) + + +def _split_xml_paths(paths): + """Split input XML paths into JUnit reports and one coverage report. Args: - xml_element (ET): ElementTree object. - root (bool, optional): Is root object. Defaults to True. + paths (list): Input XML paths. Returns: - dict: data as dictionary + tuple: JUnit paths and coverage path. """ - if root: - return {xml_element.tag: xml_to_dict(xml_element, False)} - dictionary = copy(xml_element.attrib) - if xml_element.text: - dictionary["_text"] = xml_element.text - for x in xml_element.findall("./*"): - if x.tag not in dictionary: - dictionary[x.tag] = [] - dictionary[x.tag].append(xml_to_dict(x, False)) - return dictionary + junit_paths = [] + coverage_paths = [] + for path in paths: + root = _xml_root(path) + if root.tag == "coverage": + coverage_paths.append(path) + elif root.tag in {"testsuite", "testsuites"}: + junit_paths.append(path) + else: + raise ValueError(f"Unknown XML report type {root.tag!r} in {path}.") + + if not coverage_paths: + raise ValueError("No coverage XML report was provided.") + if len(coverage_paths) > 1: + raise ValueError("Expected exactly one coverage XML report.") + if not junit_paths: + raise ValueError("No JUnit XML reports were provided.") + + return junit_paths, coverage_paths[0] + + +def _iter_testsuites(root): + """Yield all testsuite elements from a JUnit XML root.""" + if root.tag == "testsuite": + yield root + return + + yield from root.findall(".//testsuite") + + +def _workflow_group_from_path(path): + """Infer workflow test group label from a JUnit XML file name.""" + match = JUNIT_REPORT_PATTERN.fullmatch(Path(path).name) + if match is None: + return Path(path).stem.replace("_", " ") + + group = GROUP_LABELS[match.group("group")] + runner = RUNNER_LABELS.get(match.group("runner"), match.group("runner")) + return f"{group} ({runner})" + + +def _testcase_status(testcase): + """Return the status of a JUnit testcase element.""" + if testcase.find("error") is not None: + return "error" + if testcase.find("failure") is not None: + return "failed" + if testcase.find("skipped") is not None: + return "skipped" + return "passed" + + +def _shorten_classname(classname): + """Shorten pytest class names for display.""" + prefixes = ( + "tests.unit_tests.", + "tests.integration_tests.", + "tests.tutorial_tests.", + "tests.benchmarks.", + ) + for prefix in prefixes: + if classname.startswith(prefix): + return classname[len(prefix) :] + return classname + + +def _format_test_name(name): + """Highlight pytest parametrization values in test names.""" + return re.sub(r"\[(.*?)\]", r"[**\1**]", name) + + +def _parse_junit_report(path): + """Parse one JUnit XML report into a TestReport.""" + root = _xml_root(path) + group = _workflow_group_from_path(path) + suites = list(_iter_testsuites(root)) + cases = [] + + for suite in suites: + for testcase in suite.findall("testcase"): + cases.append( + TestCase( + group=group, + classname=_shorten_classname(testcase.get("classname", "")), + name=_format_test_name(testcase.get("name", "")), + status=_testcase_status(testcase), + time=float(testcase.get("time", 0.0)), + ) + ) + + passed = sum(testcase.status == "passed" for testcase in cases) + skipped = sum(testcase.status == "skipped" for testcase in cases) + failures = sum(testcase.status == "failed" for testcase in cases) + errors = sum(testcase.status == "error" for testcase in cases) + runtime = sum(float(suite.get("time", 0.0)) for suite in suites) + + return TestReport( + group=group, + tests=len(cases), + passed=passed, + skipped=skipped, + failures=failures, + errors=errors, + time=runtime, + cases=cases, + ) def create_md_table(data_list, header): @@ -54,8 +195,12 @@ def create_md_table(data_list, header): str: table string """ - def add_seperators(row): - """Add markdown table seperators. + def markdown_cell(value): + """Format a value as markdown table cell.""" + return str(value).replace("|", r"\|").replace("\n", "
") + + def add_separators(row): + """Add markdown table separators. Args: row (list): List of row data. @@ -63,16 +208,19 @@ def add_seperators(row): Returns: str: single row for markdown table """ - return "|" + "|".join([str(s) for s in row]) + "|" + return "|" + "|".join([markdown_cell(s) for s in row]) + "|" + + if not data_list: + return "_No entries._" - table = [add_seperators(header)] - table.append(add_seperators(["--"] * len(header))) - table.extend([add_seperators(k) for k in data_list]) + table = [add_separators(header)] + table.append(add_separators(["--"] * len(header))) + table.extend([add_separators(k) for k in data_list]) return "\n".join(table) -def collapsable(full_text, summary): - """Create collapsable section. +def collapsible(full_text, summary): + """Create collapsible section. Args: full_text (str): Full text. @@ -84,83 +232,137 @@ def collapsable(full_text, summary): return f"
\n{summary}\n\n{full_text}\n\n
" "" -def generate_md_summary(path_to_junit_xml, path_to_coverage_xml): +def collapsable(full_text, summary): + """Create collapsible section. + + Keep the old misspelled function name for compatibility. + """ + return collapsible(full_text, summary) + + +def _format_time(seconds): + """Format a time value for markdown output.""" + return f"{seconds:.3f}" + + +def _format_test_count(count): + """Format a test count with the correct singular or plural label.""" + return f"{count} test" if count == 1 else f"{count} tests" + + +def _report_summary(report): + """Create a compact text summary for one grouped report.""" + failed = report.failures + report.errors + status_summary = f"{report.passed} passed" + if report.skipped: + status_summary += f", {report.skipped} skipped" + if failed: + status_summary += f", {failed} failed or errored" + return f"{_format_test_count(report.tests)} took {int(report.time)}s ({status_summary})." + + +def _overview_rows(reports): + """Create the workflow group overview table rows.""" + return [ + [ + report.group, + report.tests, + report.passed, + report.skipped, + report.failures, + report.errors, + _format_time(report.time), + ] + for report in reports + ] + + +def _case_rows(cases): + """Create markdown table rows for testcase entries.""" + return [ + [ + testcase.group, + testcase.classname, + testcase.name, + testcase.status, + _format_time(testcase.time), + ] + for testcase in cases + ] + + +def generate_md_summary(*paths): """Generate markdown summary. Args: - path_to_junit_xml (str): Path to junit xml file. - path_to_coverage_xml (str): Path to coverage xml file. + paths (str): Paths to JUnit XML files and one coverage XML file. The + order is flexible; report types are detected from the XML root tag. Returns: str: pytest summary. """ - root = ET.fromstring(Path(path_to_junit_xml).read_text(encoding="utf-8")) - junit_report = xml_to_dict(root) - - root = ET.fromstring(Path(path_to_coverage_xml).read_text(encoding="utf-8")) - coverage_summary = xml_to_dict(root) - - testing_time = junit_report["testsuites"]["testsuite"][0]["time"] - total_number_of_tests = junit_report["testsuites"]["testsuite"][0]["tests"] - unit_tests = [] - integration_tests = [] - failed = [] - for k in junit_report["testsuites"]["testsuite"][0]["testcase"]: - k.pop("system-out") - k.pop("system-err") - k["time"] = float(k["time"]) - k["name"] = re.sub(r"\[(.*?)\]", r"[**\1**]", k["name"]) - - if k.pop("failure", False): - failed.append(list(k.values())) - if k["classname"].startswith("tests.unit_tests"): - k["classname"] = k["classname"][len("tests.unit_tests.") :] - unit_tests.append(list(k.values())) - elif k["classname"].startswith("tests.integration_tests"): - k["classname"] = k["classname"][len("tests.integration_tests.") :] - integration_tests.append(list(k.values())) + flattened_paths = [] + for path in paths: + if isinstance(path, (list, tuple)): + flattened_paths.extend(path) else: - raise ValueError(f"Unknown test type {k['classname']}.") + flattened_paths.append(path) - integration_tests = sorted(integration_tests, key=lambda x: -x[-1]) - unit_tests = sorted(unit_tests, key=lambda x: -x[-1]) + junit_paths, coverage_path = _split_xml_paths(flattened_paths) + reports = [_parse_junit_report(path) for path in junit_paths] + coverage_root = _xml_root(coverage_path) - text = "# :blue_heart: Pytest summary\n" + total_number_of_tests = sum(report.tests for report in reports) + testing_time = sum(report.time for report in reports) + failed_cases = [ + testcase + for report in reports + for testcase in report.cases + if testcase.status in {"failed", "error"} + ] - text += f"\n### {total_number_of_tests} tests took {int(float(testing_time))}s.\n" + text = "# Pytest summary\n" - text += "\n## :umbrella: Coverage \n\n" - text += f'\n - by line rate **{int(float(coverage_summary["coverage"]["line-rate"]) * 100)}%**' text += ( - f'\n - by branch rate **{int(float(coverage_summary["coverage"]["branch-rate"]) * 100)}%**' + f"\n### {_format_test_count(total_number_of_tests)} took {int(testing_time)}s " + f"across {len(reports)} workflow report(s).\n" ) - text += "\n\n## :bullettrain_side: Integration tests\n\n" - text += collapsable( - "\n > only showing the top 50 slowest tests\n\n" - + create_md_table(integration_tests[:50], header=["Test Path", "Name", "Time (s)"]), - f"{len(integration_tests)} integration tests took " - f"{int(sum((k[-1] for k in integration_tests)))}s.", - ) + text += "\n## Coverage\n\n" + text += f'\n - by line rate **{int(float(coverage_root.get("line-rate", 0.0)) * 100)}%**' + text += f'\n - by branch rate **{int(float(coverage_root.get("branch-rate", 0.0)) * 100)}%**' - text += "\n\n## :speedboat: Unit tests\n\n" - text += collapsable( - "\n > only showing the top 50 slowest tests\n\n" - + create_md_table(unit_tests[:50], header=["Test Path", "Name", "Time (s)"]), - f"{len(unit_tests)} unit tests took {int(sum((k[-1] for k in unit_tests)))}s.", + text += "\n\n## Workflow Groups\n\n" + text += create_md_table( + _overview_rows(reports), + header=["Group", "Tests", "Passed", "Skipped", "Failures", "Errors", "Time (s)"], ) - text += "\n\n" - if failed: - text += "\n\n## :worried: Failed tests\n\n" - text += f"\n{len(failed)} test(s) failed.\n\n" - text += create_md_table(failed, header=["Test Path", "Name", "Time (s)"]) + for report in reports: + slowest_cases = sorted(report.cases, key=lambda testcase: -testcase.time)[:MAX_SLOW_TESTS] + text += f"\n\n## {report.group}\n\n" + text += collapsible( + f"\n > only showing the top {MAX_SLOW_TESTS} slowest tests\n\n" + + create_md_table( + _case_rows(slowest_cases), + header=["Group", "Test Path", "Name", "Status", "Time (s)"], + ), + _report_summary(report), + ) + + if failed_cases: + text += "\n\n## Failed Tests\n\n" + text += f"\n{_format_test_count(len(failed_cases))} failed or errored.\n\n" + text += create_md_table( + _case_rows(failed_cases), + header=["Group", "Test Path", "Name", "Status", "Time (s)"], + ) return text if __name__ == "__main__": try: - print(generate_md_summary(sys.argv[1], sys.argv[2])) - except: # pylint: disable=bare-except - print("Could not generate the summary :sob:") + print(generate_md_summary(*sys.argv[1:])) + except Exception as error: # pylint: disable=broad-except + print(f"Could not generate the summary: {error}") From e9331983e9259e0b32db55c94f78bac7ce3885f1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 22:40:25 +0200 Subject: [PATCH 144/200] ci: remove junit report from collection since it is published per job step --- .github/workflows/local_testsuite.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 109a8b4c1..70568d18d 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -270,13 +270,6 @@ jobs: reports/fourc-ubuntu/test_junit_fourc_Linux.xml \ reports/tutorials-fourc-ubuntu/test_junit_tutorials_fourc_Linux.xml \ >> "$GITHUB_STEP_SUMMARY" - - name: Publish combined junit pytest report - if: success() || failure() - uses: mikepenz/action-junit-report@v6 - with: - report_paths: "reports/**/*.xml" - annotate_only: true - job_summary: false - name: Upload combined coverage report uses: actions/upload-pages-artifact@v5 with: From fd12d7f034a0620e4d42e16b4027d9f658d93cc6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Tue, 12 May 2026 22:54:54 +0200 Subject: [PATCH 145/200] docs: instructions on how to change dependencies --- CONTRIBUTING.md | 47 +++++++++++++++++++++++++++++++++ doc/source/faqs/requirements.md | 4 +++ 2 files changed, 51 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4f47995fa..785b23809 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -80,6 +80,53 @@ Like every codebase, QUEENS follows some project-specific coding conventions. Be - If relative paths within the QUEENS source are needed, use the [relative_path_from_queens_source](src/queens/utils/path.py#L24) function. - Decorate the init method of QUEENS objects with the `log_init_args` decorator from [src/queens/utils/logger_settings.py](src/queens/utils/logger_settings.py#L248). This automatically logs the arguments passed to the init. - We only allow disabling pylint warnings for specific lines, not for entire files. If you disable warnings, please use the long pylint description, not just the code. + +##### Changing dependencies +QUEENS declares dependencies in `pyproject.toml` and locks the Pixi environments in `pixi.lock`. +For a short overview of the available environments, see the +[requirements FAQ](doc/source/faqs/requirements.md). This section describes how to add, remove, or +update dependencies. + +When changing dependencies, keep the PEP-style dependency declarations and the Pixi declarations in +sync: +- Runtime dependencies belong in `[project].dependencies` and the matching + `[tool.pixi.feature.base]` dependency section. +- Optional runtime dependencies belong in `[project.optional-dependencies]` and a matching + `[tool.pixi.feature.]` section. +- Development-only tools belong in `[dependency-groups].dev` and the matching + `[tool.pixi.feature.dev]` dependency section. +- In Pixi sections, use `dependencies` for Conda packages and `pypi-dependencies` for packages that + must be installed from PyPI or a Git source. +- Do not add test, linting, formatting, documentation, or release tooling to the base runtime + dependencies unless it is actually needed by QUEENS at runtime. + +After editing `pyproject.toml`, run the dependency integrity check. The same check is installed as a +pre-commit hook and also runs in CI: +```bash +pixi run -e queens-dev pre-commit run check-pyproject-dependency-integrity --files pyproject.toml +``` + +If dependency declarations changed, refresh the lockfile and commit it together with +`pyproject.toml`: +```bash +pixi lock +git add pyproject.toml pixi.lock +``` + +The CI pipeline checks this as well: if dependency-relevant sections in `pyproject.toml` changed and +`pixi lock --check --dry-run` would update `pixi.lock`, the code quality job fails. Before opening +or updating a pull request, it is useful to verify the lockfile locally: +```bash +pixi lock --check --dry-run +``` + +Finally, reinstall or update the affected Pixi environment and run a focused test or smoke check: +```bash +pixi install --environment queens-dev +pixi run -e queens-dev install-editable +pixi run -e queens-dev pytest +``` + ##### Commit messages Please provide meaningful commit messages based on the [Conventional Commits guidelines](https://www.conventionalcommits.org/en/v1.0.0/). diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index f795a20ab..ed3ad0aed 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -14,3 +14,7 @@ environments are declared in `pyproject.toml` and locked in `pixi.lock`: - `queens-all`: runtime extras without development tools For installation information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). + +## Changing the requirements +For instructions on adding, removing, or updating dependencies, see the +[contributing guide](../contributing.md#changing-dependencies). From cb27716014e70996f868e36fb7f8ed5fbf57349b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 11:40:33 +0200 Subject: [PATCH 146/200] ci: add dependabot automatic updating of actions --- .github/dependabot.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..2d0f59c3c --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,15 @@ +--- +version: 2 +updates: + - package-ecosystem: github-actions + directories: + - / + - /.github/actions/setup-queens-pixi + schedule: + interval: monthly + groups: + github-actions: + patterns: + - "*" + cooldown: + default-days: 7 From 1540676597b75807f4d32d0e108b22fc554cee7c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 13 May 2026 09:44:43 +0000 Subject: [PATCH 147/200] build(deps): bump the github-actions group across 2 directories with 2 updates Bumps the github-actions group with 1 update in the / directory: [webiny/action-conventional-commits](https://github.com/webiny/action-conventional-commits). Bumps the github-actions group with 1 update in the /.github/actions/setup-queens-pixi directory: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi). Updates `webiny/action-conventional-commits` from 1.3.0 to 1.4.2 - [Release notes](https://github.com/webiny/action-conventional-commits/releases) - [Commits](https://github.com/webiny/action-conventional-commits/compare/v1.3.0...v1.4.2) Updates `prefix-dev/setup-pixi` from 0.9.4 to 0.9.5 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/v0.9.4...v0.9.5) --- updated-dependencies: - dependency-name: webiny/action-conventional-commits dependency-version: 1.4.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] --- .github/actions/setup-queens-pixi/action.yml | 2 +- .github/workflows/code_quality.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index aed40d6c7..499f752a1 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -34,7 +34,7 @@ inputs: runs: using: composite steps: - - uses: prefix-dev/setup-pixi@v0.9.4 + - uses: prefix-dev/setup-pixi@v0.9.5 with: pixi-version: ${{ inputs.pixi-version }} cache: ${{ inputs.cache }} diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index dc99e1b84..784b0f66d 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -175,7 +175,7 @@ jobs: uses: apache/skywalking-eyes/header@v0.8.0 - name: Check conventional commit messages - uses: webiny/action-conventional-commits@v1.3.0 + uses: webiny/action-conventional-commits@v1.4.2 - name: Run isort run: | From d30c84f1da80e233868ee1f7c1ecbdbfd9efd9e8 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 14:42:14 +0200 Subject: [PATCH 148/200] docs: fix link to section --- doc/source/faqs/requirements.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index ed3ad0aed..523cf516d 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -17,4 +17,4 @@ For installation information see the [README.md](https://github.com/queens-py/qu ## Changing the requirements For instructions on adding, removing, or updating dependencies, see the -[contributing guide](../contributing.md#changing-dependencies). +[contributing guide](../contributing.md). From 5da1a16a591a2720538da3cdf3019d301dc70427 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 14:42:29 +0200 Subject: [PATCH 149/200] docs: remove double information --- doc/README.md | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/doc/README.md b/doc/README.md index 9e86ba8d8..7de0d323d 100644 --- a/doc/README.md +++ b/doc/README.md @@ -7,12 +7,7 @@ We believe that documentation is essential and therefore welcome any improvement ## :woman_teacher: Build the documentation To build the documentation, first set up the QUEENS development environment as described in the -[README](../README.md): - -```bash -pixi install --environment queens-dev -pixi run -e queens-dev install-editable -``` +[README](../README.md). Next, register the environment as a Jupyter kernel with: From 7345b98062122053f19e717b2bd421f10aae9dd0 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 16:04:06 +0200 Subject: [PATCH 150/200] ci: add workflow for automatic dependecy upgrades --- .github/workflows/update_pixi_lock.yml | 43 ++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 .github/workflows/update_pixi_lock.yml diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml new file mode 100644 index 000000000..155286733 --- /dev/null +++ b/.github/workflows/update_pixi_lock.yml @@ -0,0 +1,43 @@ +# yamllint disable +name: Update Pixi lockfile + +on: + workflow_dispatch: + schedule: + - cron: "0 5 1 * *" + +permissions: + contents: write + pull-requests: write + +jobs: + update-pixi-lock: + name: Update Pixi lockfile + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v6 + - name: Set up Pixi + uses: prefix-dev/setup-pixi@v0.9.4 + with: + pixi-version: v0.67.2 + run-install: false + - name: Update Pixi lockfile + run: | + set -euo pipefail + + pixi update --json | pixi exec pixi-diff-to-markdown > pixi_lock_update.md + - name: Create pull request + uses: peter-evans/create-pull-request@v8 + with: + token: ${{ secrets.GITHUB_TOKEN }} + commit-message: Update Pixi lockfile + title: Update Pixi lockfile + body-path: pixi_lock_update.md + branch: update-pixi-lock + base: main + labels: pixi + delete-branch: true + add-paths: pixi.lock From f181e6ac93e5c92953da7fee2ec473b771f16624 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 16:06:01 +0200 Subject: [PATCH 151/200] ci: add gitattributes file for pixi.lock --- .gitattributes | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 000000000..997504b46 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff From 3b9e9882211bd4a48e9d1caec91f55e1de0cc289 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 16:49:36 +0200 Subject: [PATCH 152/200] build: make queens-base the default environment, remove queens-base --- pixi.lock | 11939 +++++++++++++++++------------------------------ pyproject.toml | 6 +- 2 files changed, 4202 insertions(+), 7743 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5f2fc6dc6..ab66d35d9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,344 +11,6 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda - 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queens-base + default queens-all queens-dev activate-environment: queens-dev diff --git a/README.md b/README.md index 8ee560396..ee6798b0f 100644 --- a/README.md +++ b/README.md @@ -73,11 +73,12 @@ pip install ".[all]" We recommend a modern project-based workflow based on [Pixi](https://pixi.sh/latest/) especially for development. After cloning the repository, installing with Pixi is as easy as: ```bash -pixi install --environment queens-base -pixi run -e queens-base install-editable +pixi install +pixi run install-editable ``` -Use the `queens-base` environment for core QUEENS or `queens-all` for runtime extras without development tools. -Run `pixi run -e install-editable` once for each Pixi environment you want to use. +The default Pixi environment contains the core QUEENS dependencies. Use `queens-all` for runtime +extras without development tools. For named Pixi environments, run +`pixi run -e install-editable` once for each environment you want to use. ### Development installation For development, we recommend using [Pixi](https://pixi.sh/latest/) together with the `queens-dev` environment. diff --git a/doc/README.md b/doc/README.md index 7de0d323d..fa759cfda 100644 --- a/doc/README.md +++ b/doc/README.md @@ -18,7 +18,7 @@ pixi run -e queens-dev python -m ipykernel install --user --name queens --displa When building the documentation on your machine for the first time or after adding new modules or classes to QUEENS, one needs to first rebuild the `autodoc index` by running: ```bash -cd +cd pixi run -e queens-dev sphinx-apidoc -o doc/source src/ -fMT ``` diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index 523cf516d..e6b3010ac 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -9,9 +9,9 @@ QUEENS declares its Python dependencies in `pyproject.toml`. For development and CI-like reproducibility, dependencies are managed with Pixi. The Pixi environments are declared in `pyproject.toml` and locked in `pixi.lock`: -- `queens-base`: core QUEENS dependencies -- `queens-dev`: full contributor setup, including development tools, tutorials, and 4C support +- `default`: core QUEENS dependencies - `queens-all`: runtime extras without development tools +- `queens-dev`: full contributor setup, including development tools, tutorials, and 4C support For installation information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). diff --git a/tests/README.md b/tests/README.md index efc18ab9c..bd3764469 100644 --- a/tests/README.md +++ b/tests/README.md @@ -55,7 +55,7 @@ add its relative path to exactly one list in notebook has no marker assignment. ### :four_leaf_clover: Integration tests with 4C -For the integration tests in QUEENS that require the multiphysics simulation framework [4C](https://github.com/4C-multiphysics/4C), the user needs to create a **symbolic link** to the 4C-executable and store it under `/config`: +For the integration tests in QUEENS that require the multiphysics simulation framework [4C](https://github.com/4C-multiphysics/4C), the user needs to create a **symbolic link** to the 4C-executable and store it under `/config`: ``` -ln -s /config/4C_build +ln -s /config/4C_build ``` diff --git a/tests/integration_tests/fourc/conftest.py b/tests/integration_tests/fourc/conftest.py index 41484cf33..1a6c3e5e2 100644 --- a/tests/integration_tests/fourc/conftest.py +++ b/tests/integration_tests/fourc/conftest.py @@ -40,6 +40,6 @@ def fixture_setup_symbolic_links_fourc(fourc_link): "4C! \n" "You can create the necessary symbolic link on Linux via:\n" "-------------------------------------------------------------------------\n" - "ln -s /config/4C_build\n" + "ln -s /config/4C_build\n" "-------------------------------------------------------------------------\n" ) from error diff --git a/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb b/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb index 1245936fd..6b11c296c 100644 --- a/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb +++ b/tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb @@ -145,9 +145,9 @@ "\n", "As mentioned before, for 4C, these are already provided by the QUEENS community.\n", "\n", - "> Note: This tutorial assumes a working local 4C installation. Please create a symbolic link to your 4C build directory and store it under `/config/4C_build` via this command:\n", + "> Note: This tutorial assumes a working local 4C installation. Please create a symbolic link to your 4C build directory and store it under `/config/4C_build` via this command:\n", "> ```\n", - "> ln -s /config/4C_build\n", + "> ln -s /config/4C_build\n", "> ```" ] }, diff --git a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb index fb827e3b2..23d943eee 100644 --- a/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb +++ b/tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb @@ -212,9 +212,9 @@ "source": [ "As we can see, we set the material parameter to be constant in each element. We can think about this random field as a domain that has some type of defect where the mechanical properties are different.\n", "\n", - "> Note: This tutorial assumes a working local 4C installation. Please create a symbolic link to your 4C build directory and store it under `/config/4C_build` via this command:\n", + "> Note: This tutorial assumes a working local 4C installation. Please create a symbolic link to your 4C build directory and store it under `/config/4C_build` via this command:\n", "> ```\n", - "> ln -s /config/4C_build\n", + "> ln -s /config/4C_build\n", "> ```" ] }, From e451cb65d681a2dc55fe1fe17b421def9a68c1da Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 17:25:39 +0200 Subject: [PATCH 154/200] ci: unify use of pixi to make maintenance easier --- .github/actions/setup-queens-pixi/action.yml | 9 ++++++++- .github/workflows/update_pixi_lock.yml | 5 +++-- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 499f752a1..a40e18a8f 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -1,5 +1,7 @@ name: Setup QUEENS pixi environment -description: Set up pixi, install QUEENS editable into the selected environment, and optionally ensure rsync is available. +description: > + Set up pixi, install QUEENS editable into the selected environment, + and optionally ensure rsync is available. inputs: pixi-version: @@ -14,6 +16,10 @@ inputs: description: Whether setup-pixi should write to the cache. required: false default: "false" + run-install: + description: Whether setup-pixi should install the selected pixi environments. + required: false + default: "true" environments: description: Whitespace-separated list of pixi environments to install. required: false @@ -39,6 +45,7 @@ runs: pixi-version: ${{ inputs.pixi-version }} cache: ${{ inputs.cache }} cache-write: ${{ inputs.cache-write }} + run-install: ${{ inputs.run-install }} environments: ${{ inputs.environments }} frozen: true activate-environment: ${{ inputs.activate-environment }} diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index 155286733..625d1c594 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -20,10 +20,11 @@ jobs: steps: - uses: actions/checkout@v6 - name: Set up Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: ./.github/actions/setup-queens-pixi with: - pixi-version: v0.67.2 run-install: false + install-editable: false + ensure-rsync: false - name: Update Pixi lockfile run: | set -euo pipefail From b3c8b47697911f5de201af7a3b827d5fdadea44f Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 13 May 2026 17:37:12 +0200 Subject: [PATCH 155/200] refactor: activate yamllint for workflow yml files --- .github/workflows/build_documentation.yml | 3 +- .github/workflows/code_quality.yml | 21 +++++---- .github/workflows/local_testsuite.yml | 57 +++++++++++++++++++---- .github/workflows/test_pypi_build.yml | 7 +-- .github/workflows/update_pixi_lock.yml | 3 +- 5 files changed, 66 insertions(+), 25 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 07e7cb81a..4dfa618f1 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -1,7 +1,6 @@ -# yamllint disable name: Build documentation -on: +"on": pull_request: push: branches: diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 88292fc6c..acb077d55 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -1,7 +1,6 @@ -# yamllint disable name: Code quality -on: +"on": schedule: - cron: "0 1 * * *" pull_request: @@ -76,7 +75,8 @@ jobs: exit "${pyproject_check_status}" fi fi - echo "Pyproject.toml dependency sections changed compared to ${base_ref}: ${pyproject_changed}" + echo "Pyproject.toml dependency sections changed compared to ${base_ref}:" \ + "${pyproject_changed}" echo "::endgroup::" echo "::group::Check if pixi.lock would be updated by pixi lock..." @@ -112,7 +112,9 @@ jobs: { echo "### Pixi Environment Integrity" echo "" - echo "- dependency-relevant \`pyproject.toml\` changes vs \`${base_ref}\`: ${pyproject_changed}" + echo "- dependency-relevant \`pyproject.toml\` changes:" + echo " - compare ref: \`${base_ref}\`" + echo " - changed: ${pyproject_changed}" echo "- \`pixi.lock\` would change if refreshed: ${lock_update_possible}" if [ "${pyproject_changed}" = "true" ]; then @@ -168,7 +170,11 @@ jobs: set -euo pipefail echo "::group::Create an rc file for the license header check..." - python .gitlab/pipeline_utils/create_licenserc.py --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" --text_file "license_header.tmpl" --output_file ".licenserc.yaml" --placeholder "license_header" + python .gitlab/pipeline_utils/create_licenserc.py \ + --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" \ + --text_file "license_header.tmpl" \ + --output_file ".licenserc.yaml" \ + --placeholder "license_header" echo "::endgroup::" - name: Check license headers @@ -205,11 +211,6 @@ jobs: pylint --rcfile=.pylintrc --disable=duplicate-code tests/integration_tests/ echo "::endgroup::" - # echo "::group::Create code quality report..." - # pylint src/ tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0 - # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json - # echo "::endgroup::" - - name: Run ruff run: | set -euo pipefail diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 70568d18d..962a2a0af 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -1,7 +1,6 @@ -# yamllint disable name: Testsuite -on: +"on": schedule: - cron: "0 1 * * *" pull_request: @@ -41,10 +40,19 @@ jobs: environments: queens-dev activate-environment: queens-dev - name: Run pytest for unit tests and integration tests + env: + COVERAGE_FILE: .coverage.core.${{ runner.os }} run: | set -euo pipefail - COVERAGE_FILE=".coverage.core.${{ runner.os }}" pytest -v -m "${{ matrix.pytest_markers }}" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_core_${{ runner.os }}.xml + pytest -v \ + -m "${{ matrix.pytest_markers }}" \ + --cov \ + --cov-report=term \ + $TEST_TIMING_OPTION \ + --color=yes \ + -o junit_logging=all \ + --junitxml="test_junit_core_${{ runner.os }}.xml" - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -85,10 +93,19 @@ jobs: environments: queens-dev activate-environment: queens-dev - name: Run pytest for tutorial tests + env: + COVERAGE_FILE: .coverage.tutorials.${{ runner.os }} run: | set -euo pipefail - COVERAGE_FILE=".coverage.tutorials.${{ runner.os }}" pytest -v -m "tutorial_tests" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_${{ runner.os }}.xml + pytest -v \ + -m "tutorial_tests" \ + --cov \ + --cov-report=term \ + $TEST_TIMING_OPTION \ + --color=yes \ + -o junit_logging=all \ + --junitxml="test_junit_tutorials_${{ runner.os }}.xml" - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -129,10 +146,19 @@ jobs: run: | ln -s /home/user/4C/bin/ config/4C_build - name: Run pytest for 4C integration tests + env: + COVERAGE_FILE: .coverage.fourc.${{ runner.os }} run: | set -euo pipefail - COVERAGE_FILE=".coverage.fourc.${{ runner.os }}" pytest -v -m "integration_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_fourc_${{ runner.os }}.xml + pytest -v \ + -m "integration_tests_fourc" \ + --cov \ + --cov-report=term \ + $TEST_TIMING_OPTION \ + --color=yes \ + -o junit_logging=all \ + --junitxml="test_junit_fourc_${{ runner.os }}.xml" - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -173,10 +199,19 @@ jobs: run: | ln -s /home/user/4C/bin/ config/4C_build - name: Run pytest for 4C tutorial tests + env: + COVERAGE_FILE: .coverage.tutorials_fourc.${{ runner.os }} run: | set -euo pipefail - COVERAGE_FILE=".coverage.tutorials_fourc.${{ runner.os }}" pytest -v -m "tutorial_tests_fourc" --cov --cov-report=term $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit_tutorials_fourc_${{ runner.os }}.xml + pytest -v \ + -m "tutorial_tests_fourc" \ + --cov \ + --cov-report=term \ + $TEST_TIMING_OPTION \ + --color=yes \ + -o junit_logging=all \ + --junitxml="test_junit_tutorials_fourc_${{ runner.os }}.xml" - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -254,9 +289,15 @@ jobs: cp reports/core-ubuntu/.coverage.core.Linux .coverage.core.Linux cp reports/tutorials-ubuntu/.coverage.tutorials.Linux .coverage.tutorials.Linux cp reports/fourc-ubuntu/.coverage.fourc.Linux .coverage.fourc.Linux - cp reports/tutorials-fourc-ubuntu/.coverage.tutorials_fourc.Linux .coverage.tutorials_fourc.Linux + cp \ + reports/tutorials-fourc-ubuntu/.coverage.tutorials_fourc.Linux \ + .coverage.tutorials_fourc.Linux - pixi run --locked -e queens-dev coverage combine .coverage.core.Linux .coverage.tutorials.Linux .coverage.fourc.Linux .coverage.tutorials_fourc.Linux + pixi run --locked -e queens-dev coverage combine \ + .coverage.core.Linux \ + .coverage.tutorials.Linux \ + .coverage.fourc.Linux \ + .coverage.tutorials_fourc.Linux pixi run --locked -e queens-dev coverage html -d html_coverage_report pixi run --locked -e queens-dev coverage xml -o xml_coverage_report.xml pixi run --locked -e queens-dev coverage report diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 4613f8f61..3cba24026 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -1,7 +1,6 @@ -# yamllint disable name: Test PyPI build -on: +"on": schedule: - cron: "0 1 * * *" pull_request: @@ -15,7 +14,9 @@ permissions: jobs: test_pypi_build: - name: PyPI build test (${{ matrix.os }}, ${{ matrix.install_target }}, ${{ matrix.requiredness }}) + name: >- + PyPI build test + (${{ matrix.os }}, ${{ matrix.install_target }}, ${{ matrix.requiredness }}) runs-on: ${{ matrix.os }} continue-on-error: ${{ matrix.allow_failure }} strategy: diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index 625d1c594..75ff279bd 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -1,7 +1,6 @@ -# yamllint disable name: Update Pixi lockfile -on: +"on": workflow_dispatch: schedule: - cron: "0 5 1 * *" From 95882f862c74584c97bf00e5babb2205ff7d8fa6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 14 May 2026 00:09:47 +0200 Subject: [PATCH 156/200] ci: bump pixi version, fix pixi version --- .github/actions/setup-queens-pixi/action.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index a40e18a8f..0ddb6057b 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -4,10 +4,6 @@ description: > and optionally ensure rsync is available. inputs: - pixi-version: - description: Pixi version to install. - required: false - default: v0.67.0 cache: description: Whether setup-pixi should enable caching. required: false @@ -42,7 +38,7 @@ runs: steps: - uses: prefix-dev/setup-pixi@v0.9.5 with: - pixi-version: ${{ inputs.pixi-version }} + pixi-version: v0.68.1 cache: ${{ inputs.cache }} cache-write: ${{ inputs.cache-write }} run-install: ${{ inputs.run-install }} From ffcc328d1a2c3c62df887b4f320f6eb5ca07b6d1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 14 May 2026 11:04:59 +0200 Subject: [PATCH 157/200] build: remove environment name prefix queens- --- .github/actions/setup-queens-pixi/action.yml | 4 +-- .github/workflows/build_documentation.yml | 4 +-- .github/workflows/code_quality.yml | 8 +++--- .github/workflows/local_testsuite.yml | 28 +++++++++---------- .gitlab/.gitlab-ci.yml | 6 ++-- CONTRIBUTING.md | 12 ++++---- README.md | 14 +++++----- doc/README.md | 6 ++-- doc/source/_ext/templates/introduction.md.j2 | 2 +- doc/source/faqs/requirements.md | 4 +-- pixi.lock | 4 +-- pyproject.toml | 4 +-- src/queens/utils/remote_build.py | 2 +- src/queens/utils/remote_operations.py | 2 +- src/queens_interfaces/fourc/README.md | 8 +++--- .../fourc/random_material_preprocessor.py | 2 +- tests/README.md | 2 +- 17 files changed, 56 insertions(+), 56 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 0ddb6057b..a601650d6 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -19,11 +19,11 @@ inputs: environments: description: Whitespace-separated list of pixi environments to install. required: false - default: queens-dev + default: dev activate-environment: description: Pixi environment to activate and use for the editable install. required: false - default: queens-dev + default: dev install-editable: description: Whether to install QUEENS editable into the selected pixi environment. required: false diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 4dfa618f1..65fac512c 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -28,8 +28,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index acb077d55..1b3853dc0 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -31,9 +31,9 @@ jobs: cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: >- default - queens-all - queens-dev - activate-environment: queens-dev + all + dev + activate-environment: dev ensure-rsync: false - name: Check dependency declaration integrity run: | @@ -162,7 +162,7 @@ jobs: set -euo pipefail echo "::group::Check compatibility with licenses of dependencies..." - pip-licenses --python=.pixi/envs/queens-all/bin/python + pip-licenses --python=.pixi/envs/all/bin/python echo "::endgroup::" - name: Create licenserc diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 962a2a0af..198768be9 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -37,8 +37,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev - name: Run pytest for unit tests and integration tests env: COVERAGE_FILE: .coverage.core.${{ runner.os }} @@ -90,8 +90,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev - name: Run pytest for tutorial tests env: COVERAGE_FILE: .coverage.tutorials.${{ runner.os }} @@ -140,8 +140,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build @@ -193,8 +193,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev - name: Create links to 4C run: | ln -s /home/user/4C/bin/ config/4C_build @@ -249,8 +249,8 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - environments: queens-dev - activate-environment: queens-dev + environments: dev + activate-environment: dev ensure-rsync: false - name: Download raw core test reports from Ubuntu uses: actions/download-artifact@v8 @@ -293,14 +293,14 @@ jobs: reports/tutorials-fourc-ubuntu/.coverage.tutorials_fourc.Linux \ .coverage.tutorials_fourc.Linux - pixi run --locked -e queens-dev coverage combine \ + pixi run --locked -e dev coverage combine \ .coverage.core.Linux \ .coverage.tutorials.Linux \ .coverage.fourc.Linux \ .coverage.tutorials_fourc.Linux - pixi run --locked -e queens-dev coverage html -d html_coverage_report - pixi run --locked -e queens-dev coverage xml -o xml_coverage_report.xml - pixi run --locked -e queens-dev coverage report + pixi run --locked -e dev coverage html -d html_coverage_report + pixi run --locked -e dev coverage xml -o xml_coverage_report.xml + pixi run --locked -e dev coverage report python .github/xml_summaries_to_md.py \ xml_coverage_report.xml \ diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index 4f572c0d1..a437cce54 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -11,13 +11,13 @@ variables: REMOTE_BUILD_DIR: value: "/home/queens/builds/queens-$CI_PIPELINE_ID" LNM_REMOTE_PYTHON: - value: "$REMOTE_BUILD_DIR/.pixi/envs/queens-dev/bin/python" + value: "$REMOTE_BUILD_DIR/.pixi/envs/dev/bin/python" description: "Python path on LNM clusters" LNM_REMOTE_ADDRESS: value: "thought" description: "Hostname of LNM cluster" IMCS_REMOTE_PYTHON: - value: "$REMOTE_BUILD_DIR/.pixi/envs/queens-dev/bin/python" + value: "$REMOTE_BUILD_DIR/.pixi/envs/dev/bin/python" description: "Python path on IMCS clusters" IMCS_REMOTE_ADDRESS: value: "charon.bauv.unibw-muenchen.de" @@ -26,7 +26,7 @@ variables: value: "v0.67.0" description: "Pinned pixi version used by the CI pipeline" PIXI_ENVIRONMENT: - value: "queens-dev" + value: "dev" description: "Pixi workspace environment used in CI jobs" #--------------------------------------------------------------------------------------------------- # Define stages diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 785b23809..62fa01b87 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -49,8 +49,8 @@ Install QUEENS as described in the [README.md](https://github.com/queens-py/quee For contributions, use the Pixi development environment and expose your local clone inside it: ```bash -pixi install --environment queens-dev -pixi run -e queens-dev install-editable +pixi install --environment dev +pixi run -e dev install-editable ``` @@ -103,7 +103,7 @@ sync: After editing `pyproject.toml`, run the dependency integrity check. The same check is installed as a pre-commit hook and also runs in CI: ```bash -pixi run -e queens-dev pre-commit run check-pyproject-dependency-integrity --files pyproject.toml +pixi run -e dev pre-commit run check-pyproject-dependency-integrity --files pyproject.toml ``` If dependency declarations changed, refresh the lockfile and commit it together with @@ -122,9 +122,9 @@ pixi lock --check --dry-run Finally, reinstall or update the affected Pixi environment and run a focused test or smoke check: ```bash -pixi install --environment queens-dev -pixi run -e queens-dev install-editable -pixi run -e queens-dev pytest +pixi install --environment dev +pixi run -e dev install-editable +pixi run -e dev pytest ``` ##### Commit messages diff --git a/README.md b/README.md index ee6798b0f..c17508927 100644 --- a/README.md +++ b/README.md @@ -76,23 +76,23 @@ After cloning the repository, installing with Pixi is as easy as: pixi install pixi run install-editable ``` -The default Pixi environment contains the core QUEENS dependencies. Use `queens-all` for runtime +The default Pixi environment contains the core QUEENS dependencies. Use `all` for runtime extras without development tools. For named Pixi environments, run `pixi run -e install-editable` once for each environment you want to use. ### Development installation -For development, we recommend using [Pixi](https://pixi.sh/latest/) together with the `queens-dev` environment. -`queens-dev` contains the full contributor setup, including development tools, tutorials, and the +For development, we recommend using [Pixi](https://pixi.sh/latest/) together with the `dev` environment. +`dev` contains the full contributor setup, including development tools, tutorials, and the 4C interface dependencies. Clone the repository and install with: ```bash -pixi install --environment queens-dev -pixi run -e queens-dev install-editable +pixi install --environment dev +pixi run -e dev install-editable ``` Useful development commands then look like: ```bash -pixi run -e queens-dev pytest -pixi run -e queens-dev pre-commit run --all-files +pixi run -e dev pytest +pixi run -e dev pre-commit run --all-files ``` diff --git a/doc/README.md b/doc/README.md index fa759cfda..7c42f8d63 100644 --- a/doc/README.md +++ b/doc/README.md @@ -12,21 +12,21 @@ To build the documentation, first set up the QUEENS development environment as d Next, register the environment as a Jupyter kernel with: ```bash -pixi run -e queens-dev python -m ipykernel install --user --name queens --display-name "Python (queens)" +pixi run -e dev python -m ipykernel install --user --name queens --display-name "Python (queens)" ``` When building the documentation on your machine for the first time or after adding new modules or classes to QUEENS, one needs to first rebuild the `autodoc index` by running: ```bash cd -pixi run -e queens-dev sphinx-apidoc -o doc/source src/ -fMT +pixi run -e dev sphinx-apidoc -o doc/source src/ -fMT ``` To actually build the html-documentation, navigate into the doc folder and run the make command: ```bash cd doc -pixi run -e queens-dev sphinx-build -b html -d build/doctrees source build/html -W +pixi run -e dev sphinx-build -b html -d build/doctrees source build/html -W ``` You can now view the documentation in your favorite browser by opening `build/html/index.html`. diff --git a/doc/source/_ext/templates/introduction.md.j2 b/doc/source/_ext/templates/introduction.md.j2 index 9109a168e..e89524f13 100644 --- a/doc/source/_ext/templates/introduction.md.j2 +++ b/doc/source/_ext/templates/introduction.md.j2 @@ -88,7 +88,7 @@ resolution and editable installs aligned with CI. ### Testing installation To test for a successful installation, run the test suite: ``` -pixi run -e queens-dev pytest +pixi run -e dev pytest ``` Consult the [documentation of QUEENS tests](testing) for more details on testing. diff --git a/doc/source/faqs/requirements.md b/doc/source/faqs/requirements.md index e6b3010ac..a24ae8e76 100644 --- a/doc/source/faqs/requirements.md +++ b/doc/source/faqs/requirements.md @@ -10,8 +10,8 @@ For development and CI-like reproducibility, dependencies are managed with Pixi. environments are declared in `pyproject.toml` and locked in `pixi.lock`: - `default`: core QUEENS dependencies -- `queens-all`: runtime extras without development tools -- `queens-dev`: full contributor setup, including development tools, tutorials, and 4C support +- `all`: runtime extras without development tools +- `dev`: full contributor setup, including development tools, tutorials, and 4C support For installation information see the [README.md](https://github.com/queens-py/queens/blob/main/README.md). diff --git a/pixi.lock b/pixi.lock index ab66d35d9..e013bce22 100644 --- a/pixi.lock +++ b/pixi.lock @@ -926,7 +926,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/39/1f/54ddd9171840bbf2437287ffab18268d7ccbca7752a7f290252ddabbcef8/numpysane-0.42.tar.gz - pypi: git+https://github.com/nchopin/particles.git#f71e94a21a11c73b58e2d694775b1b1d379b8854 - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - queens-all: + all: channels: - url: https://conda.anaconda.org/conda-forge/ - url: https://conda.anaconda.org/nodefaults/ @@ -1878,7 +1878,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/90/d6/42d441eeceac1d8fc7d2a7480654db661282dd1f94deef344c5421ba0c3c/rapidyaml-0.12.1-cp312-cp312-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/54/4b/ee27938d1b2c443e89a9a10e00d2d19aa5ee300cd3d61140644e93bb083e/regex-2026.5.9-cp312-cp312-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/4a/49/bb935b2e68cf31e2b2face9d0841ac97447b6d0387d0c2d2255c7a2867da/scikit_activeml-1.0.0-py3-none-any.whl - queens-dev: + dev: channels: - url: https://conda.anaconda.org/conda-forge/ - url: https://conda.anaconda.org/nodefaults/ diff --git a/pyproject.toml b/pyproject.toml index 46dfed38b..06d5dbe68 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -271,8 +271,8 @@ fourcipp = ">=1.91.0" [tool.pixi.environments] default = { features = ["base"], no-default-feature = true, solve-group = "default"} -queens-all = { features = ["base","tutorials", "fourc"], no-default-feature = true, solve-group = "default"} -queens-dev = { features = ["base", "dev", "tutorials", "fourc"], no-default-feature = true, solve-group = "default"} +all = { features = ["base","tutorials", "fourc"], no-default-feature = true, solve-group = "default"} +dev = { features = ["base", "dev", "tutorials", "fourc"], no-default-feature = true, solve-group = "default"} [dependency-groups] dev = [ diff --git a/src/queens/utils/remote_build.py b/src/queens/utils/remote_build.py index ae42f8170..bd36ad0cf 100644 --- a/src/queens/utils/remote_build.py +++ b/src/queens/utils/remote_build.py @@ -45,7 +45,7 @@ parser.add_argument( "--pixi-environment", type=str, - default="queens-all", + default="all", help="pixi workspace environment to install on the remote host", ) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 3303280af..209d84191 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -330,7 +330,7 @@ def copy_from_remote( def build_remote_environment( self, - pixi_environment: str = "queens-all", + pixi_environment: str = "all", ) -> None: """Build the remote QUEENS pixi environment. diff --git a/src/queens_interfaces/fourc/README.md b/src/queens_interfaces/fourc/README.md index 365c6014d..4862c5bcb 100644 --- a/src/queens_interfaces/fourc/README.md +++ b/src/queens_interfaces/fourc/README.md @@ -12,12 +12,12 @@ In order to create random material fields in combination with 4C, QUEENS require python -m pip install ".[fourc]" ``` -For Pixi project-based workflow, use the `queens-all` environment +For Pixi project-based workflow, use the `all` environment that includes the 4C interface dependencies without development tools: ```bash -pixi install --environment queens-all -pixi run -e queens-all install-editable +pixi install --environment all +pixi run -e all install-editable ``` -For development, use the `queens-dev` Pixi environment that includes the `fourc` feature. +For development, use the `dev` Pixi environment that includes the `fourc` feature. For more setup details, see the top-level [README.md](https://github.com/queens-py/queens/blob/main/README.md). diff --git a/src/queens_interfaces/fourc/random_material_preprocessor.py b/src/queens_interfaces/fourc/random_material_preprocessor.py index 7857c742a..e243dfe2f 100644 --- a/src/queens_interfaces/fourc/random_material_preprocessor.py +++ b/src/queens_interfaces/fourc/random_material_preprocessor.py @@ -24,7 +24,7 @@ raise ImportError( "The required packages to construct random fields in QUEENS for 4C are not installed." " Install QUEENS with the 'fourc' extra, e.g. `python -m pip install \".[fourc]\"`, " - "or use a Pixi environment with the fourc feature such as `queens-dev` or `queens-all`." + "or use a Pixi environment with the fourc feature such as `dev` or `all`." ) from exc diff --git a/tests/README.md b/tests/README.md index bd3764469..aa3eb4d8b 100644 --- a/tests/README.md +++ b/tests/README.md @@ -19,7 +19,7 @@ QUEENS is tested using [pytest](https://docs.pytest.org/en/stable/index.html). F development, run tests through the Pixi development environment, for example: ```bash -pixi run -e queens-dev pytest +pixi run -e dev pytest ``` For a comprehensive list of pytest commands, see [here](https://docs.pytest.org/en/stable/how-to/usage.html). Some additional useful commands to test QUEENS are listed in the following: From 55e94e7ca2229fecea1edb3c1be10af7ab52153c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 14 May 2026 11:07:33 +0200 Subject: [PATCH 158/200] ci: remove unnecessary pixi run calls --- .github/workflows/local_testsuite.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 198768be9..60bf14e0c 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -293,14 +293,14 @@ jobs: reports/tutorials-fourc-ubuntu/.coverage.tutorials_fourc.Linux \ .coverage.tutorials_fourc.Linux - pixi run --locked -e dev coverage combine \ + coverage combine \ .coverage.core.Linux \ .coverage.tutorials.Linux \ .coverage.fourc.Linux \ .coverage.tutorials_fourc.Linux - pixi run --locked -e dev coverage html -d html_coverage_report - pixi run --locked -e dev coverage xml -o xml_coverage_report.xml - pixi run --locked -e dev coverage report + coverage html -d html_coverage_report + coverage xml -o xml_coverage_report.xml + coverage report python .github/xml_summaries_to_md.py \ xml_coverage_report.xml \ From ab16dec6014227800bae4cd68b3479fe0dbc01c9 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 22 May 2026 00:02:22 +0200 Subject: [PATCH 159/200] fix: remove debugging print statements --- .../iterators/test_sobol_index_gp_uncertainty.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py b/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py index 7e2eaaac0..eb637855e 100644 --- a/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py +++ b/tests/integration_tests/iterators/test_sobol_index_gp_uncertainty.py @@ -357,8 +357,5 @@ def test_sobol_index_gp_uncertainty_mean_ishigami(global_settings): ] ) - print(results["first_order"].values) - print(results["total_order"].values) - np.testing.assert_allclose(results["first_order"].values, expected_s1, atol=1e-05) np.testing.assert_allclose(results["total_order"].values, expected_st, atol=1e-05) From 804e8fd24814bcc9fe36f1b60cd04dc8f62e83be Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 22 May 2026 00:10:37 +0200 Subject: [PATCH 160/200] fix: remove duplicate test The same is tested in other tests: setting a seed and drawing. These test should also cover asserting that the same samples are drawn and thus are more detailed. --- .../models/test_gaussian_neural_network.py | 21 ------------------- 1 file changed, 21 deletions(-) diff --git a/tests/integration_tests/models/test_gaussian_neural_network.py b/tests/integration_tests/models/test_gaussian_neural_network.py index 715ef0765..37978cf4c 100644 --- a/tests/integration_tests/models/test_gaussian_neural_network.py +++ b/tests/integration_tests/models/test_gaussian_neural_network.py @@ -41,27 +41,6 @@ def fixture_my_model(): return model -def test_gaussian_neural_network_default_initializer_trains_with_seed(): - """Test seeded training with the default kernel initializer.""" - rng = np.random.default_rng(1) - x_train = rng.normal(size=(16, 3)) - y_train = np.sum(x_train, axis=1).reshape(-1, 1) - model = GaussianNeuralNetwork( - activation_per_hidden_layer_lst=["elu"], - nodes_per_hidden_layer_lst=[5], - adams_training_rate=0.001, - batch_size=8, - num_epochs=1, - seed=42, - data_scaling="standard_scaler", - nugget_std=1.0e-05, - verbosity_on=False, - ) - - model.setup(x_train, y_train) - model.train() - - X_TEST_ONE_DIM = np.linspace(-5, 5, 20).reshape(-1, 1) From a9de4937f4c398de87ab68c0c114c761fea05217 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 22 May 2026 00:16:45 +0200 Subject: [PATCH 161/200] docs: unify description of seed --- src/queens/models/surrogates/gaussian_neural_network.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/queens/models/surrogates/gaussian_neural_network.py b/src/queens/models/surrogates/gaussian_neural_network.py index 4391343ae..1421ed83c 100644 --- a/src/queens/models/surrogates/gaussian_neural_network.py +++ b/src/queens/models/surrogates/gaussian_neural_network.py @@ -46,8 +46,7 @@ class GaussianNeuralNetwork(Surrogate): Attributes: nn_model (tf.model): Tensorflow based Bayesian neural network model num_epochs (int): Number of training epochs for variational optimization - seed (int): Random seed used for initialization of stochastic gradient decent - optimizer + seed (int): Seed for pseudo-random number generation verbosity_on (bool): Boolean for model verbosity during training. True=verbose batch_size (int): Size of data-batch (smaller than the training data size) scaler_x (obj): Scaler for inputs From 6c461822f9f1a1d1eea0b18712689df3aa5f65f9 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 22 May 2026 00:24:01 +0200 Subject: [PATCH 162/200] ci: rename job --- .github/workflows/code_quality.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 1b3853dc0..f4f16f503 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -18,7 +18,7 @@ env: jobs: run_code_checks: - name: code checks + name: Check code quality runs-on: ubuntu-latest defaults: run: From 1e4b3678bb9170d45e7d14771a3d62a8a89d08ed Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 22 May 2026 00:30:21 +0200 Subject: [PATCH 163/200] ci: remove groups in single group steps --- .github/workflows/code_quality.yml | 25 ++++++------------------- 1 file changed, 6 insertions(+), 19 deletions(-) diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index f4f16f503..37911998e 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -161,21 +161,19 @@ jobs: run: | set -euo pipefail - echo "::group::Check compatibility with licenses of dependencies..." pip-licenses --python=.pixi/envs/all/bin/python - echo "::endgroup::" - - name: Create licenserc + - name: Create a licenserc file run: | set -euo pipefail - echo "::group::Create an rc file for the license header check..." python .gitlab/pipeline_utils/create_licenserc.py \ --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" \ --text_file "license_header.tmpl" \ --output_file ".licenserc.yaml" \ --placeholder "license_header" - echo "::endgroup::" + + echo "Created an rc file for the license header check." - name: Check license headers uses: apache/skywalking-eyes/header@v0.8.0 @@ -187,50 +185,39 @@ jobs: run: | set -euo pipefail - echo "::group::Run isort..." isort --check-only src/* tests - echo "::endgroup::" - name: Run black run: | set -euo pipefail - echo "::group::Run black..." black --check src/* tests - echo "::endgroup::" - name: Run pylint run: | set -euo pipefail - echo "::group::Run pylint on src..." + echo "Run pylint on src:" pylint --rcfile=.pylintrc --ignore=integration_tests src/ tests/ - echo "::endgroup::" - echo "::group::Run pylint on integration tests..." + echo + echo "Run pylint on integration tests:" pylint --rcfile=.pylintrc --disable=duplicate-code tests/integration_tests/ - echo "::endgroup::" - name: Run ruff run: | set -euo pipefail - echo "::group::Run ruff..." ruff check - echo "::endgroup::" - name: Run nbstripout run: | set -euo pipefail - echo "::group::Run nbstripout..." find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + - echo "::endgroup::" - name: Run mypy run: | set -euo pipefail - echo "::group::Check type hinting with mypy..." mypy . - echo "::endgroup::" From 2d234eaef0522ea730c8bac8f5bb5e2f22a86662 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 24 May 2026 13:07:52 +0200 Subject: [PATCH 164/200] ci: introduce action to run pytest --- .github/actions/run-pytest-suite/action.yml | 41 ++++++++++ .github/workflows/local_testsuite.yml | 90 ++++++--------------- 2 files changed, 67 insertions(+), 64 deletions(-) create mode 100644 .github/actions/run-pytest-suite/action.yml diff --git a/.github/actions/run-pytest-suite/action.yml b/.github/actions/run-pytest-suite/action.yml new file mode 100644 index 000000000..d48507475 --- /dev/null +++ b/.github/actions/run-pytest-suite/action.yml @@ -0,0 +1,41 @@ +name: Run pytest suite +description: Run a marked pytest suite with coverage and a JUnit report. + +inputs: + name: + description: Suite name used in coverage and JUnit filenames. + required: true + markers: + description: Pytest marker expression to select tests. + required: true + +runs: + using: composite + steps: + - name: Run pytest + shell: bash + env: + PYTEST_MARKERS: ${{ inputs.markers }} + TEST_SUITE_NAME: ${{ inputs.name }} + run: | + set -euo pipefail + + export COVERAGE_FILE=".coverage.${TEST_SUITE_NAME}" + junit_file="test_junit_${TEST_SUITE_NAME}.xml" + + pytest_args=( + -v + -m "${PYTEST_MARKERS}" + --cov + --cov-report=term + --color=yes + -o junit_logging=all + --junitxml="${junit_file}" + ) + + if [ -n "${TEST_TIMING_OPTION:-}" ]; then + read -r -a timing_args <<< "${TEST_TIMING_OPTION}" + pytest_args+=("${timing_args[@]}") + fi + + pytest "${pytest_args[@]}" diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 60bf14e0c..bcb209e97 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -25,9 +25,7 @@ jobs: matrix: include: - os: ubuntu-latest - pytest_markers: "unit_tests or integration_tests" - os: macos-latest - pytest_markers: "unit_tests or integration_tests" defaults: run: shell: bash -l {0} @@ -40,19 +38,10 @@ jobs: environments: dev activate-environment: dev - name: Run pytest for unit tests and integration tests - env: - COVERAGE_FILE: .coverage.core.${{ runner.os }} - run: | - set -euo pipefail - - pytest -v \ - -m "${{ matrix.pytest_markers }}" \ - --cov \ - --cov-report=term \ - $TEST_TIMING_OPTION \ - --color=yes \ - -o junit_logging=all \ - --junitxml="test_junit_core_${{ runner.os }}.xml" + uses: ./.github/actions/run-pytest-suite + with: + name: core.${{ runner.os }} + markers: "unit_tests or integration_tests" - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -68,7 +57,7 @@ jobs: include-hidden-files: true path: | .coverage.core.${{ runner.os }} - test_junit_core_${{ runner.os }}.xml + test_junit_core.${{ runner.os }}.xml if-no-files-found: error retention-days: 7 @@ -93,19 +82,10 @@ jobs: environments: dev activate-environment: dev - name: Run pytest for tutorial tests - env: - COVERAGE_FILE: .coverage.tutorials.${{ runner.os }} - run: | - set -euo pipefail - - pytest -v \ - -m "tutorial_tests" \ - --cov \ - --cov-report=term \ - $TEST_TIMING_OPTION \ - --color=yes \ - -o junit_logging=all \ - --junitxml="test_junit_tutorials_${{ runner.os }}.xml" + uses: ./.github/actions/run-pytest-suite + with: + name: tutorials.${{ runner.os }} + markers: tutorial_tests - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -121,7 +101,7 @@ jobs: include-hidden-files: true path: | .coverage.tutorials.${{ runner.os }} - test_junit_tutorials_${{ runner.os }}.xml + test_junit_tutorials.${{ runner.os }}.xml if-no-files-found: error retention-days: 7 @@ -146,19 +126,10 @@ jobs: run: | ln -s /home/user/4C/bin/ config/4C_build - name: Run pytest for 4C integration tests - env: - COVERAGE_FILE: .coverage.fourc.${{ runner.os }} - run: | - set -euo pipefail - - pytest -v \ - -m "integration_tests_fourc" \ - --cov \ - --cov-report=term \ - $TEST_TIMING_OPTION \ - --color=yes \ - -o junit_logging=all \ - --junitxml="test_junit_fourc_${{ runner.os }}.xml" + uses: ./.github/actions/run-pytest-suite + with: + name: fourc.${{ runner.os }} + markers: integration_tests_fourc - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -174,7 +145,7 @@ jobs: include-hidden-files: true path: | .coverage.fourc.${{ runner.os }} - test_junit_fourc_${{ runner.os }}.xml + test_junit_fourc.${{ runner.os }}.xml if-no-files-found: error retention-days: 7 @@ -199,19 +170,10 @@ jobs: run: | ln -s /home/user/4C/bin/ config/4C_build - name: Run pytest for 4C tutorial tests - env: - COVERAGE_FILE: .coverage.tutorials_fourc.${{ runner.os }} - run: | - set -euo pipefail - - pytest -v \ - -m "tutorial_tests_fourc" \ - --cov \ - --cov-report=term \ - $TEST_TIMING_OPTION \ - --color=yes \ - -o junit_logging=all \ - --junitxml="test_junit_tutorials_fourc_${{ runner.os }}.xml" + uses: ./.github/actions/run-pytest-suite + with: + name: tutorials_fourc.${{ runner.os }} + markers: tutorial_tests_fourc - name: Publish junit pytest report if: success() || failure() uses: mikepenz/action-junit-report@v6 @@ -227,7 +189,7 @@ jobs: include-hidden-files: true path: | .coverage.tutorials_fourc.${{ runner.os }} - test_junit_tutorials_fourc_${{ runner.os }}.xml + test_junit_tutorials_fourc.${{ runner.os }}.xml if-no-files-found: error retention-days: 7 @@ -304,12 +266,12 @@ jobs: python .github/xml_summaries_to_md.py \ xml_coverage_report.xml \ - reports/core-ubuntu/test_junit_core_Linux.xml \ - reports/core-macos/test_junit_core_macOS.xml \ - reports/tutorials-ubuntu/test_junit_tutorials_Linux.xml \ - reports/tutorials-macos/test_junit_tutorials_macOS.xml \ - reports/fourc-ubuntu/test_junit_fourc_Linux.xml \ - reports/tutorials-fourc-ubuntu/test_junit_tutorials_fourc_Linux.xml \ + reports/core-ubuntu/test_junit_core.Linux.xml \ + reports/core-macos/test_junit_core.macOS.xml \ + reports/tutorials-ubuntu/test_junit_tutorials.Linux.xml \ + reports/tutorials-macos/test_junit_tutorials.macOS.xml \ + reports/fourc-ubuntu/test_junit_fourc.Linux.xml \ + reports/tutorials-fourc-ubuntu/test_junit_tutorials_fourc.Linux.xml \ >> "$GITHUB_STEP_SUMMARY" - name: Upload combined coverage report uses: actions/upload-pages-artifact@v5 From 89a991657af4eadf1305b0137a09e10152566b8b Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 24 May 2026 15:23:07 +0200 Subject: [PATCH 165/200] ci: move artifact handling into pytest action move artifact upload etc. into the predefined action thus reducing code duplication --- .github/actions/run-pytest-suite/action.yml | 53 ++++++++++-- .github/workflows/local_testsuite.yml | 92 +++------------------ 2 files changed, 55 insertions(+), 90 deletions(-) diff --git a/.github/actions/run-pytest-suite/action.yml b/.github/actions/run-pytest-suite/action.yml index d48507475..6438abd33 100644 --- a/.github/actions/run-pytest-suite/action.yml +++ b/.github/actions/run-pytest-suite/action.yml @@ -1,9 +1,9 @@ name: Run pytest suite -description: Run a marked pytest suite with coverage and a JUnit report. +description: Run a marked pytest suite and publish its reports. inputs: - name: - description: Suite name used in coverage and JUnit filenames. + test-suite-name: + description: Test suite name used in coverage, JUnit, and artifact filenames. required: true markers: description: Pytest marker expression to select tests. @@ -12,17 +12,29 @@ inputs: runs: using: composite steps: + - name: Prepare report names + id: report-names + shell: bash + env: + TEST_SUITE_NAME: ${{ inputs.test-suite-name }} + run: | + set -euo pipefail + + echo "coverage-file=.coverage.${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT" + echo "junit-file=test_junit_${TEST_SUITE_NAME}.xml" >> "$GITHUB_OUTPUT" + echo "artifact-name=raw_test_reports_${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT" + - name: Run pytest + id: pytest shell: bash + continue-on-error: true env: + COVERAGE_FILE: ${{ steps.report-names.outputs.coverage-file }} + JUNIT_FILE: ${{ steps.report-names.outputs.junit-file }} PYTEST_MARKERS: ${{ inputs.markers }} - TEST_SUITE_NAME: ${{ inputs.name }} run: | set -euo pipefail - export COVERAGE_FILE=".coverage.${TEST_SUITE_NAME}" - junit_file="test_junit_${TEST_SUITE_NAME}.xml" - pytest_args=( -v -m "${PYTEST_MARKERS}" @@ -30,7 +42,7 @@ runs: --cov-report=term --color=yes -o junit_logging=all - --junitxml="${junit_file}" + --junitxml="${JUNIT_FILE}" ) if [ -n "${TEST_TIMING_OPTION:-}" ]; then @@ -39,3 +51,28 @@ runs: fi pytest "${pytest_args[@]}" + + - name: Publish junit pytest report + if: always() + uses: mikepenz/action-junit-report@v6 + with: + report_paths: ${{ steps.report-names.outputs.junit-file }} + annotate_only: true + job_summary: false + + - name: Upload raw test reports + if: always() + uses: actions/upload-artifact@v7 + with: + name: ${{ steps.report-names.outputs.artifact-name }} + include-hidden-files: true + path: | + ${{ steps.report-names.outputs.coverage-file }} + ${{ steps.report-names.outputs.junit-file }} + if-no-files-found: error + retention-days: 7 + + - name: Fail if pytest failed + if: steps.pytest.outcome == 'failure' + shell: bash + run: exit 1 diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index bcb209e97..aea89a724 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -40,26 +40,8 @@ jobs: - name: Run pytest for unit tests and integration tests uses: ./.github/actions/run-pytest-suite with: - name: core.${{ runner.os }} + test-suite-name: core.${{ runner.os }} markers: "unit_tests or integration_tests" - - name: Publish junit pytest report - if: success() || failure() - uses: mikepenz/action-junit-report@v6 - with: - report_paths: "test_junit_*.xml" - annotate_only: true - job_summary: false - - name: Upload raw core test reports - if: success() || failure() - uses: actions/upload-artifact@v7 - with: - name: raw-test-reports-core-${{ runner.os }} - include-hidden-files: true - path: | - .coverage.core.${{ runner.os }} - test_junit_core.${{ runner.os }}.xml - if-no-files-found: error - retention-days: 7 run_tests_tutorials: name: tutorial tests (${{ matrix.os }}) @@ -84,26 +66,8 @@ jobs: - name: Run pytest for tutorial tests uses: ./.github/actions/run-pytest-suite with: - name: tutorials.${{ runner.os }} + test-suite-name: tutorials.${{ runner.os }} markers: tutorial_tests - - name: Publish junit pytest report - if: success() || failure() - uses: mikepenz/action-junit-report@v6 - with: - report_paths: "test_junit_*.xml" - annotate_only: true - job_summary: false - - name: Upload raw tutorial test reports - if: success() || failure() - uses: actions/upload-artifact@v7 - with: - name: raw-test-reports-tutorials-${{ runner.os }} - include-hidden-files: true - path: | - .coverage.tutorials.${{ runner.os }} - test_junit_tutorials.${{ runner.os }}.xml - if-no-files-found: error - retention-days: 7 run_tests_fourc: name: 4C integration tests (ubuntu-latest) @@ -128,26 +92,8 @@ jobs: - name: Run pytest for 4C integration tests uses: ./.github/actions/run-pytest-suite with: - name: fourc.${{ runner.os }} + test-suite-name: fourc.${{ runner.os }} markers: integration_tests_fourc - - name: Publish junit pytest report - if: success() || failure() - uses: mikepenz/action-junit-report@v6 - with: - report_paths: "test_junit_*.xml" - annotate_only: true - job_summary: false - - name: Upload raw 4C test reports - if: success() || failure() - uses: actions/upload-artifact@v7 - with: - name: raw-test-reports-fourc-${{ runner.os }} - include-hidden-files: true - path: | - .coverage.fourc.${{ runner.os }} - test_junit_fourc.${{ runner.os }}.xml - if-no-files-found: error - retention-days: 7 run_tests_tutorials_fourc: name: 4C tutorial tests (ubuntu-latest) @@ -172,26 +118,8 @@ jobs: - name: Run pytest for 4C tutorial tests uses: ./.github/actions/run-pytest-suite with: - name: tutorials_fourc.${{ runner.os }} + test-suite-name: tutorials_fourc.${{ runner.os }} markers: tutorial_tests_fourc - - name: Publish junit pytest report - if: success() || failure() - uses: mikepenz/action-junit-report@v6 - with: - report_paths: "test_junit_*.xml" - annotate_only: true - job_summary: false - - name: Upload raw 4C tutorial test reports - if: success() || failure() - uses: actions/upload-artifact@v7 - with: - name: raw-test-reports-tutorials-fourc-${{ runner.os }} - include-hidden-files: true - path: | - .coverage.tutorials_fourc.${{ runner.os }} - test_junit_tutorials_fourc.${{ runner.os }}.xml - if-no-files-found: error - retention-days: 7 report_test_results: name: report test results @@ -217,32 +145,32 @@ jobs: - name: Download raw core test reports from Ubuntu uses: actions/download-artifact@v8 with: - name: raw-test-reports-core-Linux + name: raw_test_reports_core.Linux path: reports/core-ubuntu - name: Download raw core test reports from macOS uses: actions/download-artifact@v8 with: - name: raw-test-reports-core-macOS + name: raw_test_reports_core.macOS path: reports/core-macos - name: Download raw tutorial test reports from Ubuntu uses: actions/download-artifact@v8 with: - name: raw-test-reports-tutorials-Linux + name: raw_test_reports_tutorials.Linux path: reports/tutorials-ubuntu - name: Download raw tutorial test reports from macOS uses: actions/download-artifact@v8 with: - name: raw-test-reports-tutorials-macOS + name: raw_test_reports_tutorials.macOS path: reports/tutorials-macos - name: Download raw 4C test reports uses: actions/download-artifact@v8 with: - name: raw-test-reports-fourc-Linux + name: raw_test_reports_fourc.Linux path: reports/fourc-ubuntu - name: Download raw 4C tutorial test reports uses: actions/download-artifact@v8 with: - name: raw-test-reports-tutorials-fourc-Linux + name: raw_test_reports_tutorials_fourc.Linux path: reports/tutorials-fourc-ubuntu - name: Combine Ubuntu coverage data and build reports run: | From f973e188b805b9cc97b62ffa4cf8fd76ae812a3e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Sun, 24 May 2026 15:36:57 +0200 Subject: [PATCH 166/200] refactor: remove extra string concatenation --- .github/xml_summaries_to_md.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/xml_summaries_to_md.py b/.github/xml_summaries_to_md.py index 466bc623b..49fc6e1f5 100644 --- a/.github/xml_summaries_to_md.py +++ b/.github/xml_summaries_to_md.py @@ -229,7 +229,7 @@ def collapsible(full_text, summary): Returns: str: collapse section """ - return f"
\n{summary}\n\n{full_text}\n\n
" "" + return f"
\n{summary}\n\n{full_text}\n\n
" def collapsable(full_text, summary): From d4eaa74a537d7c93b9fd2f7b8c8b6de4e712d8af Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 25 May 2026 11:20:36 +0200 Subject: [PATCH 167/200] build: fix ruff version mismatch --- .pre-commit-config.yaml | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a286a4d10..7d7f6effa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,13 +1,5 @@ default_stages: [pre-commit, pre-merge-commit, pre-push, manual] repos: - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.2 # Ruff version - hooks: - # Run the linter. - # Needs to placed before black, isort, and other formatters - - id: ruff - types_or: [ python, pyi ] - args: [--fix] - repo: local hooks: - id: trailing-whitespace @@ -42,6 +34,11 @@ repos: language: system files: '^pyproject\.toml$' pass_filenames: true + - id: ruff-check + name: ruff check + entry: ruff check --fix --force-exclude + language: system + types_or: [ python, pyi, jupyter, pyproject ] - id: docformatter name: docformatter entry: docformatter From 3c647c22340070c6bd8eb95e155f64437e4c6231 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Mon, 25 May 2026 11:30:32 +0200 Subject: [PATCH 168/200] docs: fix typo and formatting --- test_utils/get_queens_example_from_readme.py | 1 - test_utils/integration_tests.py | 7 ++++++- test_utils/tutorial_tests.py | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/test_utils/get_queens_example_from_readme.py b/test_utils/get_queens_example_from_readme.py index d2295e9e3..be510f5e4 100644 --- a/test_utils/get_queens_example_from_readme.py +++ b/test_utils/get_queens_example_from_readme.py @@ -14,7 +14,6 @@ # """Extract QUEENS example from the readme.""" - from pathlib import Path from queens.utils.path import relative_path_from_root diff --git a/test_utils/integration_tests.py b/test_utils/integration_tests.py index ef5af0c14..9a3fa5322 100644 --- a/test_utils/integration_tests.py +++ b/test_utils/integration_tests.py @@ -34,7 +34,12 @@ def assert_monte_carlo_iterator_results(results, expected_mean, expected_var): def assert_surrogate_model_output( - output, mean_ref, var_ref, grad_mean_ref=None, grad_var_ref=None, decimals=(2, 2, 2, 2) + output, + mean_ref, + var_ref, + grad_mean_ref=None, + grad_var_ref=None, + decimals=(2, 2, 2, 2), ): """Assert the equality of the output with the provided reference values. diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index 6c2db3f24..16401fa28 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -20,7 +20,7 @@ def inject_notebook_execution_context(tb, notebook_dir): Args: tb (testbook): testbook object for inserting code into the notebook - notebook_dir (str | Path): Directory conainting the notebook + notebook_dir (str | Path): Directory containing the notebook Returns: None From 7c63b98efe8371fbc5e42874ab33514bf781b815 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 27 May 2026 15:41:05 +0200 Subject: [PATCH 169/200] ci: extract definition of bash --- .github/workflows/build_documentation.yml | 4 ++-- .github/workflows/code_quality.yml | 21 +-------------------- .github/workflows/local_testsuite.yml | 12 +++++------- .github/workflows/test_pypi_build.yml | 8 +------- .github/workflows/update_pixi_lock.yml | 4 +--- 5 files changed, 10 insertions(+), 39 deletions(-) diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 65fac512c..4ce453c2b 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -21,7 +21,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -44,7 +44,7 @@ jobs: env: PYTHONPATH: ${{ github.workspace }} run: | - set -euxo pipefail + set -x sphinx-apidoc -o doc/source src/ -fMT cd doc xvfb-run -a sphinx-build -b html -d build/doctrees source build/html -W diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 37911998e..9c0c6d8fc 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -37,7 +37,6 @@ jobs: ensure-rsync: false - name: Check dependency declaration integrity run: | - set -euo pipefail # Validate that the PEP-style dependency declarations in pyproject.toml # stay aligned with the pixi dependency sections. python3 tools/dependencies/check_pyproject_dependency_integrity.py \ @@ -46,8 +45,6 @@ jobs: - name: Check pixi environment integrity id: environment_integrity run: | - set -euo pipefail - base_ref="main" pyproject_diff_file="$(mktemp)" git fetch --no-tags --depth=1 origin "${base_ref}" @@ -159,14 +156,10 @@ jobs: - name: Check compatibility of licenses of dependencies run: | - set -euo pipefail - pip-licenses --python=.pixi/envs/all/bin/python - name: Create a licenserc file run: | - set -euo pipefail - python .gitlab/pipeline_utils/create_licenserc.py \ --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" \ --text_file "license_header.tmpl" \ @@ -183,20 +176,14 @@ jobs: - name: Run isort run: | - set -euo pipefail - isort --check-only src/* tests - name: Run black run: | - set -euo pipefail - black --check src/* tests - name: Run pylint run: | - set -euo pipefail - echo "Run pylint on src:" pylint --rcfile=.pylintrc --ignore=integration_tests src/ tests/ @@ -206,18 +193,12 @@ jobs: - name: Run ruff run: | - set -euo pipefail - ruff check - name: Run nbstripout run: | - set -euo pipefail - find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + - name: Run mypy run: | - set -euo pipefail - mypy . diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index aea89a724..0de872818 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -28,7 +28,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -54,7 +54,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -77,7 +77,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -103,7 +103,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -132,7 +132,7 @@ jobs: - run_tests_tutorials_fourc defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -174,8 +174,6 @@ jobs: path: reports/tutorials-fourc-ubuntu - name: Combine Ubuntu coverage data and build reports run: | - set -euo pipefail - cp reports/core-ubuntu/.coverage.core.Linux .coverage.core.Linux cp reports/tutorials-ubuntu/.coverage.tutorials.Linux .coverage.tutorials.Linux cp reports/fourc-ubuntu/.coverage.fourc.Linux .coverage.fourc.Linux diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 3cba24026..377ea8615 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -45,7 +45,7 @@ jobs: requiredness: optional defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: actions/setup-python@v6 @@ -53,14 +53,10 @@ jobs: python-version: "3.12" - name: Build wheel and sdist run: | - set -euo pipefail - python -m pip install --upgrade pip build python -m build - name: Install built wheel in clean virtual environment run: | - set -euo pipefail - python -m venv .venv-pypi-smoke source .venv-pypi-smoke/bin/activate python -m pip install --upgrade pip @@ -69,8 +65,6 @@ jobs: python -m pip install pytest pytest-mock mock - name: Run pure PyPI smoke checks run: | - set -euo pipefail - source .venv-pypi-smoke/bin/activate python -c "import queens" pytest -v -m "unit_tests" \ diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index 75ff279bd..01789b6dc 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest defaults: run: - shell: bash -l {0} + shell: bash -l -euo pipefail {0} steps: - uses: actions/checkout@v6 - name: Set up Pixi @@ -26,8 +26,6 @@ jobs: ensure-rsync: false - name: Update Pixi lockfile run: | - set -euo pipefail - pixi update --json | pixi exec pixi-diff-to-markdown > pixi_lock_update.md - name: Create pull request uses: peter-evans/create-pull-request@v8 From 5f95f7c97335c2ed43f664cd8a0a75b7c2913fd3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 27 May 2026 15:54:53 +0200 Subject: [PATCH 170/200] ci: simplify bash --- .github/actions/run-pytest-suite/action.yml | 8 ++------ .github/workflows/local_testsuite.yml | 6 +++--- .github/workflows/update_pixi_lock.yml | 2 +- 3 files changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/actions/run-pytest-suite/action.yml b/.github/actions/run-pytest-suite/action.yml index 6438abd33..b1a230ed3 100644 --- a/.github/actions/run-pytest-suite/action.yml +++ b/.github/actions/run-pytest-suite/action.yml @@ -14,27 +14,23 @@ runs: steps: - name: Prepare report names id: report-names - shell: bash + shell: bash -eo pipefail {0} env: TEST_SUITE_NAME: ${{ inputs.test-suite-name }} run: | - set -euo pipefail - echo "coverage-file=.coverage.${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT" echo "junit-file=test_junit_${TEST_SUITE_NAME}.xml" >> "$GITHUB_OUTPUT" echo "artifact-name=raw_test_reports_${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT" - name: Run pytest id: pytest - shell: bash + shell: bash -eo pipefail {0} continue-on-error: true env: COVERAGE_FILE: ${{ steps.report-names.outputs.coverage-file }} JUNIT_FILE: ${{ steps.report-names.outputs.junit-file }} PYTEST_MARKERS: ${{ inputs.markers }} run: | - set -euo pipefail - pytest_args=( -v -m "${PYTEST_MARKERS}" diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 0de872818..77ccdbf0d 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -28,7 +28,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -54,7 +54,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -132,7 +132,7 @@ jobs: - run_tests_tutorials_fourc defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -euo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index 01789b6dc..c92ffa473 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -euo pipefail {0} steps: - uses: actions/checkout@v6 - name: Set up Pixi From 22a3732a0c4a58f41df9c76f5277a4073fe85795 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 27 May 2026 16:20:04 +0200 Subject: [PATCH 171/200] ci: simplify bash even more --- .github/actions/run-pytest-suite/action.yml | 4 ++-- .github/actions/setup-queens-pixi/action.yml | 4 ---- .github/workflows/build_documentation.yml | 2 +- .github/workflows/code_quality.yml | 2 +- .github/workflows/local_testsuite.yml | 10 +++++----- .github/workflows/test_pypi_build.yml | 2 +- .github/workflows/update_pixi_lock.yml | 2 +- 7 files changed, 11 insertions(+), 15 deletions(-) diff --git a/.github/actions/run-pytest-suite/action.yml b/.github/actions/run-pytest-suite/action.yml index b1a230ed3..8980c7d1b 100644 --- a/.github/actions/run-pytest-suite/action.yml +++ b/.github/actions/run-pytest-suite/action.yml @@ -14,7 +14,7 @@ runs: steps: - name: Prepare report names id: report-names - shell: bash -eo pipefail {0} + shell: bash env: TEST_SUITE_NAME: ${{ inputs.test-suite-name }} run: | @@ -24,7 +24,7 @@ runs: - name: Run pytest id: pytest - shell: bash -eo pipefail {0} + shell: bash continue-on-error: true env: COVERAGE_FILE: ${{ steps.report-names.outputs.coverage-file }} diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index a601650d6..63176d25e 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -50,21 +50,17 @@ runs: if: ${{ inputs.install-editable != 'false' }} shell: bash run: | - set -euo pipefail pixi run --locked -e "${{ inputs.activate-environment }}" install-editable - name: Mark repo as safe for git shell: bash run: | - set -euo pipefail git config --global --add safe.directory "${GITHUB_WORKSPACE}" - name: Ensure rsync is available if: ${{ inputs.ensure-rsync != 'false' }} shell: bash run: | - set -euo pipefail - if command -v rsync >/dev/null 2>&1; then rsync --version elif [ "${RUNNER_OS}" = "Linux" ]; then diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml index 4ce453c2b..cf07b2f8c 100644 --- a/.github/workflows/build_documentation.yml +++ b/.github/workflows/build_documentation.yml @@ -21,7 +21,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -l -eo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 9c0c6d8fc..d78351aca 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi diff --git a/.github/workflows/local_testsuite.yml b/.github/workflows/local_testsuite.yml index 77ccdbf0d..36c9d048f 100644 --- a/.github/workflows/local_testsuite.yml +++ b/.github/workflows/local_testsuite.yml @@ -28,7 +28,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -54,7 +54,7 @@ jobs: - os: macos-latest defaults: run: - shell: bash -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -77,7 +77,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -l -eo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -103,7 +103,7 @@ jobs: options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash -l -eo pipefail {0} steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi @@ -132,7 +132,7 @@ jobs: - run_tests_tutorials_fourc defaults: run: - shell: bash -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - uses: ./.github/actions/setup-queens-pixi diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 377ea8615..e1040d2be 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -45,7 +45,7 @@ jobs: requiredness: optional defaults: run: - shell: bash -l -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - uses: actions/setup-python@v6 diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index c92ffa473..087da1fcb 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest defaults: run: - shell: bash -euo pipefail {0} + shell: bash steps: - uses: actions/checkout@v6 - name: Set up Pixi From 07a1ace47bd94d9b4095b6c5afb28236392bc9f6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Wed, 27 May 2026 16:21:51 +0200 Subject: [PATCH 172/200] ci: remove unused default environmnet --- .github/workflows/code_quality.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index d78351aca..a12a192dc 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -30,7 +30,6 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} environments: >- - default all dev activate-environment: dev From 5790e7ff30ebedb253721580bba9fb174e3042c5 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 11:35:44 +0200 Subject: [PATCH 173/200] ci: use entire src folder as reference for coverage --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 06d5dbe68..737f19d31 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -120,7 +120,7 @@ markers = [ ] [tool.coverage.run] -source = ["queens"] +source = ["src"] parallel = true branch = true relative_files = true From 60f28af023095fe062435c7ce3c72f15ebdb6604 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 13:40:08 +0200 Subject: [PATCH 174/200] ci: add one source of truth for pixi version --- .github/actions/setup-queens-pixi/action.yml | 9 ++++++++- .gitlab/.gitlab-ci.yml | 5 ++--- .pixi-version | 1 + 3 files changed, 11 insertions(+), 4 deletions(-) create mode 100644 .pixi-version diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 63176d25e..02e79f838 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -36,9 +36,16 @@ inputs: runs: using: composite steps: + - name: Read pixi version + id: pixi-version + shell: bash + run: | + pixi_version="$(tr -d '[:space:]' < "${GITHUB_WORKSPACE}/.pixi-version")" + echo "version=${pixi_version}" >> "$GITHUB_OUTPUT" + - uses: prefix-dev/setup-pixi@v0.9.5 with: - pixi-version: v0.68.1 + pixi-version: ${{ steps.pixi-version.outputs.version }} cache: ${{ inputs.cache }} cache-write: ${{ inputs.cache-write }} run-install: ${{ inputs.run-install }} diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index a437cce54..9eb10757b 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -22,9 +22,6 @@ variables: IMCS_REMOTE_ADDRESS: value: "charon.bauv.unibw-muenchen.de" description: "Hostname of IMCS cluster" - PIXI_VERSION: - value: "v0.67.0" - description: "Pinned pixi version used by the CI pipeline" PIXI_ENVIRONMENT: value: "dev" description: "Pixi workspace environment used in CI jobs" @@ -50,6 +47,7 @@ workflow: .check_pixi_available: before_script: - | + export PIXI_VERSION="$(tr -d '[:space:]' < .pixi-version)" export PATH="$HOME/.pixi/bin:$PATH" if ! command -v pixi >/dev/null 2>&1; then curl -fsSL https://pixi.sh/install.sh | PIXI_VERSION="$PIXI_VERSION" PIXI_HOME="$HOME/.pixi" bash @@ -91,6 +89,7 @@ imcs-build_pixi_env: .build_pixi_env_cluster: stage: build script: + - export PIXI_VERSION="$(tr -d '[:space:]' < .pixi-version)" - | ssh queens@$REMOTE_ADDRESS "bash -lc ' export PATH=\"\$HOME/.pixi/bin:\$PATH\" diff --git a/.pixi-version b/.pixi-version new file mode 100644 index 000000000..161052e0a --- /dev/null +++ b/.pixi-version @@ -0,0 +1 @@ +v0.68.1 From 5b096fb83a7abc6dc64332d19b5cb1b7e6b034dc Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 13:43:03 +0200 Subject: [PATCH 175/200] fix: remove unused file --- composed.conda-lock.yml | 17228 -------------------------------------- 1 file changed, 17228 deletions(-) delete mode 100644 composed.conda-lock.yml diff --git a/composed.conda-lock.yml b/composed.conda-lock.yml deleted file mode 100644 index 4a6262bfb..000000000 --- a/composed.conda-lock.yml +++ /dev/null @@ -1,17228 +0,0 @@ -# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). 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hash: - sha256: 806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b - category: main - optional: false From d25975c646d27a8acae35694c5d49e4954b583f8 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 13:53:43 +0200 Subject: [PATCH 176/200] build: expose yamllint config outside precommit hook, add yamllint code quality check --- .github/actions/setup-queens-pixi/action.yml | 1 + .github/workflows/code_quality.yml | 4 ++++ .pre-commit-config.yaml | 4 ---- .yamllint | 15 +++++++++++++++ 4 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 .yamllint diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 02e79f838..db8175c2f 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -1,3 +1,4 @@ +--- name: Setup QUEENS pixi environment description: > Set up pixi, install QUEENS editable into the selected environment, diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index a12a192dc..73b04c7b0 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -201,3 +201,7 @@ jobs: - name: Run mypy run: | mypy . + + - name: Run yamllint + run: | + yamllint -f=colored . diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7d7f6effa..9697db808 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -71,13 +71,9 @@ repos: name: yamllint entry: yamllint args: - - > # This is needed to lint the jinja templates - -d={extends: default, rules: {braces: {max-spaces-inside: 1} - , brackets: disable, document-start: disable, "line-length": {"max": 100}}} - -f=colored language: python types: ["yaml"] - exclude: '^composed\.conda-lock\.yml$' - id: pylint name: pylint entry: pylint diff --git a/.yamllint b/.yamllint new file mode 100644 index 000000000..a0a0f0019 --- /dev/null +++ b/.yamllint @@ -0,0 +1,15 @@ +--- +extends: default + +ignore: | + .pixi/ + .venv/ + +rules: + # Allow single spaces inside braces for Jinja templates. + braces: + max-spaces-inside: 1 + brackets: disable + document-start: disable + line-length: + max: 100 From 617cdd12bd2ca74837727c166588bb98267ae6c3 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 13:58:50 +0200 Subject: [PATCH 177/200] build: manage version with pixi --- .pre-commit-config.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9697db808..7f2d38fb9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -107,9 +107,8 @@ repos: ^src/queens/(schedulers|stochastic_optimizers|visualization)/| ^src/queens/(main.py|global_settings.py) ).*$ - - repo: https://github.com/kynan/nbstripout - rev: 0.8.1 - hooks: - id: nbstripout name: Strip outputs from Jupyter notebooks + entry: nbstripout + language: system files: \.ipynb$ From 5f1e16ae08cb2792578d12aa32d330ac6ddbffbb Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 14:05:34 +0200 Subject: [PATCH 178/200] ci: collect all test but ignore problematic cases, add explanation --- .github/workflows/test_pypi_build.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index e1040d2be..4c561fd05 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -68,6 +68,11 @@ jobs: source .venv-pypi-smoke/bin/activate python -c "import queens" pytest -v -m "unit_tests" \ + # test fails due to path errors in this setup --ignore=tests/unit_tests/utils/test_path_utils.py \ + # test fails due to path errors in this setup --ignore=tests/unit_tests/data_processors/test_txt_file.py \ - tests/unit_tests/ + # test collection would fail due to missing testbook in the `base` and `all` envs + --ignore=tests/tutorial_tests \ + # test collection would fail due to missing testbook in the `base` and `all` envs + --ignore=tests/integration_tests/cluster/test_cluster.py From eb83358f3b2f7d2e4a6f048e6af900b8d87c77d6 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 15:03:51 +0200 Subject: [PATCH 179/200] ci: run pre-commit hooks and code quality in same order, add missing code checks from pre-commit hooks to code quality checks --- .github/workflows/code_quality.yml | 26 ++++++++++++++++---------- .pre-commit-config.yaml | 1 - 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml index 73b04c7b0..e22702eef 100644 --- a/.github/workflows/code_quality.yml +++ b/.github/workflows/code_quality.yml @@ -157,6 +157,12 @@ jobs: run: | pip-licenses --python=.pixi/envs/all/bin/python + - name: Run basic pre-commit checks + run: | + pre-commit run trailing-whitespace --all-files + pre-commit run end-of-file-fixer --all-files + pre-commit run check-added-large-files --all-files + - name: Create a licenserc file run: | python .gitlab/pipeline_utils/create_licenserc.py \ @@ -170,6 +176,10 @@ jobs: - name: Check license headers uses: apache/skywalking-eyes/header@v0.8.0 + - name: Run ruff + run: | + ruff check + - name: Check conventional commit messages uses: webiny/action-conventional-commits@v1.4.2 @@ -181,6 +191,10 @@ jobs: run: | black --check src/* tests + - name: Run yamllint + run: | + yamllint -f=colored . + - name: Run pylint run: | echo "Run pylint on src:" @@ -190,18 +204,10 @@ jobs: echo "Run pylint on integration tests:" pylint --rcfile=.pylintrc --disable=duplicate-code tests/integration_tests/ - - name: Run ruff - run: | - ruff check - - - name: Run nbstripout - run: | - find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + - - name: Run mypy run: | mypy . - - name: Run yamllint + - name: Run nbstripout run: | - yamllint -f=colored . + find . -path './.pixi' -prune -o -name '*.ipynb' -exec nbstripout --verify {} + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7f2d38fb9..4858588e6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,6 @@ repos: entry: check-added-large-files language: python types: [text] - exclude: '^(composed\.conda-lock\.yml|pixi\.lock)$' - id: check-license-header name: check for correct license header entry: licenseheaders From 5b34b108519615b82fc5a6e68b52d7fd26710090 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 15:09:39 +0200 Subject: [PATCH 180/200] ci: restrict pypi test collection to unit_tests as many packages miss in base env --- .github/workflows/test_pypi_build.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 4c561fd05..034fa5689 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -72,7 +72,4 @@ jobs: --ignore=tests/unit_tests/utils/test_path_utils.py \ # test fails due to path errors in this setup --ignore=tests/unit_tests/data_processors/test_txt_file.py \ - # test collection would fail due to missing testbook in the `base` and `all` envs - --ignore=tests/tutorial_tests \ - # test collection would fail due to missing testbook in the `base` and `all` envs - --ignore=tests/integration_tests/cluster/test_cluster.py + tests/unit_tests/ From 486d0f4041e154f09cdfa7b4275f4c7ce3c048ee Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 15:25:59 +0200 Subject: [PATCH 181/200] docs: add explanation for jupyter kernel --- doc/README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/doc/README.md b/doc/README.md index 7c42f8d63..b1bb68260 100644 --- a/doc/README.md +++ b/doc/README.md @@ -1,6 +1,7 @@ # :book: HTML documentation -We use [Sphinx](https://www.sphinx-doc.org/en/master/#) to generate the [QUEENS documentation](https://queens-py.github.io/queens). It automatically builds the html documentation from the docstrings. +We use [Sphinx](https://www.sphinx-doc.org/en/master/#) to generate the [QUEENS documentation](https://queens-py.github.io/queens). +It automatically builds the html documentation from the docstrings. We believe that documentation is essential and therefore welcome any improvements :blush: @@ -9,13 +10,15 @@ We believe that documentation is essential and therefore welcome any improvement To build the documentation, first set up the QUEENS development environment as described in the [README](../README.md). -Next, register the environment as a Jupyter kernel with: +Next, register the environment as a Jupyter kernel such that the tutorial notbooks can be run while +building the documentation: ```bash pixi run -e dev python -m ipykernel install --user --name queens --display-name "Python (queens)" ``` -When building the documentation on your machine for the first time or after adding new modules or classes to QUEENS, one needs to first rebuild the `autodoc index` by running: +When building the documentation on your machine for the first time or after adding new modules or +classes to QUEENS, one needs to first rebuild the `autodoc index` by running: ```bash cd From 5d96d0ef70bad7ea137cbe184ac5d025609f0256 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 15:48:50 +0200 Subject: [PATCH 182/200] ci: remove comments that break shell command --- .github/workflows/test_pypi_build.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index 034fa5689..e1040d2be 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -68,8 +68,6 @@ jobs: source .venv-pypi-smoke/bin/activate python -c "import queens" pytest -v -m "unit_tests" \ - # test fails due to path errors in this setup --ignore=tests/unit_tests/utils/test_path_utils.py \ - # test fails due to path errors in this setup --ignore=tests/unit_tests/data_processors/test_txt_file.py \ tests/unit_tests/ From 80ee1f680f5e9e3e5539c4da185ab77584818d54 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 16:16:56 +0200 Subject: [PATCH 183/200] fix: use absolute path for notebooks in test suite --- .../integration_tests/cluster/test_cluster.py | 9 ++++--- .../test_1_grid_iterator_rosenbrock.py | 14 +++++------ ...ertainty_propagation_and_quantification.py | 12 ++++++---- .../tutorial_tests/tutorial_tests_markers.py | 24 +++++++++++++------ 4 files changed, 38 insertions(+), 21 deletions(-) diff --git a/tests/integration_tests/cluster/test_cluster.py b/tests/integration_tests/cluster/test_cluster.py index 5b3a64d89..a6774efc0 100644 --- a/tests/integration_tests/cluster/test_cluster.py +++ b/tests/integration_tests/cluster/test_cluster.py @@ -259,7 +259,9 @@ def test_fourc_mc_cluster( @staticmethod @testbook( - "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb", + relative_path_from_root( + "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" + ), ) def test_4c_remote_tutorial( tb, @@ -271,8 +273,9 @@ def test_4c_remote_tutorial( ): """Test for tutorial 3: Remote 4C simulation with grid iterator. - The notebook is run with injected lines of code to replace placeholders. - It is checked that the replaced dict entries already exist in the notebook. + The notebook is run with injected lines of code to replace + placeholders. It is checked that the replaced dict entries + already exist in the notebook. """ kwargs_dicts = [basic_jobscript_kwargs, remote_connection_kwargs, minimal_cluster_kwargs] dict_names = [ diff --git a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py index 136c091da..d59ccf1ab 100644 --- a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py +++ b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py @@ -17,10 +17,11 @@ import numpy as np from testbook import testbook +from queens.utils.path import relative_path_from_root from test_utils.tutorial_tests import inject_mock_base_dir from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook -NOTEBOOK_PATH = "tutorials/1_grid_iterator_rosenbrock.ipynb" +NOTEBOOK_PATH = relative_path_from_root("tutorials/1_grid_iterator_rosenbrock.ipynb") pytestmark = markers_for_notebook(NOTEBOOK_PATH) @@ -31,17 +32,16 @@ def test_output_tutorial_1(tb, tmp_path): """Parameterized test case for tutorial 1: Grid Iterator Rosenbrock. - The notebook is run with injected lines of codes for testing - that the final results are as expected. + The notebook is run with injected lines of codes for testing that + the final results are as expected. """ optimal_fun = 2.957935e-11 optimal_x = np.array([0.99999463, 0.99998915]).tolist() - # inject testing cells tb.inject( - """np.testing.assert_allclose(X1, X1_QUEENS) -np.testing.assert_allclose(X2, X2_QUEENS) -np.testing.assert_allclose(Z, Z_QUEENS)""", + "np.testing.assert_allclose(X1, X1_QUEENS)\n" + "np.testing.assert_allclose(X2, X2_QUEENS)\n" + "np.testing.assert_allclose(Z, Z_QUEENS)", after=28, run=False, ) diff --git a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py index f70c2cb84..3373ff65e 100644 --- a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py +++ b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py @@ -17,10 +17,13 @@ import numpy as np from testbook import testbook +from queens.utils.path import relative_path_from_root from test_utils.tutorial_tests import inject_mock_base_dir from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook -NOTEBOOK_PATH = "tutorials/2_uncertainty_propagation_and_quantification.ipynb" +NOTEBOOK_PATH = relative_path_from_root( + "tutorials/2_uncertainty_propagation_and_quantification.ipynb" +) pytestmark = markers_for_notebook(NOTEBOOK_PATH) @@ -30,10 +33,11 @@ timeout=-1, ) def test_output_tutorial_2(tb, tmp_path): - """Parameterized test case for tutorial 2: Uncertainty Propagation and Quantification. + """Parameterized test case for tutorial 2. - The notebook is run with injected lines of codes for testing - that the final results are as expected. + The tutorial is on Uncertainty Propagation and Quantification. The + notebook is run with injected lines of codes for testing that the + final results are as expected. """ mu = np.array([0.006638095218949362, 0.0063343892089076466, 0.0021987605285805315]).tolist() x = np.array([0.203125, 0.5, 0.796875]).tolist() diff --git a/tests/tutorial_tests/tutorial_tests_markers.py b/tests/tutorial_tests/tutorial_tests_markers.py index 32d76e1b3..a04c71e68 100644 --- a/tests/tutorial_tests/tutorial_tests_markers.py +++ b/tests/tutorial_tests/tutorial_tests_markers.py @@ -20,23 +20,33 @@ import pytest +from queens.utils.path import relative_path_from_root + TUTORIAL_NOTEBOOKS_BY_MARKER = { "tutorial_tests": [ - "tutorials/1_grid_iterator_rosenbrock.ipynb", - "tutorials/2_uncertainty_propagation_and_quantification.ipynb", + relative_path_from_root("tutorials/1_grid_iterator_rosenbrock.ipynb").as_posix(), + relative_path_from_root( + "tutorials/2_uncertainty_propagation_and_quantification.ipynb" + ).as_posix(), ], "tutorial_tests_fourc": [ - "tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb", - "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" - "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb", + relative_path_from_root( + "tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb" + ).as_posix(), + relative_path_from_root( + "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" + "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb" + ).as_posix(), ], "tutorial_tests_remote": [ - "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" + relative_path_from_root( + "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" + ).as_posix(), ], } ALL_TUTORIAL_NOTEBOOKS = tuple( - sorted(path.as_posix() for path in Path("tutorials").rglob("*.ipynb")) + sorted(path.as_posix() for path in relative_path_from_root(Path("tutorials")).rglob("*.ipynb")) ) From c75212d382309bbb5ec3558e1cd0d16d9f1fba64 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 17:58:09 +0200 Subject: [PATCH 184/200] feat: generalize path finding of root and src dirs that also work in pypi tests --- .github/workflows/test_pypi_build.yml | 5 +- src/queens/utils/path.py | 61 ++++++++++++++++++++++- tests/unit_tests/utils/test_path_utils.py | 53 +++++++++++++++++++- 3 files changed, 112 insertions(+), 7 deletions(-) diff --git a/.github/workflows/test_pypi_build.yml b/.github/workflows/test_pypi_build.yml index e1040d2be..91bf34e6f 100644 --- a/.github/workflows/test_pypi_build.yml +++ b/.github/workflows/test_pypi_build.yml @@ -67,7 +67,4 @@ jobs: run: | source .venv-pypi-smoke/bin/activate python -c "import queens" - pytest -v -m "unit_tests" \ - --ignore=tests/unit_tests/utils/test_path_utils.py \ - --ignore=tests/unit_tests/data_processors/test_txt_file.py \ - tests/unit_tests/ + pytest -v -m "unit_tests" tests/unit_tests/ diff --git a/src/queens/utils/path.py b/src/queens/utils/path.py index 6b5cfa9f1..fcd317d7a 100644 --- a/src/queens/utils/path.py +++ b/src/queens/utils/path.py @@ -14,11 +14,68 @@ # """Path utilities for QUEENS.""" +import tomllib from pathlib import Path from typing import Sequence -PATH_TO_QUEENS_SOURCE = Path(__file__).parents[1] -PATH_TO_ROOT = Path(__file__).parents[3] +import queens + +PROJECT_NAME = "queens" + + +def _is_queens_project_root(path: Path) -> bool: + """Check whether a path is the QUEENS project root. + + This is done by looking for the pyproject.toml file. To ensure that + it is the QUEENS root, the name of the project defined in the file + should match. + """ + pyproject_file = path / "pyproject.toml" + if not pyproject_file.is_file(): + return False + + try: + with pyproject_file.open("rb") as pyproject: + pyproject_data = tomllib.load(pyproject) + except (OSError, tomllib.TOMLDecodeError): + return False + + return pyproject_data.get("project", {}).get("name") == PROJECT_NAME + + +def _find_path_to_root(package_candidate: Path) -> Path: + """Find the QUEENS project root from source or installed package contexts. + + Start from a candidate and as a fallback try to find the root: + 1. Check whether the guessed source root is really root. + 2. If not, check whether the current directory or one of its parents is root. + 3. If not, search below the current directory for a root checkout + """ + package_candidate = package_candidate.resolve() + if _is_queens_project_root(package_candidate): + return package_candidate + + # search the parents (upwards) + cwd = Path.cwd().resolve() + for candidate in (cwd, *cwd.parents): + if _is_queens_project_root(candidate): + return candidate + + # search downwards within cwd + for pyproject_file in cwd.rglob("pyproject.toml"): + candidate = pyproject_file.parent + if _is_queens_project_root(candidate): + return candidate + + raise RuntimeError( + "Could not determine the QUEENS project root. Expected a pyproject.toml " + f"with [project].name = {PROJECT_NAME!r} at {package_candidate}, the current working " + f"directory {cwd}, one of its parents, or one of its subdirectories." + ) + + +PATH_TO_QUEENS_SOURCE = Path(queens.__file__).parent +PATH_TO_ROOT = _find_path_to_root(Path(__file__).parents[3]) def relative_path_from_queens_source(relative_path: str) -> Path: diff --git a/tests/unit_tests/utils/test_path_utils.py b/tests/unit_tests/utils/test_path_utils.py index 70aad0765..af6537a8f 100644 --- a/tests/unit_tests/utils/test_path_utils.py +++ b/tests/unit_tests/utils/test_path_utils.py @@ -18,9 +18,11 @@ import pytest +import queens from queens.utils.path import ( PATH_TO_QUEENS_SOURCE, PATH_TO_ROOT, + _find_path_to_root, check_if_path_exists, create_folder_if_not_existent, is_empty, @@ -31,6 +33,15 @@ THIS_PATH = Path(__file__).parent +def _write_pyproject(path, project_name): + """Write a minimal pyproject.toml with the given project name.""" + path.mkdir(parents=True, exist_ok=True) + (path / "pyproject.toml").write_text( + f'[project]\nname = "{project_name}"\n', + encoding="utf-8", + ) + + @pytest.fixture(name="path_to_root") def fixture_path_to_root(): """Path to root.""" @@ -40,7 +51,7 @@ def fixture_path_to_root(): @pytest.fixture(name="path_to_queens_source") def fixture_path_to_queens_source(): """Path to QUEENS source.""" - return THIS_PATH.parents[2] / "src/queens" + return Path(queens.__file__).parent def test_path_to_queens_source(path_to_queens_source): @@ -53,6 +64,46 @@ def test_path_to_root(path_to_root): assert PATH_TO_ROOT == path_to_root +def test_find_path_to_root_falls_back_to_current_working_directory(tmp_path, monkeypatch): + """Test path to root fallback from an installed package location.""" + installed_candidate = tmp_path / ".venv" / "lib" / "python3.12" / "site-packages" + installed_candidate.mkdir(parents=True) + checkout = tmp_path / "checkout" + _write_pyproject(checkout, "queens") + + monkeypatch.chdir(checkout) + + assert _find_path_to_root(installed_candidate) == checkout + + +def test_find_path_to_root_falls_back_to_current_working_directory_subdirectories( + tmp_path, monkeypatch +): + """Test path to root fallback via pyproject.toml below the cwd.""" + installed_candidate = tmp_path / ".venv" / "lib" / "python3.12" / "site-packages" + _write_pyproject(installed_candidate, "not-queens") + workspace = tmp_path / "workspace" + checkout = workspace / "queens" + _write_pyproject(checkout, "queens") + + monkeypatch.chdir(workspace) + + assert _find_path_to_root(installed_candidate) == checkout + + +def test_find_path_to_root_raises_if_queens_pyproject_is_missing(tmp_path, monkeypatch): + """Test path to root fallback fails without a QUEENS pyproject.toml.""" + installed_candidate = tmp_path / ".venv" / "lib" / "python3.12" / "site-packages" + _write_pyproject(installed_candidate, "not-queens") + workspace = tmp_path / "workspace" + _write_pyproject(workspace, "not-queens") + + monkeypatch.chdir(workspace) + + with pytest.raises(RuntimeError, match="Could not determine the QUEENS project root"): + _find_path_to_root(installed_candidate) + + def test_check_if_path_exists(): """Test if path exists.""" current_folder = Path(__file__).parent From e99969050a5208f077eb65bd7626b07adb5983e4 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 23:15:53 +0200 Subject: [PATCH 185/200] refactor: move helper functions to tests_utils --- test_utils/tutorial_tests.py | 130 +++++++++++++++ tests/conftest.py | 2 +- .../test_1_grid_iterator_rosenbrock.py | 3 +- ...ertainty_propagation_and_quantification.py | 3 +- tests/tutorial_tests/test_tutorials.py | 11 +- .../tutorial_tests/tutorial_tests_markers.py | 148 ------------------ 6 files changed, 142 insertions(+), 155 deletions(-) delete mode 100644 tests/tutorial_tests/tutorial_tests_markers.py diff --git a/test_utils/tutorial_tests.py b/test_utils/tutorial_tests.py index 16401fa28..e29c2d163 100644 --- a/test_utils/tutorial_tests.py +++ b/test_utils/tutorial_tests.py @@ -14,6 +14,14 @@ # """Utility methods used by the tutorial tests.""" +from collections import Counter +from itertools import chain +from pathlib import Path + +import pytest + +from queens.utils.path import relative_path_from_root + def inject_notebook_execution_context(tb, notebook_dir): """Inject the notebook directory as Python path and working directory. @@ -64,3 +72,125 @@ def inject_mock_base_dir(tb, tmp_path): """, before=0, ) + + +TUTORIAL_NOTEBOOKS_BY_MARKER = { + "tutorial_tests": [ + relative_path_from_root("tutorials/1_grid_iterator_rosenbrock.ipynb").as_posix(), + relative_path_from_root( + "tutorials/2_uncertainty_propagation_and_quantification.ipynb" + ).as_posix(), + ], + "tutorial_tests_fourc": [ + relative_path_from_root( + "tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb" + ).as_posix(), + relative_path_from_root( + "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" + "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb" + ).as_posix(), + ], + "tutorial_tests_remote": [ + relative_path_from_root( + "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" + ).as_posix(), + ], +} +ALL_TUTORIAL_NOTEBOOKS = tuple( + sorted(path.as_posix() for path in relative_path_from_root(Path("tutorials")).rglob("*.ipynb")) +) + + +def _format_paths(paths): + """Format paths for collection error messages.""" + return "\n".join(f" - {path}" for path in sorted(paths)) + + +def _duplicate_paths(paths): + """Return paths that occur more than once.""" + return sorted(path for path, count in Counter(paths).items() if count > 1) + + +def _validate_tutorial_notebook_markers(): + """Ensure every tutorial notebook has at least one explicit marker.""" + discovered_notebooks = set(ALL_TUTORIAL_NOTEBOOKS) + marked_notebooks = set(chain.from_iterable(TUTORIAL_NOTEBOOKS_BY_MARKER.values())) + missing_notebooks = discovered_notebooks - marked_notebooks + stale_notebooks = marked_notebooks - discovered_notebooks + base_notebooks = set(TUTORIAL_NOTEBOOKS_BY_MARKER["tutorial_tests"]) + specialized_notebooks = set( + chain.from_iterable( + notebook_paths + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if marker_name != "tutorial_tests" + ) + ) + overlapping_base_notebooks = base_notebooks & specialized_notebooks + + duplicate_marker_assignments = { + marker_name: duplicates + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if (duplicates := _duplicate_paths(notebook_paths)) + } + + if not ( + missing_notebooks + or stale_notebooks + or overlapping_base_notebooks + or duplicate_marker_assignments + ): + return + + error_parts = ["Tutorial notebook marker assignments are out of sync."] + if missing_notebooks: + error_parts.append( + "Add marker assignments for these notebooks:\n" f"{_format_paths(missing_notebooks)}" + ) + if stale_notebooks: + error_parts.append( + "Remove marker assignments for missing notebooks:\n" f"{_format_paths(stale_notebooks)}" + ) + if overlapping_base_notebooks: + error_parts.append( + "Remove tutorial_tests from notebooks with specialized tutorial markers:\n" + f"{_format_paths(overlapping_base_notebooks)}" + ) + if duplicate_marker_assignments: + duplicate_entries = [ + f"{marker_name}: {notebook_path}" + for marker_name, notebook_paths in duplicate_marker_assignments.items() + for notebook_path in notebook_paths + ] + error_parts.append( + "Remove duplicate marker assignments:\n" f"{_format_paths(duplicate_entries)}" + ) + + raise pytest.UsageError("\n\n".join(error_parts)) + + +def marker_names_for_notebook(notebook_path): + """Return marker names assigned to a tutorial notebook.""" + notebook_path = Path(notebook_path).as_posix() + return [ + marker_name + for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() + if notebook_path in notebook_paths + ] + + +def markers_for_notebook(notebook_path): + """Return pytest markers assigned to a tutorial notebook.""" + return [ + getattr(pytest.mark, marker_name) + for marker_name in marker_names_for_notebook(notebook_path) + ] + + +def notebook_param(notebook_path): + """Return a pytest parameter for a tutorial notebook.""" + notebook_path = Path(notebook_path).as_posix() + return pytest.param( + notebook_path, + marks=markers_for_notebook(notebook_path), + id=notebook_path, + ) diff --git a/tests/conftest.py b/tests/conftest.py index b471db118..9d6b85968 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -26,7 +26,7 @@ from queens.utils import config_directories from queens.utils.logger_settings import reset_logging from queens.utils.path import relative_path_from_root -from tests.tutorial_tests.tutorial_tests_markers import TUTORIAL_NOTEBOOKS_BY_MARKER +from test_utils.tutorial_tests import TUTORIAL_NOTEBOOKS_BY_MARKER _logger = logging.getLogger(__name__) diff --git a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py index d59ccf1ab..fe7f54a60 100644 --- a/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py +++ b/tests/tutorial_tests/test_1_grid_iterator_rosenbrock.py @@ -18,8 +18,7 @@ from testbook import testbook from queens.utils.path import relative_path_from_root -from test_utils.tutorial_tests import inject_mock_base_dir -from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook +from test_utils.tutorial_tests import inject_mock_base_dir, markers_for_notebook NOTEBOOK_PATH = relative_path_from_root("tutorials/1_grid_iterator_rosenbrock.ipynb") diff --git a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py index 3373ff65e..92961177a 100644 --- a/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py +++ b/tests/tutorial_tests/test_2_uncertainty_propagation_and_quantification.py @@ -18,8 +18,7 @@ from testbook import testbook from queens.utils.path import relative_path_from_root -from test_utils.tutorial_tests import inject_mock_base_dir -from tests.tutorial_tests.tutorial_tests_markers import markers_for_notebook +from test_utils.tutorial_tests import inject_mock_base_dir, markers_for_notebook NOTEBOOK_PATH = relative_path_from_root( "tutorials/2_uncertainty_propagation_and_quantification.ipynb" diff --git a/tests/tutorial_tests/test_tutorials.py b/tests/tutorial_tests/test_tutorials.py index 09e832e73..5670e0a04 100644 --- a/tests/tutorial_tests/test_tutorials.py +++ b/tests/tutorial_tests/test_tutorials.py @@ -19,8 +19,15 @@ import pytest from testbook import testbook -from test_utils.tutorial_tests import inject_mock_base_dir, inject_notebook_execution_context -from tests.tutorial_tests.tutorial_tests_markers import ALL_TUTORIAL_NOTEBOOKS, notebook_param +from test_utils.tutorial_tests import ( + ALL_TUTORIAL_NOTEBOOKS, + _validate_tutorial_notebook_markers, + inject_mock_base_dir, + inject_notebook_execution_context, + notebook_param, +) + +_validate_tutorial_notebook_markers() TUTORIAL_NOTEBOOKS_WITH_DEDICATED_TESTS = { path.stem.removeprefix("test_") diff --git a/tests/tutorial_tests/tutorial_tests_markers.py b/tests/tutorial_tests/tutorial_tests_markers.py deleted file mode 100644 index a04c71e68..000000000 --- a/tests/tutorial_tests/tutorial_tests_markers.py +++ /dev/null @@ -1,148 +0,0 @@ -# -# SPDX-License-Identifier: LGPL-3.0-or-later -# Copyright (c) 2024-2025, QUEENS contributors. -# -# This file is part of QUEENS. -# -# QUEENS is free software: you can redistribute it and/or modify it under the terms of the GNU -# Lesser General Public License as published by the Free Software Foundation, either version 3 of -# the License, or (at your option) any later version. QUEENS is distributed in the hope that it will -# be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You -# should have received a copy of the GNU Lesser General Public License along with QUEENS. If not, -# see . -# -"""Marker assignments for tutorial notebooks.""" - -from collections import Counter -from itertools import chain -from pathlib import Path - -import pytest - -from queens.utils.path import relative_path_from_root - -TUTORIAL_NOTEBOOKS_BY_MARKER = { - "tutorial_tests": [ - relative_path_from_root("tutorials/1_grid_iterator_rosenbrock.ipynb").as_posix(), - relative_path_from_root( - "tutorials/2_uncertainty_propagation_and_quantification.ipynb" - ).as_posix(), - ], - "tutorial_tests_fourc": [ - relative_path_from_root( - "tutorials/3_orchestrating_4c_simulations/3_orchestrating_4c_simulations.ipynb" - ).as_posix(), - relative_path_from_root( - "tutorials/4_quantifying_uncertainty_due_to_heterogeneous_material_fields/" - "4_quantifying_uncertainty_due_to_heterogeneous_material_fields.ipynb" - ).as_posix(), - ], - "tutorial_tests_remote": [ - relative_path_from_root( - "tutorials/5_grid_iterator_4c_remote/5_grid_iterator_4c_remote.ipynb" - ).as_posix(), - ], -} - -ALL_TUTORIAL_NOTEBOOKS = tuple( - sorted(path.as_posix() for path in relative_path_from_root(Path("tutorials")).rglob("*.ipynb")) -) - - -def _format_paths(paths): - """Format paths for collection error messages.""" - return "\n".join(f" - {path}" for path in sorted(paths)) - - -def _duplicate_paths(paths): - """Return paths that occur more than once.""" - return sorted(path for path, count in Counter(paths).items() if count > 1) - - -def _validate_tutorial_notebook_markers(): - """Ensure every tutorial notebook has at least one explicit marker.""" - discovered_notebooks = set(ALL_TUTORIAL_NOTEBOOKS) - marked_notebooks = set(chain.from_iterable(TUTORIAL_NOTEBOOKS_BY_MARKER.values())) - missing_notebooks = discovered_notebooks - marked_notebooks - stale_notebooks = marked_notebooks - discovered_notebooks - base_notebooks = set(TUTORIAL_NOTEBOOKS_BY_MARKER["tutorial_tests"]) - specialized_notebooks = set( - chain.from_iterable( - notebook_paths - for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() - if marker_name != "tutorial_tests" - ) - ) - overlapping_base_notebooks = base_notebooks & specialized_notebooks - - duplicate_marker_assignments = { - marker_name: duplicates - for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() - if (duplicates := _duplicate_paths(notebook_paths)) - } - - if not ( - missing_notebooks - or stale_notebooks - or overlapping_base_notebooks - or duplicate_marker_assignments - ): - return - - error_parts = ["Tutorial notebook marker assignments are out of sync."] - if missing_notebooks: - error_parts.append( - "Add marker assignments for these notebooks:\n" f"{_format_paths(missing_notebooks)}" - ) - if stale_notebooks: - error_parts.append( - "Remove marker assignments for missing notebooks:\n" f"{_format_paths(stale_notebooks)}" - ) - if overlapping_base_notebooks: - error_parts.append( - "Remove tutorial_tests from notebooks with specialized tutorial markers:\n" - f"{_format_paths(overlapping_base_notebooks)}" - ) - if duplicate_marker_assignments: - duplicate_entries = [ - f"{marker_name}: {notebook_path}" - for marker_name, notebook_paths in duplicate_marker_assignments.items() - for notebook_path in notebook_paths - ] - error_parts.append( - "Remove duplicate marker assignments:\n" f"{_format_paths(duplicate_entries)}" - ) - - raise pytest.UsageError("\n\n".join(error_parts)) - - -_validate_tutorial_notebook_markers() - - -def marker_names_for_notebook(notebook_path): - """Return marker names assigned to a tutorial notebook.""" - notebook_path = Path(notebook_path).as_posix() - return [ - marker_name - for marker_name, notebook_paths in TUTORIAL_NOTEBOOKS_BY_MARKER.items() - if notebook_path in notebook_paths - ] - - -def markers_for_notebook(notebook_path): - """Return pytest markers assigned to a tutorial notebook.""" - return [ - getattr(pytest.mark, marker_name) - for marker_name in marker_names_for_notebook(notebook_path) - ] - - -def notebook_param(notebook_path): - """Return a pytest parameter for a tutorial notebook.""" - notebook_path = Path(notebook_path).as_posix() - return pytest.param( - notebook_path, - marks=markers_for_notebook(notebook_path), - id=notebook_path, - ) From dba074937218f0f471300edbf6d35359a405eb99 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Thu, 28 May 2026 23:58:21 +0200 Subject: [PATCH 186/200] ci: ensure editable queens install --- .gitlab/.gitlab-ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index 9eb10757b..b95399efc 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -62,6 +62,7 @@ workflow: stage: build script: - pixi install --frozen -e "$PIXI_ENVIRONMENT" + - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable - pixi list --frozen -e "$PIXI_ENVIRONMENT" > pipeline_pixi_environment.txt artifacts: name: "pixi_env-$CI_PIPELINE_ID.txt" @@ -98,6 +99,7 @@ imcs-build_pixi_env: fi pixi --version '" + - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable - pixi run --frozen -e "$PIXI_ENVIRONMENT" python src/queens/utils/remote_build.py --host=$REMOTE_ADDRESS --user=queens --remote-queens-repository=$REMOTE_BUILD_DIR From 27342f8c4944df5127d9b89a7ed6919c3af0f650 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 00:18:49 +0200 Subject: [PATCH 187/200] ci: add gitlab strategy variables --- .gitlab/.gitlab-ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index b95399efc..23df98f78 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -2,6 +2,9 @@ --- #--------------------------------------------------------------------------------------------------- variables: + GIT_STRATEGY: clone + GIT_CHECKOUT: "true" + GIT_CLEAN_FLAGS: -ffdx LNM_TESTS: value: "1" description: "Run cluster tests at LNM" From bdfc074e766b6f1c41a828877228a26a7c325623 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 00:23:25 +0200 Subject: [PATCH 188/200] fix: install editable queens on remote --- src/queens/utils/remote_operations.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/queens/utils/remote_operations.py b/src/queens/utils/remote_operations.py index 209d84191..e253c0b79 100644 --- a/src/queens/utils/remote_operations.py +++ b/src/queens/utils/remote_operations.py @@ -361,7 +361,8 @@ def build_remote_environment( 'bash -lc \'export PATH="$HOME/.pixi/bin:$PATH";' f" cd {self.remote_queens_repository}; " f"rm -rf .pixi/envs/{pixi_environment}; " - f"pixi install --frozen --environment {pixi_environment};'" + f"pixi install --locked --environment {pixi_environment}; " + f"pixi run --locked --environment {pixi_environment} install-editable;'" ) result = self.run(command_string, echo=True, in_stream=False) From 713b820a84ae1d74474d759d60a2d13481014dff Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 00:49:57 +0200 Subject: [PATCH 189/200] ci: ensure install editable queens on pytest call --- .gitlab/.gitlab-ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index 23df98f78..e8e277981 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -192,6 +192,7 @@ charon-build_4C: - .check_pixi_available stage: tests script: + - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable - pixi run --locked -e "$PIXI_ENVIRONMENT" pytest tests/integration_tests/cluster/ -v -m $CLUSTER_MARKER --no-cov -o log_cli=true --log-cli-level=DEBUG --remote-user=queens From 50aa61d69d3291312f071400bd024b72e7eda597 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 00:52:05 +0200 Subject: [PATCH 190/200] ci: switch to locked env --- .gitlab/.gitlab-ci.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index e8e277981..512b4a9de 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -64,9 +64,9 @@ workflow: - .check_pixi_available stage: build script: - - pixi install --frozen -e "$PIXI_ENVIRONMENT" - - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable - - pixi list --frozen -e "$PIXI_ENVIRONMENT" > pipeline_pixi_environment.txt + - pixi install --locked -e "$PIXI_ENVIRONMENT" + - pixi run --locked -e "$PIXI_ENVIRONMENT" install-editable + - pixi list --locked -e "$PIXI_ENVIRONMENT" > pipeline_pixi_environment.txt artifacts: name: "pixi_env-$CI_PIPELINE_ID.txt" paths: @@ -102,8 +102,8 @@ imcs-build_pixi_env: fi pixi --version '" - - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable - - pixi run --frozen -e "$PIXI_ENVIRONMENT" python src/queens/utils/remote_build.py + - pixi run --locked -e "$PIXI_ENVIRONMENT" install-editable + - pixi run --locked -e "$PIXI_ENVIRONMENT" python src/queens/utils/remote_build.py --host=$REMOTE_ADDRESS --user=queens --remote-queens-repository=$REMOTE_BUILD_DIR --pixi-environment=$PIXI_ENVIRONMENT @@ -192,7 +192,7 @@ charon-build_4C: - .check_pixi_available stage: tests script: - - pixi run --frozen -e "$PIXI_ENVIRONMENT" install-editable + - pixi run --locked -e "$PIXI_ENVIRONMENT" install-editable - pixi run --locked -e "$PIXI_ENVIRONMENT" pytest tests/integration_tests/cluster/ -v -m $CLUSTER_MARKER --no-cov -o log_cli=true --log-cli-level=DEBUG --remote-user=queens From 4b7f57e4f5516f72ee9e05b7bfa3007943a391e1 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 01:05:11 +0200 Subject: [PATCH 191/200] build: update pixi.lock to v7 --- pixi.lock | 25649 ++++++++++++++++++++++++++-------------------------- 1 file changed, 12823 insertions(+), 12826 deletions(-) diff --git a/pixi.lock b/pixi.lock index e013bce22..abd507dca 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,30 +1,23 @@ -version: 6 +version: 7 +platforms: +- name: linux-64 +- name: osx-arm64 environments: - default: + all: channels: - url: https://conda.anaconda.org/conda-forge/ - url: https://conda.anaconda.org/nodefaults/ indexes: - https://pypi.org/simple - options: - pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/_x86_64-microarch-level-1-3_x86_64.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-49.0-unix_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.5-py312h5d8c7f2_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/arviz-0.23.4-pyhcf101f3_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-ha62d5e7_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda @@ -49,72 +42,36 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/blas-2.306-mkl.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/blas-devel-3.11.0-6_hcf00494_mkl.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/bokeh-3.9.0-pyhd8ed1ab_0.conda - 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loguru + - numpy + - rapidyaml + - regex + - pre-commit ; extra == 'dev' + - pytest ; extra == 'dev' + - pytest-cov ; extra == 'dev' + - pip-tools ; extra == 'dev' + - pytest-xdist ; extra == 'dev' + requires_python: '>=3.10' From 1578e15657f8adf79aa30b99b4109f8e5aa76fea Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 10:24:06 +0200 Subject: [PATCH 192/200] ci: add optional use of existign 4C build --- .gitlab/.gitlab-ci.yml | 58 ++++++++++++++++++++++++++++++++++++------ 1 file changed, 50 insertions(+), 8 deletions(-) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index 512b4a9de..eb53d11bf 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -11,6 +11,9 @@ variables: IMCS_TESTS: value: "1" description: "Run cluster tests at IMCS" + BUILD_4C: + value: "1" + description: "Build 4C in CI. Set to 0 to check for an existing remote 4C executable" REMOTE_BUILD_DIR: value: "/home/queens/builds/queens-$CI_PIPELINE_ID" LNM_REMOTE_PYTHON: @@ -167,7 +170,7 @@ thought-build_4C: tags: - lnm-build rules: - - if: $LNM_TESTS == "1" + - if: '$LNM_TESTS == "1" && $BUILD_4C == "1"' charon-build_4C: extends: @@ -182,7 +185,40 @@ charon-build_4C: tags: - imcs-build rules: - - if: $IMCS_TESTS == "1" + - if: '$IMCS_TESTS == "1" && $BUILD_4C == "1"' + +.check_4C: + stage: build + script: + - | + ssh "queens@$REMOTE_ADDRESS" \ + "bash -lc 'if test -f ~/workspace/fourc_build/4C; then \ + ls -l ~/workspace/fourc_build/4C; \ + else \ + echo Missing required 4C executable: ~/workspace/fourc_build/4C >&2; \ + echo Set BUILD_4C to 1 to build it automatically. >&2; \ + exit 1; \ + fi'" + +thought-check_4C: + extends: + - .check_4C + variables: + REMOTE_ADDRESS: $LNM_REMOTE_ADDRESS + tags: + - lnm-build + rules: + - if: '$LNM_TESTS == "1" && $BUILD_4C == "0"' + +charon-check_4C: + extends: + - .check_4C + variables: + REMOTE_ADDRESS: $IMCS_REMOTE_ADDRESS + tags: + - imcs-build + rules: + - if: '$IMCS_TESTS == "1" && $BUILD_4C == "0"' #--------------------------------------------------------------------------------------------------- # Cluster tests @@ -217,9 +253,12 @@ lnm-cluster_tests: CLUSTER_MARKER: "lnm_cluster" REMOTE_PYTHON: $LNM_REMOTE_PYTHON needs: - - lnm-build_pixi_env - - thought-build_pixi_env - - thought-build_4C + - job: lnm-build_pixi_env + - job: thought-build_pixi_env + - job: thought-build_4C + optional: true + - job: thought-check_4C + optional: true tags: - lnm-ubuntu rules: @@ -232,9 +271,12 @@ imcs-cluster_tests: CLUSTER_MARKER: "imcs_cluster" REMOTE_PYTHON: $IMCS_REMOTE_PYTHON needs: - - imcs-build_pixi_env - - charon-build_pixi_env - - charon-build_4C + - job: imcs-build_pixi_env + - job: charon-build_pixi_env + - job: charon-build_4C + optional: true + - job: charon-check_4C + optional: true tags: - imcs-ubuntu rules: From 547b05d8a96e893cc4168883fba509befa799591 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 10:25:24 +0200 Subject: [PATCH 193/200] ci: run cleanup immediately once tests finish --- .gitlab/.gitlab-ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index eb53d11bf..e56975191 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -299,6 +299,8 @@ thought-cluster-remove_build_dir: - thought-build_pixi_env variables: REMOTE_ADDRESS: $LNM_REMOTE_ADDRESS + needs: + - job: lnm-cluster_tests tags: - lnm-build rules: @@ -311,6 +313,8 @@ charon-cluster-remove_build_dir: - charon-build_pixi_env variables: REMOTE_ADDRESS: $IMCS_REMOTE_ADDRESS + needs: + - job: imcs-cluster_tests tags: - imcs-build rules: From 1689be8ef2fc5ab50c3b934d9f92fcc32939d786 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 10:52:25 +0200 Subject: [PATCH 194/200] ci: fix needs statements --- .gitlab/.gitlab-ci.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.gitlab/.gitlab-ci.yml b/.gitlab/.gitlab-ci.yml index e56975191..e3459a070 100644 --- a/.gitlab/.gitlab-ci.yml +++ b/.gitlab/.gitlab-ci.yml @@ -300,7 +300,10 @@ thought-cluster-remove_build_dir: variables: REMOTE_ADDRESS: $LNM_REMOTE_ADDRESS needs: + - job: thought-build_pixi_env - job: lnm-cluster_tests + optional: true + artifacts: false tags: - lnm-build rules: @@ -314,7 +317,10 @@ charon-cluster-remove_build_dir: variables: REMOTE_ADDRESS: $IMCS_REMOTE_ADDRESS needs: + - job: charon-build_pixi_env - job: imcs-cluster_tests + optional: true + artifacts: false tags: - imcs-build rules: From 964bb64edc84607e6498c6f97494749eb633ab3e Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 13:37:31 +0200 Subject: [PATCH 195/200] ci: periodic, automatic update of pixi version --- .github/workflows/update_pixi_lock.yml | 90 +++++++++++++++++++++++--- 1 file changed, 82 insertions(+), 8 deletions(-) diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_pixi_lock.yml index 087da1fcb..362839c7a 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_pixi_lock.yml @@ -1,4 +1,4 @@ -name: Update Pixi lockfile +name: Update Pixi "on": workflow_dispatch: @@ -10,14 +10,67 @@ permissions: pull-requests: write jobs: - update-pixi-lock: - name: Update Pixi lockfile + update-pixi: + name: Update Pixi runs-on: ubuntu-latest defaults: run: shell: bash steps: - uses: actions/checkout@v6 + - name: Find latest Pixi release + id: pixi_release + env: + GH_TOKEN: ${{ github.token }} + run: | + latest_version="$( + gh api \ + -H "Accept: application/vnd.github+json" \ + --paginate \ + "/repos/prefix-dev/pixi/releases" | + jq -rs ' + [ + .[][] + | select(.draft | not) + | select(.prerelease | not) + | .tag_name as $tag + | select($tag | test("^v[0-9]+\\.[0-9]+\\.[0-9]+$")) + | ($tag | capture( + "^v(?[0-9]+)\\.(?[0-9]+)\\.(?[0-9]+)$" + )) as $version + | { + tag: $tag, + major: ($version.major | tonumber), + minor: ($version.minor | tonumber), + patch: ($version.patch | tonumber) + } + ] + | sort_by(.major, .minor, .patch) + | last + | .tag + ' + )" + + if [ -z "${latest_version}" ] || [ "${latest_version}" = "null" ]; then + echo "No stable Pixi release tag matching vMAJOR.MINOR.PATCH found." + exit 1 + fi + + current_version="$(tr -d '[:space:]' < .pixi-version)" + echo "current_version=${current_version}" >> "$GITHUB_OUTPUT" + echo "latest_version=${latest_version}" >> "$GITHUB_OUTPUT" + + if [ "${current_version}" = "${latest_version}" ]; then + echo "version_changed=false" >> "$GITHUB_OUTPUT" + echo "Pixi is already up to date: ${current_version}" + else + echo "version_changed=true" >> "$GITHUB_OUTPUT" + echo "Pixi update available: ${current_version} -> ${latest_version}" + fi + - name: Update Pixi version file + if: ${{ steps.pixi_release.outputs.version_changed == 'true' }} + run: | + printf '%s\n' "${{ steps.pixi_release.outputs.latest_version }}" > .pixi-version - name: Set up Pixi uses: ./.github/actions/setup-queens-pixi with: @@ -27,15 +80,36 @@ jobs: - name: Update Pixi lockfile run: | pixi update --json | pixi exec pixi-diff-to-markdown > pixi_lock_update.md + - name: Write pull request body + env: + CURRENT_PIXI_VERSION: ${{ steps.pixi_release.outputs.current_version }} + LATEST_PIXI_VERSION: ${{ steps.pixi_release.outputs.latest_version }} + VERSION_CHANGED: ${{ steps.pixi_release.outputs.version_changed }} + run: | + { + if [ "${VERSION_CHANGED}" = "false" ]; then + echo "Pixi is already up to date at \`${CURRENT_PIXI_VERSION}\`." + else + echo "Update Pixi from \`${CURRENT_PIXI_VERSION}\` to" \ + "\`${LATEST_PIXI_VERSION}\`." + echo "" + echo "Release: https://github.com/prefix-dev/pixi/releases/tag/${LATEST_PIXI_VERSION}" + fi + + echo "" + cat pixi_lock_update.md + } > pixi_update.md - name: Create pull request uses: peter-evans/create-pull-request@v8 with: token: ${{ secrets.GITHUB_TOKEN }} - commit-message: Update Pixi lockfile - title: Update Pixi lockfile - body-path: pixi_lock_update.md - branch: update-pixi-lock + commit-message: "build: update dependencies" + title: Update dependencies + body-path: pixi_update.md + branch: update-dependencies base: main labels: pixi delete-branch: true - add-paths: pixi.lock + add-paths: | + .pixi-version + pixi.lock From 978d609458d9d5cf0a65e75a0120db42f6fa9a01 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 13:41:07 +0200 Subject: [PATCH 196/200] ci: fix naming --- .../{update_pixi_lock.yml => update_dependencies.yml} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{update_pixi_lock.yml => update_dependencies.yml} (98%) diff --git a/.github/workflows/update_pixi_lock.yml b/.github/workflows/update_dependencies.yml similarity index 98% rename from .github/workflows/update_pixi_lock.yml rename to .github/workflows/update_dependencies.yml index 362839c7a..9f74d238a 100644 --- a/.github/workflows/update_pixi_lock.yml +++ b/.github/workflows/update_dependencies.yml @@ -1,4 +1,4 @@ -name: Update Pixi +name: Update Dependencies "on": workflow_dispatch: @@ -11,7 +11,7 @@ permissions: jobs: update-pixi: - name: Update Pixi + name: Update Dependencies runs-on: ubuntu-latest defaults: run: From c044e80bb61d480126412dee1779e621b5811163 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 13:50:08 +0200 Subject: [PATCH 197/200] ci: deactivate caching for non-install --- .github/workflows/update_dependencies.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 9f74d238a..f98019654 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -74,6 +74,7 @@ jobs: - name: Set up Pixi uses: ./.github/actions/setup-queens-pixi with: + cache: false run-install: false install-editable: false ensure-rsync: false From 498c1ffb4cfbe3db3a0f7fd68c9ae504fa4085e7 Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 13:55:33 +0200 Subject: [PATCH 198/200] ci: frozen cannot be true if install is false --- .github/actions/setup-queens-pixi/action.yml | 6 +++++- .github/workflows/update_dependencies.yml | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index db8175c2f..22eb194a4 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -33,6 +33,10 @@ inputs: description: Whether to verify that rsync is available, installing it if necessary. required: false default: "true" + frozen: + description: Whether to install with frozen requirements. + required: false + default: "true" runs: using: composite @@ -51,7 +55,7 @@ runs: cache-write: ${{ inputs.cache-write }} run-install: ${{ inputs.run-install }} environments: ${{ inputs.environments }} - frozen: true + frozen: ${{ inputs.frozen }} activate-environment: ${{ inputs.activate-environment }} - name: Install QUEENS in workspace diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index f98019654..6142fb32c 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -75,6 +75,7 @@ jobs: uses: ./.github/actions/setup-queens-pixi with: cache: false + frozen: false run-install: false install-editable: false ensure-rsync: false From 2f7c1940934c2d48927328d46eb5ee1140af142c Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 15:34:28 +0200 Subject: [PATCH 199/200] ci: switch default value for environment --- .github/actions/setup-queens-pixi/action.yml | 4 ++-- .github/workflows/update_dependencies.yml | 3 --- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/actions/setup-queens-pixi/action.yml b/.github/actions/setup-queens-pixi/action.yml index 22eb194a4..aed4eb401 100644 --- a/.github/actions/setup-queens-pixi/action.yml +++ b/.github/actions/setup-queens-pixi/action.yml @@ -20,11 +20,11 @@ inputs: environments: description: Whitespace-separated list of pixi environments to install. required: false - default: dev + default: default activate-environment: description: Pixi environment to activate and use for the editable install. required: false - default: dev + default: default install-editable: description: Whether to install QUEENS editable into the selected pixi environment. required: false diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 6142fb32c..6b41beff1 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -74,9 +74,6 @@ jobs: - name: Set up Pixi uses: ./.github/actions/setup-queens-pixi with: - cache: false - frozen: false - run-install: false install-editable: false ensure-rsync: false - name: Update Pixi lockfile From 1ddc2b9949293bce1f0c43a257c67fa509b9863d Mon Sep 17 00:00:00 2001 From: Sebastian Brandstaeter Date: Fri, 29 May 2026 18:10:18 +0200 Subject: [PATCH 200/200] ci: switch to GitHub App managed branch creation --- .github/workflows/update_dependencies.yml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 6b41beff1..5d80098a2 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -6,8 +6,7 @@ name: Update Dependencies - cron: "0 5 1 * *" permissions: - contents: write - pull-requests: write + contents: read jobs: update-pixi: @@ -17,6 +16,14 @@ jobs: run: shell: bash steps: + - name: Create GitHub App token + id: update_dependencies_token + uses: actions/create-github-app-token@v3 + with: + client-id: ${{ vars.UPDATE_DEPENDENCIES_APP_CLIENT_ID }} + private-key: ${{ secrets.UPDATE_DEPENDENCIES_APP_PRIVATE_KEY }} + permission-contents: write + permission-pull-requests: write - uses: actions/checkout@v6 - name: Find latest Pixi release id: pixi_release @@ -101,7 +108,7 @@ jobs: - name: Create pull request uses: peter-evans/create-pull-request@v8 with: - token: ${{ secrets.GITHUB_TOKEN }} + token: ${{ steps.update_dependencies_token.outputs.token }} commit-message: "build: update dependencies" title: Update dependencies body-path: pixi_update.md