From 8dc6c64d73d86904d2add024cdfc67f248d3b0d2 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Fri, 29 Aug 2025 19:31:23 +0200 Subject: [PATCH 1/2] Migrate to Pixi for environment and CI management (#81) * Update versioning format in pyproject.toml * Removes old release drafter configuration * Add Pixi related files to .gitignore and .prettierignore * Reformats versioning configuration format * Adds pixi.toml configuration for dependency management * Adds pixi.lock * Migrate to pixi for environment and dependency management * Refines GitHub Actions workflow by removing unused job * Updates pixi workflow and task definitions * Enhances workflow with logging and environment adjustments * Updates CI workflow configurations * Add verbose flag and prevent project auto-install * Updates PyPI dependencies in pixi workflow * Simplifies pixi installation commands * Refines installation strategy for easydiffraction * Refines testing workflow in GitHub Actions * Update test-code.yaml * Update test-code.yaml * Update test-code.yaml * Removes easydiffraction from test setup * Refines test workflow naming for clarity * Refines CI for easydiffraction integration * Removes verbose flag from pixi install steps * Updates .github workflows and pixi.lock dependencies * Enforces locked dependency installation * Reenables step failure checks and functional tests * Removes obsolete PIXI_ENV_PREFIXES env var * Simplifies workflow and removes redundant setup task * Removes env setup step from test workflow * Enable caching for Pixi setup in CI workflow * Disables caching in GitHub workflow * Enhances notebook support and testing * Replaces Python setup with Pixi in CI workflow * Adds test for running tutorial scripts * Refines script testing approach for tutorials * Update workflow to handle environment-specific builds * Removes redundant script validation checks * Disables functional test execution in CI workflow * Replaces inline script with external Python tool * Updates environment handling in workflow * Adds debug information for current directory in CI * Corrects script path in setup task * Includes 'tools/' in paths to check for artifacts * Adds debug steps to CI workflow and corrects script path * Enables unit and functional test execution * Fixes task script path in configuration * Adds nightly test workflow for develop branch * Switches CI to use Pixi for environment management * Enhances notebook conversion and deployment process * Refines docs deployment workflow * Updates deployment links and uses 'pixi run' in workflows * Update versioning strategy for non-tagged commits * Fixes conditional formatting in YAML workflow * Try if: !(startsWith(github.ref , 'refs/tags/v')) * Try if: startsWith(github.ref , 'refs/tags/v') != true * Simplifies workflow with streamlined pixi commands * Enables testing stages in GitHub Actions * Remove redundant echo argument in workflow * Replaces blank echo with hyphen for readability * Enhances log output with visual indicators * Enhances logging in workflow scripts * Updates workflow task names for clarity * Update GitHub workflows and streamline environment setup * Removes obsolete shell scripts for dependencies and notebooks * Adds pixi-based installation * Adds dependencies and tutorial fetch task * Updates pixi.lock * Removes line breaks in setup guide * Improves Pixi installation guide for clarity * Add CI workflow for Pixi installation validation * Removes locked option from setup-pixi action * Removes unnecessary checkout step from workflow * Avoids Jupyter warnings by setting session name * Updates npm registry configuration for Prettier * Removes unnecessary Jupyter session name export * Add libcblas to dependencies for enhanced functionality * Expands OS matrix for workflow validation * Simplifies notebook execution command * Simplifies environment logging format in workflows * Enhances deployment links in documentation workflow * Refines Pixi installation guide section * Enhances Jupyter setup instructions * Refines deployment URL handling in workflow * Replaces curl with Python script for fetching tutorials * Sets easydiffraction as editable and adds execution command * Adds lazy loading for improved import performance * Add tutorial download and listing utilities * Enhances EasyDiffraction CLI and tutorial setup * Updates pixi.lock * Quote Python command in Pixi task addition * Consistently define environment variables in workflows * Ensures UTF-8 output consistency on all platforms * Unlocks environments in GitHub workflows * Removes locked flag from pixi install command * Enables locked installations in workflows * Refines development dependency configuration * Adds tutorial listing to EasyDiffraction workflow * Removes 'locked' config and editable mode for easydiffraction * Add GitHub Actions workflow for testing unlocked ED * Adds dev dependencies to EasyDiffraction setup * Refactors workflow for PyPI package testing * Refines CI configuration for dev environments * Updates virtual environment task configuration * Enhances pixi setup in CI workflow * Refactors extras format in pixi.toml * Switch 'locked' to 'frozen' in workflows * Moves import success prints to debug mode * Updates test command to use pytest for better test clarity * Enhances test workflow with environment-specific tasks * Updates feature flag to use environment prefix * Comments out dev-wheel environments in CI config * Removes solve-group keys from configurations * Updates pixi.lock * Renames feature sections for clarity * Updates build process to include environment variable * Refactors feature configuration for modularity * Removes default package environment * Adds new test job for Ubuntu 24.04 in CI workflow * Adds dependency for job execution order * Adds pixi.lock to artifact paths in workflow * Enhances logging for package installation * Refines CI configuration for wheel builds * Adds pyproject.toml to artifact paths * Updates artifact paths in test workflow * Updates workflow to optimize environment setup * Removes unnecessary PIXI environment setup * Updates GitHub Actions to improve build setup * Adds environment configuration to setup-pixi step * Relocates artifact download step in CI workflow * Adds debugging output to workflow * Removes unnecessary whitespace in workflow file * Adds LICENSE to artifact paths in CI workflow * Reorganizes test structure and updates soupsieve * Updates test matrix and refines test commands * Refactors CI workflows and config for Pixi usage * Updates manifest file extension in workflow * Updates file extension in workflow configuration * Removes redundant var & updates manifest setup * Fixes env_prefix handling in workflow script * Adds 'pip' to project dependencies * Reorganizes workflow and configures Pixi paths * Sets up production environment for Pixi project * Enhances version handling and tutorial management * Formats dependency configuration for readability * Refactors render_table calls for clarity * Simplifies EasyDiffraction setup with pixi install * Removes redundant pixi toml renaming step * Enhances Pixi setup instructions * Updates file path for configuration consistency * Enhances installation guide with alternative tools * Reorganizes and refines project tasks * Removes obsolete fix_find_links script * Adjusts path for pixi.toml in test workflow * Reorders tasks and installs Prettier for TOML files * Removes unnecessary newlines for cleaner markdown * Update test-code.yaml * Adds PIXI_PROJECT_MANIFEST and adjusts pixi setup * Refines Pixi setup and enhances docs * Streamlines package version check in workflow * Refactors documentation workflow and assets handling * Refines doc cleanup script for specific asset types * Refactor docs build process with pixi tasks * Refactors doc build steps and adds delay in tests * Corrects pixi command syntax in test workflow * Refines environment-specific command execution * Add GitHub API token authentication to fetch release * Adds GITHUB_TOKEN to workflow environment * Standardizes string quote style in utils.py * Refines Pixi workflow and enhances documentation tasks * Enables full testing matrix in CI workflows * Simplifies EasyDiffraction tutorial download process * Adds jupyterquiz to dev dependencies * Fix URL for downloading the pixi configuration file in CI workflow * Update ipython version to 9.5.0 in pixi.lock --- .github/release-drafter.yml | 40 - .github/workflows/build-docs.yml | 125 +- .github/workflows/publish-pypi.yml | 2 +- .github/workflows/test-code.yaml | 251 +- .github/workflows/test-package-pypi.yaml | 54 + .github/workflows/test-tutorials-nightly.yaml | 10 + .github/workflows/test-tutorials.yaml | 135 +- .github/workflows/validate-pixi.yaml | 75 + .gitignore | 3 + .prettierignore | 3 +- DEVELOPMENT.md | 170 +- docs/installation-and-setup/index.md | 124 +- docs/mkdocs.yml | 7 +- pixi.lock | 17496 ++++++++++++++++ pixi.toml | 165 + pixi/prod/pixi.toml | 25 + pixi/wheel/pixi.toml | 26 + pycrysfml.md | 26 + pyproject.toml | 5 +- src/easydiffraction/__init__.py | 122 +- src/easydiffraction/__main__.py | 34 + src/easydiffraction/analysis/analysis.py | 22 +- .../calculators/calculator_crysfml.py | 3 +- .../analysis/calculators/calculator_cryspy.py | 3 +- .../analysis/calculators/calculator_pdffit.py | 3 +- src/easydiffraction/utils/utils.py | 295 +- tests/__init__.py | 3 + tests/functional_tests/__init__.py | 3 + tests/functional_tests/fitting/__init__.py | 3 + tests/unit_tests/__init__.py | 3 + tests/unit_tests/analysis/__init__.py | 3 + .../analysis/calculators/__init__.py | 3 + .../analysis/collections/__init__.py | 3 + .../analysis/minimizers/__init__.py | 3 + tests/unit_tests/core/__init__.py | 3 + tests/unit_tests/experiments/__init__.py | 3 + .../experiments/collections/__init__.py | 3 + .../experiments/components/__init__.py | 3 + tests/unit_tests/sample_models/__init__.py | 3 + .../sample_models/collections/__init__.py | 3 + .../sample_models/components/__init__.py | 3 + ...{prepare_docs.sh => add_assets_to_docs.sh} | 12 +- tools/build_docs.sh | 4 - tools/cleanup_docs.sh | 12 +- ...ate_mkdocs-yml.py => create_mkdocs_yml.py} | 0 tools/install_deps.sh | 2 - tools/run_notebooks.sh | 6 - tools/test_scripts.py | 25 + ...repare_notebooks.py => tweak_notebooks.py} | 5 +- ...{update_spdx-headers.py => update_spdx.py} | 0 50 files changed, 18784 insertions(+), 551 deletions(-) delete mode 100644 .github/release-drafter.yml create mode 100644 .github/workflows/test-package-pypi.yaml create mode 100644 .github/workflows/test-tutorials-nightly.yaml create mode 100644 .github/workflows/validate-pixi.yaml create mode 100644 pixi.lock create mode 100644 pixi.toml create mode 100644 pixi/prod/pixi.toml create mode 100644 pixi/wheel/pixi.toml create mode 100644 pycrysfml.md create mode 100644 src/easydiffraction/__main__.py create mode 100644 tests/__init__.py create mode 100644 tests/functional_tests/__init__.py create mode 100644 tests/functional_tests/fitting/__init__.py create mode 100644 tests/unit_tests/__init__.py create mode 100644 tests/unit_tests/analysis/__init__.py create mode 100644 tests/unit_tests/analysis/calculators/__init__.py create mode 100644 tests/unit_tests/analysis/collections/__init__.py create mode 100644 tests/unit_tests/analysis/minimizers/__init__.py create mode 100644 tests/unit_tests/core/__init__.py create mode 100644 tests/unit_tests/experiments/__init__.py create mode 100644 tests/unit_tests/experiments/collections/__init__.py create mode 100644 tests/unit_tests/experiments/components/__init__.py create mode 100644 tests/unit_tests/sample_models/__init__.py create mode 100644 tests/unit_tests/sample_models/collections/__init__.py create mode 100644 tests/unit_tests/sample_models/components/__init__.py rename tools/{prepare_docs.sh => add_assets_to_docs.sh} (65%) delete mode 100755 tools/build_docs.sh rename tools/{create_mkdocs-yml.py => create_mkdocs_yml.py} (100%) delete mode 100755 tools/install_deps.sh delete mode 100755 tools/run_notebooks.sh create mode 100644 tools/test_scripts.py rename tools/{prepare_notebooks.py => tweak_notebooks.py} (95%) rename tools/{update_spdx-headers.py => update_spdx.py} (100%) diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml deleted file mode 100644 index 7a4e6ef7..00000000 --- a/.github/release-drafter.yml +++ /dev/null @@ -1,40 +0,0 @@ -# This file is used to configure the Release Drafter GitHub Action -# https://github.com/marketplace/actions/release-drafter - -name-template: 'easydiffraction $RESOLVED_VERSION' -tag-template: 'v$RESOLVED_VERSION' - -categories: - - title: 'Added' - labels: - - '[scope] significant' - - '[scope] enhancement' - - title: 'Fixed' - labels: - - '[scope] bug' - - title: 'Changed' - labels: - - '[scope] maintenance' - - title: 'Documentation' - labels: - - '[scope] documentation' - -change-template: '- $TITLE (#$NUMBER)' -change-title-escapes: '\<*_&' - -version-resolver: - major: - labels: - - '[scope] significant' - minor: - labels: - - '[scope] enhancement' - patch: - labels: - - '[scope] bug' - - '[scope] maintenance' - - '[scope] documentation' - default: patch - -template: | - $CHANGES diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index d6f31dad..3a4c49ce 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -4,7 +4,7 @@ on: # Trigger the workflow on push push: # Selected branches - branches: [develop, master, docs, patch] + branches: [develop, master, docs, patch, pixi] # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' tags: - 'v*' @@ -18,12 +18,17 @@ concurrency: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true +# Set the environment variables to be used in all jobs defined in this workflow env: - # Set the environment variables to be used in all jobs defined in this workflow - # Set the CI_BRANCH environment variable to be the branch name - # Set the NOTEBOOKS_DIR environment variable to be the directory containing the Jupyter notebooks + # CI_BRANCH - the branch name (used in mkdocs.yml) + # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml) + # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml) CI_BRANCH: ${{ github.head_ref || github.ref_name }} + GITHUB_REPOSITORY: ${{ github.repository }} NOTEBOOKS_DIR: tutorials + DEV_DEPLOYMENT_URL: + https://easyscience.github.io/${{ github.event.repository.name }} + PROD_DEPLOYMENT_URL: https://docs.easydiffraction.org/lib jobs: # Job 1: Build the static files for the documentation site @@ -31,7 +36,6 @@ jobs: strategy: matrix: os: [macos-14] # Use macOS to switch to dark mode for Plotly charts - python-version: ['3.13'] runs-on: ${{ matrix.os }} @@ -49,10 +53,6 @@ jobs: git fetch --tags --force echo "RELEASE_VERSION=$(git describe --tags --abbrev=0)" >> "$GITHUB_ENV" - # Without this step, GITHUB_REPOSITORY is not accessible from mkdocs.yml - - name: Set GITHUB_REPOSITORY env variable - run: echo "GITHUB_REPOSITORY=$GITHUB_REPOSITORY" >> "$GITHUB_ENV" - # Activate dark mode to create documentation with Plotly charts in dark mode # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/, @@ -64,85 +64,57 @@ jobs: # dark-mode on # dark-mode status - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - shell: bash - run: python -m pip install --upgrade pip + environments: >- + py313-docs + activate-environment: py313-docs + run-install: true + frozen: true + cache: false + post-cleanup: false - # Install EasyDiffraction Library to run Jupyter notebooks - # Install with the 'docs' and 'visualization' extras - - name: Install EasyDiffraction Library and its dependencies - run: python -m pip install .'[dev,docs,visualization]' - - # Clone assets extra from: - # - easyscience/assets-docs - # - easyscience/assets-branding - name: Clone easyscience/assets-docs and easyscience/assets-branding run: | cd .. git clone https://github.com/easyscience/assets-docs.git git clone https://github.com/easyscience/assets-branding.git - # Add the extra files from the easyscience/assets-docs repository - - name: Add files from easyscience/assets-docs files - run: | - cp -R ../assets-docs/docs/assets/ docs/assets/ - cp -R ../assets-docs/includes/ includes/ - cp -R ../assets-docs/overrides/ overrides/ - - # Add the extra files from the easyscience/assets-branding repository - - name: Add files from easyscience/assets-branding files - run: | - mkdir -p docs/assets/images/ - cp ../assets-branding/easydiffraction/hero/dark.png docs/assets/images/hero_dark.png - cp ../assets-branding/easydiffraction/hero/light.png docs/assets/images/hero_light.png - cp ../assets-branding/easydiffraction/logos/dark.svg docs/assets/images/logo_dark.svg - cp ../assets-branding/easydiffraction/logos/light.svg docs/assets/images/logo_light.svg - cp ../assets-branding/easydiffraction/icons/color.png docs/assets/images/favicon.png - mkdir -p overrides/.icons/ - cp ../assets-branding/easydiffraction/icons/bw.svg overrides/.icons/easydiffraction.svg - cp ../assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg + - name: Add files from cloned repositories + run: pixi run add-assets-to-docs # Convert python scripts in the notebooks directory to Jupyter notebooks - # Strip output from the notebooks, simpify cell ids and replace '# !pip' with '!pip' - # The notebooks are used to generate the documentation - - name: - Convert ${{ env.NOTEBOOKS_DIR }}/*.py to docs/${{env.NOTEBOOKS_DIR - }}/*.ipynb - run: | - cp -R ${{ env.NOTEBOOKS_DIR }}/data docs/${{ env.NOTEBOOKS_DIR }}/ - jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb - nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb - python tools/prepare_notebooks.py ${{ env.NOTEBOOKS_DIR }}/ - mv ${{ env.NOTEBOOKS_DIR }}/*.ipynb docs/${{ env.NOTEBOOKS_DIR }}/ + # Strip output from the notebooks + # Prepare the notebooks for documentation (add colab cell, etc.) + # Run the notebooks to generate the output cells using multiple cores + # The notebooks are then used to build the documentation site + - name: Convert tutorial scripts to notebooks + run: pixi run make-notebooks + + - name: Run notebooks + run: pixi run run-notebooks + + - name: Move notebooks to docs/tutorials + run: pixi run move-notebooks-to-docs # The following step is needed to avoid the following message during the build: # "Matplotlib is building the font cache; this may take a moment" - - name: Pre-build site step - run: | - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -c "import easydiffraction" + #- name: Pre-build site step + # run: pixi run python -c "import easydiffraction" # Create the mkdocs.yml configuration file # The file is created by merging two files: # - assets-docs/mkdocs.yml - the common configuration (theme, plugins, etc.) # - docs/mkdocs.yml - the project-specific configuration (project name, TOC, etc.) - name: Create mkdocs.yml file - run: python tools/create_mkdocs-yml.py + run: pixi run create-mkdocs-yml # Build the static files # Input: docs/ directory containing the Markdown files # Output: site/ directory containing the generated HTML files - name: Build site with MkDocs - run: | - export JUPYTER_PLATFORM_DIRS=1 - export PYTHONWARNINGS="ignore::RuntimeWarning" - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - mkdocs build + run: pixi run build-docs # Set up the Pages action to configure the static files to be deployed # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions @@ -155,9 +127,7 @@ jobs: # This artifact is named github-pages and is a single gzip archive containing a single tar file # The artifact is then used in the next job by actions/deploy-pages to deploy the static files to GitHub Pages # Unfortunately, the artifact is not available for download, so extra steps below are needed to do similar things - - name: - Upload built site as artifact for easyscience.github.io/${{ - github.event.repository.name }} (all branches) + - name: Upload built site as artifact for DEV deployment (all branches) uses: actions/upload-pages-artifact@v3 with: path: site/ @@ -165,7 +135,7 @@ jobs: # Upload the static files from the site/ directory to be used in the next job # This artifact is only uploaded on tagged releases (tags starting with 'v', e.g., v1.0.3) # and is used to push content to gh_pages for custom domain deployment. - - name: Upload built site as artifact for gh_pages (tagged release) + - name: Upload built site as artifact for PROD deployment (tagged release) if: startsWith(github.ref, 'refs/tags/v') uses: actions/upload-artifact@v4 with: @@ -203,11 +173,14 @@ jobs: # restrictions on the branch name need to be set for desired branches on # https://github.com/easyscience/diffraction-lib/settings/environments # Deployed pages are available at https://easyscience.github.io/diffraction-lib - - name: - Deploy to easyscience.github.io/${{ github.event.repository.name }} - (all branches) + - name: DEV deployment (all branches) uses: actions/deploy-pages@v4 + - name: Show DEV deployment url (all branches) + run: + echo "πŸ”— DEV deployment url [${{ env.DEV_DEPLOYMENT_URL }}](${{ + env.DEV_DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY + # Download built site as artifact from a previous job for gh_pages (tagged release) # This artifact is only downloaded on tagged releases (tags starting with 'v', e.g., v1.0.3) # and is used to push content to gh_pages for custom domain deployment. @@ -228,9 +201,7 @@ jobs: # Then the gh_pages branch is used to deploy the site to the custom domain. # Deploying is done with a webhook added via: # https://github.com/easyscience/diffraction-lib/settings/hooks - - name: - Deploy to gh_pages branch to trigger deployment to custom domain - (tagged release) + - name: PROD deployment to gh_pages for custom domain (tagged release) if: startsWith(github.ref, 'refs/tags/v') uses: s0/git-publish-subdir-action@develop env: @@ -238,3 +209,9 @@ jobs: REPO: self BRANCH: gh_pages FOLDER: site + + - name: Show PROD deployment url (tagged release) + if: startsWith(github.ref, 'refs/tags/v') + run: + echo "πŸ”— PROD deployment url [${{ env.PROD_DEPLOYMENT_URL }}](${{ + env.PROD_DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 7b6b73ed..805ef813 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -29,7 +29,7 @@ jobs: - name: Upgrade package installer for Python run: pip install --upgrade pip - - name: Install build frontend + - name: Install build tool run: pip install --upgrade build - name: Create Python package diff --git a/.github/workflows/test-code.yaml b/.github/workflows/test-code.yaml index 3a9d31bb..7fb814ec 100644 --- a/.github/workflows/test-code.yaml +++ b/.github/workflows/test-code.yaml @@ -10,8 +10,8 @@ # - Test the code base against the latest code in the repository # - Create the Python package # - Upload the Python package for the next job -# 3. check-package: -# - Download the Python package from the previous job +# 3. test-package: +# - Download the Python package (including extra files) from the previous job # - Install the downloaded Python package # - Test the code base against the installed package @@ -41,10 +41,10 @@ concurrency: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true +# Set the environment variables to be used in all jobs defined in this workflow env: - # Set the environment vars to be used in all jobs defined in this workflow - # Set the CI_BRANCH environment var to be the branch name - # Set the NOTEBOOKS_DIR environment var to be the dir of Jupyter notebooks + # CI_BRANCH - the branch name (used in mkdocs.yml) + # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml) CI_BRANCH: ${{ github.head_ref || github.ref_name }} NOTEBOOKS_DIR: tutorials @@ -54,7 +54,6 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: ['3.13'] runs-on: ${{ matrix.os }} @@ -62,61 +61,53 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + - name: Set up pixi (incl. environments and dependencies) + uses: prefix-dev/setup-pixi@v0.9.0 with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - shell: bash - run: python -m pip install --upgrade pip - - - name: Install Python dependencies - shell: bash - run: python -m pip install .'[dev]' - - - name: Install npm dependencies - # Install 'prettier' for code formatting of Markdown, YAML, etc. files - # Install 'prettier-plugin-toml' plugin for formatting of TOML files + environments: >- + py313-dev + activate-environment: py313-dev + run-install: true + frozen: true + cache: false + post-cleanup: false + + - name: Install extra tools (Prettier via GitHub npm mirror) shell: bash - run: > - npm install --no-save --no-audit --no-fund 'prettier@>=3.3.3' - 'prettier-plugin-toml@>=0.13.0' + run: | + pixi run npm config set registry https://registry.npmjs.org/ + pixi run install-prettier # Check the validity of pyproject.toml - name: Check validity of pyproject.toml id: check_pyproject continue-on-error: true shell: bash - run: validate-pyproject pyproject.toml + run: pixi run check-pyproject # Check code linting with Ruff in the project root - name: Check code linting id: check_code_linting continue-on-error: true shell: bash - run: ruff check . + run: pixi run check-lint-py - name: Suggestion to fix code linting issues (*.py files) if: steps.check_code_linting.outcome == 'failure' shell: bash - run: > - echo "In project root run 'ruff check . --fix' and commit changes to - fix issues." + run: echo "In project root run 'pixi run lint-py' and commit changes" # Check code formatting with Ruff in the project root - name: Check code formatting id: check_code_formatting continue-on-error: true shell: bash - run: ruff format . --check + run: pixi run check-format-py - name: Suggestion to fix code formatting issues (*.py files) if: steps.check_code_formatting.outcome == 'failure' shell: bash - run: > - echo "In project root run 'ruff format .' and commit changes to fix - issues." + run: echo "In project root run 'pixi run format-py' and commit changes" # Check formatting of Markdown, YAML, TOML, etc. files with Prettier in # the project root @@ -124,108 +115,101 @@ jobs: id: check_others_formatting continue-on-error: true shell: bash - run: npx prettier . --check --config=prettierrc.toml + run: pixi run check-format-non-py - name: Suggestion to fix non-code formatting issues (*.md, *.yml, etc.) if: steps.check_others_formatting.outcome == 'failure' shell: bash - run: > - echo "In project root run 'npx prettier . --write - --config=prettierrc.toml' and commit changes to fix issues." + run: + echo "In project root run 'pixi run format-non-py' and commit changes" - name: Force fail if any of the previous steps failed if: | steps.check_pyproject.outcome == 'failure' || steps.check_code_linting.outcome == 'failure' || - steps.check_code_formatting.outcome == 'failure' || + steps.check_code_formatting.outcome == 'failure' || steps.check_others_formatting.outcome == 'failure' run: exit 1 - # Job 2: Test code and upload coverage to Codecov. + # Job 2: Test code + # TODO: Add coverage reporting with upload to Codecov? run-tests: needs: code-quality # previous job needs to be finished first strategy: fail-fast: false matrix: - os: [ubuntu-24.04, windows-2022, macos-13, macos-14] - python-version: ['3.11', '3.12', '3.13'] + os: [ubuntu-24.04, macos-13, macos-14, windows-2022] runs-on: ${{ matrix.os }} + env: + PIXI_ENVS: 'py311-dev py312-dev py313-dev' + steps: - name: Checkout repository uses: actions/checkout@v4 with: fetch-depth: '0' # full history with tags to get the version number by versioningit - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - shell: bash - run: python -m pip install --upgrade pip - - - name: Set up conda (Windows only) - if: runner.os == 'Windows' - uses: s-weigand/setup-conda@v1 + - name: Set up pixi (incl. environments and dependencies) + uses: prefix-dev/setup-pixi@v0.9.0 with: - update-conda: true - python-version: ${{ matrix.python-version }} - conda-channels: conda-forge + environments: ${{ env.PIXI_ENVS }} + run-install: true + frozen: true + cache: false + post-cleanup: false - - name: Install libcblas for pdffit (Windows only) - if: runner.os == 'Windows' - shell: bash - run: conda install -y -c conda-forge libcblas - - - name: Install Python dependencies - shell: bash - run: python -m pip install .'[dev,visualization]' - - - name: Run Python unit tests (using src/ as the source dir) + - name: Run unit tests shell: bash run: | - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest tests/unit_tests/ --color=yes + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + pixi run -e $env unit-tests + done - - name: Run Python functional tests (using src/ as the source dir) + - name: Run functional tests shell: bash run: | - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest tests/functional_tests/ --color=yes -n auto + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + pixi run -e $env func-tests + done - # Ensures a consistent high version like 999.0.0 when not on a tagged commit + # Delete all local tags when not on a tagged commit to force versioningit + # to fall back to the configured default-tag, which is '999.0.0' in our case. # This is needed for testing the package in the next job, as its version # must be higher than the PyPI version for pip to prefer the local version. - - name: Inject fallback version tag if not on a real tag - shell: bash - run: | - if ! git describe --tags --match "v*" --exact-match > /dev/null 2>&1; then - echo "Not on release tag β€” applying fallback 'v999.0.0'" - git tag v999.0.0 - else - echo "On a valid tag" - fi - - - name: Create Python package for the next job + - name: Force using versioningit default tag (non tagged release) + if: startsWith(github.ref , 'refs/tags/v') != true + run: git tag --delete $(git tag) + + - name: Move tests inside the package shell: bash - run: python -m build --wheel --outdir dist + run: mv tests/ src/easydiffraction/tests/ - - name: - Upload zipped Python package (with tests and ${{ env.NOTEBOOKS_DIR }}) - for next job + - name: Create Python package + shell: bash + run: | + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + pixi run -e $env build + env_prefix="${env%%-*}" + echo "πŸ“¦ Moving built wheel to dist/$env_prefix/" + pixi run mkdir -p dist/$env_prefix + pixi run mv dist/*.whl dist/$env_prefix/ + done + + # More than one file/dir need to be specified in 'path', to preserve the + # structure of the dist/ directory, not only its contents. + - name: Upload Python package for the next job uses: actions/upload-artifact@v4 with: - name: - edl_py${{ matrix.python-version }}_${{ matrix.os }}_${{ runner.arch - }} + name: edl_${{ matrix.os }}_${{ runner.arch }} path: | - dist/*.whl - tests/ - ${{ env.NOTEBOOKS_DIR }}/ + dist/ + pixi/wheel/pixi.toml if-no-files-found: 'error' compression-level: 0 @@ -236,56 +220,59 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-24.04, windows-2022, macos-13, macos-14] - python-version: ['3.11', '3.12', '3.13'] + os: [ubuntu-24.04, macos-13, macos-14, windows-2022] runs-on: ${{ matrix.os }} - steps: - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - run: python -m pip install --upgrade pip - - - name: Set up conda (Windows only) - if: runner.os == 'Windows' - uses: s-weigand/setup-conda@v1 - with: - update-conda: true - python-version: ${{ matrix.python-version }} - conda-channels: conda-forge - - - name: Install libcblas for pdffit (Windows only) - if: runner.os == 'Windows' - shell: bash - run: conda install -y -c conda-forge libcblas + env: + PIXI_PROJECT_MANIFEST: 'pixi/wheel/pixi.toml' + PIXI_ENVS: 'py311-wheel py312-wheel py313-wheel' + steps: - name: - Download zipped Python package (with tests and ${{ env.NOTEBOOKS_DIR - }}) from previous job + Download zipped Python package (incl. extra files) from previous job uses: actions/download-artifact@v4 with: # name or path are taken from the upload step of the previous job - name: - edl_py${{ matrix.python-version }}_${{ matrix.os }}_${{ runner.arch - }} + name: edl_${{ matrix.os }}_${{ runner.arch }} path: . # directory to extract downloaded zipped artifacts - # The local version must be higher than the PyPI version for pip to - # prefer the local version. So, after a new release and a new tag, - # remember to merge the master branch with the develop branch, - # and then create a new feature branch from the develop branch. - - name: Install Python package from previous job with all extras + - name: Move pixi/wheel/pixi.toml to project root shell: bash - run: > - pip install 'easydiffraction[dev,visualization]' --find-links=dist + run: mv pixi/wheel/pixi.toml . + + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 + with: + environments: ${{ env.PIXI_ENVS }} + run-install: true + cache: false + post-cleanup: false - - name: Run Python unit tests (using installed package) + - name: Add easydiffraction package from the built wheel shell: bash - run: python -m pytest tests/unit_tests/ --color=yes + run: | + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + env_prefix="${env%%-*}" + echo "πŸ“¦ Looking for wheel in dist/$env_prefix/" + whl_path="$(python3 -c "import pathlib; w = sorted(pathlib.Path('dist/${env_prefix}').glob('*.whl')); print(w[0].resolve().as_uri())")" + echo "πŸ“¦ Adding easydiffraction from: $whl_path" + pixi add --feature $env_prefix --pypi "easydiffraction[dev,visualization] @ $whl_path" + pixi run -e $env easydiffraction version + done + + - name: Run unit tests (using built package from previous job) + shell: bash + run: | + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + pixi run -e $env unit-tests + done - - name: Run Python functional tests (using installed package) + - name: Run functional tests (using built package from previous job) shell: bash - run: python -m pytest tests/functional_tests/ --color=yes -n auto + run: | + for env in ${{ env.PIXI_ENVS }}; do + echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" + pixi run -e $env func-tests + done diff --git a/.github/workflows/test-package-pypi.yaml b/.github/workflows/test-package-pypi.yaml new file mode 100644 index 00000000..2b923762 --- /dev/null +++ b/.github/workflows/test-package-pypi.yaml @@ -0,0 +1,54 @@ +name: Test unpinned package from PyPI + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: + ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + test-package: + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 + with: + run-install: false + cache: false + post-cleanup: false + + - name: Download the pixi configuration file for EasyDiffraction + run: + curl -LO + https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml + + - name: Create the environment and install dependencies + run: pixi install + + - name: Run unit tests to verify the installation + run: pixi run unit-tests + + - name: Run functional tests to verify the installation + run: pixi run func-tests + + - name: List the available EasyDiffraction tutorials + run: pixi run list-tutorials + + - name: Fetch the EasyDiffraction tutorials + run: pixi run fetch-tutorials + + - name: Test tutorials as notebooks + run: pixi run test-notebooks diff --git a/.github/workflows/test-tutorials-nightly.yaml b/.github/workflows/test-tutorials-nightly.yaml new file mode 100644 index 00000000..34980ce9 --- /dev/null +++ b/.github/workflows/test-tutorials-nightly.yaml @@ -0,0 +1,10 @@ +name: Test tutorials nightly (develop) + +on: + schedule: + - cron: '0 0 * * *' # Every midnight UTC + +jobs: + call-tutorials: + if: github.ref_name == 'develop' + uses: ./.github/workflows/test-tutorials.yaml diff --git a/.github/workflows/test-tutorials.yaml b/.github/workflows/test-tutorials.yaml index 5b04b176..63e3cbf1 100644 --- a/.github/workflows/test-tutorials.yaml +++ b/.github/workflows/test-tutorials.yaml @@ -14,9 +14,10 @@ on: pull_request: branches: - '**' - # Trigger the workflow on a schedule (every day at midnight) - schedule: - - cron: '0 0 * * *' + # Trigger the workflow on workflow_call (to be called from other workflows) + # Needed, as standard schedule triggers the master branch only, but we want + # to run this workflow on develop branch. + workflow_call: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: @@ -27,22 +28,12 @@ concurrency: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true -env: - # Set the environment variables to be used in all jobs defined in this workflow - # Set the CI_BRANCH environment variable to be the branch name - # Set the NOTEBOOKS_DIR environment var to be the dir of Jupyter notebooks - # Set PYTHONIOENCODING to utf-8 to avoid encoding issues on Windows - CI_BRANCH: ${{ github.head_ref || github.ref_name }} - NOTEBOOKS_DIR: tutorials - PYTHONIOENCODING: utf-8 - jobs: # Job 1: Check code quality and consistency code-quality: strategy: matrix: os: [ubuntu-latest] - python-version: ['3.13'] runs-on: ${{ matrix.os }} @@ -50,43 +41,33 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - shell: bash - run: python -m pip install --upgrade pip - - - name: Install Python dependencies - shell: bash - run: python -m pip install .'[dev]' - - # Check Jupyter notebooks with nbQA in the tutorials directory - - name: Convert ${{ env.NOTEBOOKS_DIR }}/*.py to *.ipynb + environments: >- + py313-dev + activate-environment: py313-dev + run-install: true + frozen: true + cache: false + post-cleanup: false + + - name: Convert tutorial scripts to notebooks shell: bash - run: | - jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb - nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb - python tools/prepare_notebooks.py ${{ env.NOTEBOOKS_DIR }}/ + run: pixi run make-notebooks - - name: Check Jupyter notebooks formatting - id: check_notebooks + - name: Check notebooks formatting + id: check_formatting continue-on-error: true shell: bash - run: nbqa ruff ${{ env.NOTEBOOKS_DIR }}/ + run: pixi run check-format-notebooks - - name: Suggestion to fix notebook formatting issues (*.ipynb files) - if: steps.check_notebooks.outcome == 'failure' + - name: Suggestion to fix notebook formatting + if: steps.check_formatting.outcome == 'failure' shell: bash - run: > - echo "In project root run 'nbqa ruff ${{ env.NOTEBOOKS_DIR }}/ --fix' - and commit changes to fix issues." - - - name: Force fail if the previous step failed - if: steps.check_notebooks.outcome == 'failure' - run: exit 1 + run: | + echo "Run 'pixi run fix-format-notebooks' and commit changes." + exit 1 # Job 2: Test tutorials as Python scripts and Jupyter Notebooks test-tutorials: @@ -95,8 +76,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-24.04, windows-2022, macos-13, macos-14] - python-version: ['3.13'] + os: [ubuntu-latest, macos-latest, windows-latest] runs-on: ${{ matrix.os }} @@ -104,58 +84,25 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade package installer for Python - shell: bash - run: python -m pip install --upgrade pip - - - name: Set up conda (Windows only) - if: runner.os == 'Windows' - uses: s-weigand/setup-conda@v1 + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 with: - update-conda: true - python-version: ${{ matrix.python-version }} - conda-channels: conda-forge - - - name: Install libcblas for pdffit (Windows only) - if: runner.os == 'Windows' - shell: bash - run: conda install -y -c conda-forge libcblas - - - name: Install Python dependencies + environments: >- + py313-dev + activate-environment: py313-dev + run-install: true + frozen: true + cache: false + post-cleanup: false + + - name: Test tutorials as python scripts shell: bash - run: python -m pip install .'[dev,visualization]' + run: pixi run test-scripts - # Check if tutorials as python scripts run without errors - # Run all Python scripts in the folder tutorials/ in parallel - # -n 1: run one script per Python invocation - # -P 0: run as many in parallel as you have cores (auto mode) - - name: Run tutorials as python scripts - shell: bash - run: | - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - find ${{ env.NOTEBOOKS_DIR }}/ -name "*.py" | xargs -n 1 -P 0 python - - # Check if tutorials as Jupyter Notebooks run without errors - # Convert all Python scripts in the folder tutorials/ to Jupyter Notebooks - # Strip output from Jupyter Notebooks and rename cell ids - # Replace '# !pip' with '!pip' in Jupyter Notebooks - # Run all Jupyter Notebooks in the folder tutorials/ in parallel - # -n auto: run as many in parallel as you have cores (auto mode) - # --nbmake-timeout=600: set timeout to 600 seconds - - name: Convert ${{ env.NOTEBOOKS_DIR }}/*.py to *.ipynb + - name: Convert tutorial scripts to notebooks shell: bash - run: | - jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb - nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb - python tools/prepare_notebooks.py ${{ env.NOTEBOOKS_DIR }}/ + run: pixi run make-notebooks - - name: Run tutorials as Jupyter Notebooks (using src/ as the source dir) + - name: Test tutorials as notebooks shell: bash - run: | - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest --nbmake ${{ env.NOTEBOOKS_DIR }}/ --nbmake-timeout=600 --color=yes -n auto + run: pixi run test-notebooks diff --git a/.github/workflows/validate-pixi.yaml b/.github/workflows/validate-pixi.yaml new file mode 100644 index 00000000..c4a8fbf9 --- /dev/null +++ b/.github/workflows/validate-pixi.yaml @@ -0,0 +1,75 @@ +name: Validate installation via Pixi + +on: + # Trigger the workflow on push + push: + # Every branch + branches: + - '**' + # But do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: + - 'v*' + # Trigger the workflow on pull request + pull_request: + branches: + - '**' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: + ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + # CI_BRANCH - the branch name (used in mkdocs.yml) + # GITHUB_TOKEN - to authenticate on GitHub (e.g. increase API rate limit) + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + +jobs: + validate-pixi: + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.9.0 + with: + run-install: false + cache: false + post-cleanup: false + + - name: Initialize a new Pixi project for EasyDiffraction + run: pixi init + + - name: Add Conda dependencies + run: pixi add python==3.13 jupyterlab pixi-kernel libcblas + + - name: Add PyPI dependencies + run: > + pixi add --pypi "easydiffraction[visualization] @ + git+https://github.com/easyscience/diffraction-lib@${{env.CI_BRANCH}}" + + - name: Add a task to run EasyDiffraction from the command line + run: pixi task add easydiffraction "python -m easydiffraction" + + - name: List the available EasyDiffraction tutorials + run: pixi run easydiffraction list-tutorials + + - name: Fetch the EasyDiffraction tutorials + run: pixi run easydiffraction fetch-tutorials + + - name: Test execution of one of the tutorial notebooks + shell: bash + run: > + pixi run jupyter nbconvert --to notebook --execute + tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb --inplace + --ExecutePreprocessor.kernel_name=pixi-kernel-python3 --log-level=WARN diff --git a/.gitignore b/.gitignore index 9150f6cb..02bb32e1 100644 --- a/.gitignore +++ b/.gitignore @@ -4,6 +4,9 @@ __pycache__ .coverage .pyc +# Pixi +.pixi + # Jupyter Notebooks .ipynb_checkpoints diff --git a/.prettierignore b/.prettierignore index c2c13c52..f599168f 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1 +1,2 @@ -.pixi \ No newline at end of file +# Pixi +pixi.lock diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md index 62e6c02b..02f0b8ad 100644 --- a/DEVELOPMENT.md +++ b/DEVELOPMENT.md @@ -2,6 +2,15 @@ This is an example of a workflow that describes the development process. +## Installation and setup with Pixi + +- Install Pixi by following the instructions on the + [official Pixi Installation Guide](https://pixi.sh/latest/installation). +- Clone repositories with assets for building documentation + ```bash + git clone https://github.com/easyscience/assets-docs.git + git clone https://github.com/easyscience/assets-branding.git + ``` - Clone EasyDiffraction library repository ```bash git clone https://github.com/easyscience/diffraction-lib @@ -10,156 +19,99 @@ This is an example of a workflow that describes the development process. ```bash cd diffraction-lib ``` -- Checkout/switch to the `develop` branch - ```bash - git checkout develop - ``` -- Create a new branch from the current one - ```bash - git checkout -b new-feature - ``` -- Create Python environment and activate it +- Create the environment defined in `pixi.toml` and install all necessary + dependencies: ```bash - python3 -m venv .venv - source .venv/bin/activate + pixi install ``` -- Upgrade PIP - package installer for Python +- Install Prettier for non-Python files formatting ```bash - python -m pip install --upgrade pip + pixi run install-prettier ``` -- Install easydiffraction from root with `dev` extras for development, - `visualization` extras for Jupyter notebooks and `docs` extras for building - documentation - ```bash - pip install '.[dev,visualization,docs]' - ``` -- Install pycrysfml (pyenv python 3.12, macOS 14, Apple Silicon): + +## Making changes + +- Checkout/switch to the `develop` branch ```bash - # Install from local wheel - pip install deps/pycrysfml-0.1.6-py312-none-macosx_14_0_arm64.whl - # Try to import the module - python -c "from pycrysfml import cfml_py_utilities" - # If previous step failed, check the linked libraries - otool -L .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so - # If the library is linked to the wrong Python version, you can fix it with: - install_name_tool -change `python3-config --prefix`/Python `python3-config --prefix`/lib/libpython3.12.dylib .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so - # Check again the linked Python library - otool -L .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so - # Try to import the module again - python -c "from pycrysfml import cfml_py_utilities" + git checkout develop ``` -- Install CBLAS library, required for using the Pair Distribution Function - feature. This step is required only on Windows. +- Create a new branch from the `develop` one ```bash - # Install from the conda-forge channel - conda install libcblas -c conda-forge - # Try to import the module - python -c "import diffpy.pdffit2" + git checkout -b new-feature ``` - Make changes in the code ```bash ... ``` -- Check the validity of pyproject.toml - ```bash - validate-pyproject pyproject.toml - ``` -- Run Ruff - Python linter and code formatter (configuration is in - pyproject.toml)
Linting (overwriting files) - ```bash - ruff check . --fix - ``` - Formatting (overwriting files) + +## Checking code quality and testing + +- Check and fix code quality (configuration is in `pyproject.toml` and + `prettierrc.toml`) ```bash - ruff format . + pixi run code-quality ``` -- Install and run Prettier - code formatter for Markdown, YAML, TOML, etc. files - (configuration in prettierrc.toml)
Formatting (overwriting files) +- Run unit tests ```bash - npm install --no-save --no-audit --no-fund 'prettier@>=3.3.3' 'prettier-plugin-toml@>=0.13.0' - npx prettier . --write --config=prettierrc.toml + pixi run unit-tests ``` -- Run python unit tests +- Run functional tests ```bash - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest tests/unit_tests/ --color=yes + pixi run func-tests ``` -- Run python functional tests +- Test tutorials as python scripts ```bash - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest tests/functional_tests/ --color=yes -n auto + pixi run test-scripts ``` -- Run tutorials as python scripts +- Convert tutorial scripts to notebooks ```bash - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - find tutorials/ -name "*.py" | xargs -n 1 -P 0 python + pixi run make-notebooks ``` -- Run tutorials/_.py to _.ipynb +- Test tutorials as notebooks ```bash - jupytext tutorials/*.py --from py:percent --to ipynb - nbstripout tutorials/*.ipynb + pixi run test-notebooks ``` -- Run tutorials as Jupyter Notebooks + +## Building and checking documentation with MkDocs + +- Move notebooks to docs/tutorials ```bash - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto + pixi run move-notebooks-to-docs ``` - Add extra files to build documentation (from `../assets-docs/` and `../assets-branding/` directories) - ```bash - cp -R ../assets-docs/docs/assets/ docs/assets/ - cp -R ../assets-docs/includes/ includes/ - cp -R ../assets-docs/overrides/ overrides/ - - mkdir -p docs/assets/images/ - cp ../assets-branding/easydiffraction/hero/dark.png docs/assets/images/hero_dark.png - cp ../assets-branding/easydiffraction/hero/light.png docs/assets/images/hero_light.png - cp ../assets-branding/easydiffraction/logos/dark.svg docs/assets/images/logo_dark.svg - cp ../assets-branding/easydiffraction/logos/light.svg docs/assets/images/logo_light.svg - cp ../assets-branding/easydiffraction/icons/color.png docs/assets/images/favicon.png - - mkdir -p overrides/.icons/ - cp ../assets-branding/easydiffraction/icons/bw.svg overrides/.icons/easydiffraction.svg - cp ../assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg - - jupytext tutorials/*.py --from py:percent --to ipynb - nbstripout tutorials/*.ipynb - cp tutorials/*.ipynb docs/tutorials/ - cp -R tutorials/data docs/tutorials/ - - python tools/create_mkdocs-yml.py + pixi run add-assets-to-docs ``` - -- Build documentation with MkDocs - static site generator +- Create mkdocs.yml file + ```bash + pixi run create-mkdocs-yml + ``` +- Build documentation ```bash - export JUPYTER_PLATFORM_DIRS=1 - export PYTHONWARNINGS="ignore::RuntimeWarning" - export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}" - mkdocs serve + pixi run build-docs ``` - Test the documentation locally (built in the `site/` directory). E.g., on macOS, open the site in the default browser via the terminal - ```console + ```bash open http://127.0.0.1:8000 ``` -- Clean up after building documentation - ```console - rm -rf site/ - rm -rf docs/assets/ - rm -rf docs/tutorials/*.py - rm -rf docs/tutorials/*.ipynb - rm -rf includes/ - rm -rf overrides/ - rm -rf node_modules/ - rm mkdocs.yml +- Clean up after checking documentation + ```bash + pixi run cleanup-docs ``` + +## Committing and pushing changes + - Commit changes - ```console + ```bash git add . git commit -m "Add new feature" ``` - Push the new branch to a remote repository - ```console + ```bash git push -u origin new-feature ``` +- Create a pull request on + [EasyScience GitHub repository](https://github.com/easyscience/diffraction-lib/pulls) + and request a review from team members diff --git a/docs/installation-and-setup/index.md b/docs/installation-and-setup/index.md index 25220f91..3b81e130 100644 --- a/docs/installation-and-setup/index.md +++ b/docs/installation-and-setup/index.md @@ -6,8 +6,8 @@ icon: material/cog-box ## Requirements -EasyDiffraction is a cross-platform Python library compatible with **Python 3.10 -through 3.12**. +EasyDiffraction is a cross-platform Python library compatible with **Python 3.11 +through 3.13**. Make sure Python is installed on your system before proceeding with the installation. @@ -19,56 +19,54 @@ and recreate the environment. #### Creating and Activating a Virtual Environment: + + - Create a new virtual environment: - ```console + ```bash python3 -m venv venv ``` - - - - Activate the environment: === ":material-apple: macOS" - ```console + ```bash . venv/bin/activate ``` === ":material-linux: Linux" - ```console + ```bash . venv/bin/activate ``` === ":fontawesome-brands-windows: Windows" - ```console + ```bash . venv/Scripts/activate # Windows with Unix-like shells .\venv\Scripts\activate.bat # Windows with CMD .\venv\Scripts\activate.ps1 # Windows with PowerShell ``` - - - The terminal should now show `(venv)`, indicating that the virtual environment is active. + + #### Deactivating and Removing the Virtual Environment: + + - Exit the environment: - ```console + ```bash deactivate ``` - - - - If this environment is no longer needed, delete it: === ":material-apple: macOS" - ```console + ```bash rm -rf venv ``` === ":material-linux: Linux" - ```console + ```bash rm -rf venv ``` === ":fontawesome-brands-windows: Windows" - ```console + ```bash rmdir /s /q venv ``` @@ -88,32 +86,32 @@ We recommend installing the latest release of EasyDiffraction with the visualization of charts and tables. This can be especially useful for running the Jupyter Notebook examples. To do so, use the following command: -```console +```bash pip install 'easydiffraction[visualization]' ``` If only the core functionality is needed, the library can be installed simply with: -```console +```bash pip install easydiffraction ``` To install a specific version of EasyDiffraction, e.g., 1.0.3: -```console +```bash pip install 'easydiffraction==1.0.3' ``` To upgrade to the latest version: -```console +```bash pip install --upgrade --force-reinstall easydiffraction ``` To check the installed version: -```console +```bash pip show easydiffraction ``` @@ -124,13 +122,13 @@ for testing. To install EasyDiffraction from, e.g., the `develop` branch of GitHub: -```console +```bash pip install git+https://github.com/easyscience/diffraction-lib@develop ``` To include extra dependencies (e.g., visualization): -```console +```bash pip install 'easydiffraction[visualization] @ git+https://github.com/easyscience/diffraction-lib@develop' ``` @@ -159,28 +157,28 @@ them interactively in two ways: To run tutorials locally, install **Jupyter Notebook** or **JupyterLab**. Here are the steps to follow in the case of **Jupyter Notebook**: -- Install Jupyter Notebook: - ```console - pip install notebook +- Install Jupyter Notebook and IPython kernel: + ```bash + pip install notebook ipykernel ``` -- Download the latest EasyDiffraction tutorial examples from GitHub, e.g., using - curl: - ```console - curl --location --remote-name https://github.com/easyscience/diffraction-lib/releases/latest/download/examples.zip +- Add the virtual environment as a Jupyter kernel + ```bash + python -m ipykernel install --user --name=venv --display-name "EasyDiffraction Python kernel" ``` -- Unzip the archive: - ```console - unzip examples.zip +- Download the EasyDiffraction tutorials from GitHub Releases: + ```bash + python -m easydiffraction fetch-tutorials ``` - Launch the Jupyter Notebook server in the `examples/` directory: - ```console - jupyter notebook examples/ + ```bash + jupyter notebook tutorials/ ``` - In your web browser, go to: - ```console + ```bash http://localhost:8888/ ``` -- Open one of the `*.ipynb` files. +- Open one of the `*.ipynb` files and select the `EasyDiffraction Python kernel` + to get started. ### Run Tutorials via Google Colab @@ -195,3 +193,51 @@ To use Google Colab: This is the fastest way to start experimenting with EasyDiffraction, without setting up Python on your system. + +## Installing with Pixi alternative { #installing-with-pixi data-toc-label="Installing with Pixi" } + +[Pixi](https://pixi.sh) is a modern package and environment manager for Python +and Conda-compatible packages. It simplifies dependency management, environment +isolation, and reproducibility. + +The following simple steps provide an alternative setup method for +EasyDiffraction using Pixi, replacing the traditional virtual environment +approach. + + + +- Install Pixi by following the instructions on the + [official Pixi Installation Guide](https://pixi.sh/latest/installation). +- Create a dedicated directory for the EasyDiffraction and navigate into it: + ```bash + mkdir easydiffraction + cd easydiffraction + ``` +- Download the pixi configuration file for EasyDiffraction: + + === "curl" + ```bash + curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml + ``` + === "wget" + ```bash + wget https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml + ``` + +- Create the environment defined in `pixi.toml` and install all necessary + dependencies: + ```bash + pixi install + ``` +- Fetch the EasyDiffraction tutorials to the `tutorials/` directory: + ```bash + pixi run easydiffraction fetch-tutorials + ``` +- Start JupyterLab in the `tutorials/` directory to access the notebooks: + ```bash + pixi run jupyter lab tutorials/ + ``` +- Your web browser should open automatically. Click on one of the `*.ipynb` + files and select the `Python (Pixi)` kernel to get started. + + diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index b8a41df8..ba5f16e8 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -27,9 +27,10 @@ extra: name: EasyDiffraction Library Source Code on GitHub # Jupyter notebooks -#plugins: -# - mkdocs-jupyter: -# execute_ignore: +plugins: + - mkdocs-jupyter: + execute_ignore: + - '*.ipynb' # Do not execute any notebooks # - 'quick*.ipynb' # - 'basic*.ipynb' # - 'advanced*.ipynb' diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..659680d7 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,17496 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: 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BSD + purls: + - pkg:pypi/zstandard?source=hash-mapping + size: 347160 + timestamp: 1756075776191 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 00000000..4d9f2b26 --- /dev/null +++ b/pixi.toml @@ -0,0 +1,165 @@ +[workspace] +# Channels used to fetch the packages from +channels = ["conda-forge"] +platforms = [ + "win-64", + "linux-64", + "osx-64", + "osx-arm64", +] # Platforms supported for lock file (pixi.lock) + +########## +# FEATURES +########## + +# Default feature configuration + +[dependencies] # == [feature.default.dependencies] +libcblas = "*" # CBLAS library for linear algebra. Needed for pdffit2 on Windows +pip = "*" # Needed to install from PyPI +jupyterlab = "*" # JupyterLab for notebooks +pixi-kernel = "*" # IPython kernel for Jupyter + +# Extra features for different Python versions + +# These features are used to specify the Python version for the environment. +# Each feature corresponds to a specific Python version. + +[feature.py311.dependencies] +python = "3.11.*" + +[feature.py312.dependencies] +python = "3.12.*" + +[feature.py313.dependencies] +python = "3.13.*" + +# This feature is used for local development with editable installation of +# easydiffraction. Effectively, the source code defined in the pyproject.toml +# will be used directly without installing the package. The changes are +# reflected immediately without needing to reinstall the package. +# This feature should be deleted in CI, because otherwise the pixi lock file +# created locally will be considered as outdated in CI. + +[feature.ed-local-editable.pypi-dependencies] +easydiffraction = { editable = true, path = ".", extras = [ + "dev", + "visualization", + "docs", +] } + +# This feature is used for development in CI, where the easydiffraction +# is installed from the local source code defined in the pyproject.toml, but +# not in editable mode. This ensures that the lock file update locally will +# work in CI. + +[feature.ed-local.pypi-dependencies] +easydiffraction = { path = ".", extras = ["dev", "visualization"] } + +# This feature is used to build the documentation, where the package is +# installed from PyPI with the additional dependencies needed for building +# the docs. + +[feature.ed-local-with-docs.pypi-dependencies] +easydiffraction = { path = ".", extras = ["dev", "visualization", "docs"] } + +# This feature is used when the easydiffraction package is installed from PyPI. + +[feature.ed-pypi.pypi-dependencies] +easydiffraction = { version = "*", extras = ["dev", "visualization"] } + +# This feature is used to install Node.js and Prettier for formatting +# non-Python files. + +[feature.nodejs.dependencies] +nodejs = "*" # Needed for prettier + +############## +# ENVIRONMENTS +############## + +[environments] + +# The `default` environment is always included in the lock file, so there is no +# need to specify it explicitly in the environments section. + +py311-dev = { features = ["py311", "ed-local", "nodejs"] } +py312-dev = { features = ["py312", "ed-local", "nodejs"] } +py313-dev = { features = ["py313", "ed-local", "nodejs"] } + +py313-docs = { features = ["py313", "ed-local-with-docs"] } + +py313-prod = { features = ["py313", "ed-pypi"] } + +default = { features = ["py313", "ed-local-editable"] } + +####### +# TASKS +####### + +[tasks] + +# Testing tasks +unit-tests = "python -m pytest tests/unit_tests/ --color=yes -v" +func-tests = "python -m pytest tests/functional_tests/ --color=yes -n auto -v" +unit-tests-package = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" +func-tests-package = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" +test-notebooks = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v' +test-scripts = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v' +test = { depends-on = ["unit-tests", "func-tests"] } + +# Check code quality tasks +check-pyproject = "python -m validate_pyproject pyproject.toml" +check-lint-py = "python -m ruff check ." +check-format-py = "python -m ruff format . --check" +check-format-non-py = "npx prettier . --list-different --config=prettierrc.toml" +check-format-notebooks = 'nbqa ruff tutorials/' + +# Fix code quality tasks +lint-py = "python -m ruff check . --fix" +format-py = "python -m ruff format ." +format-non-py = "npx prettier . --list-different --write --config=prettierrc.toml" +fix-format-notebooks = 'nbqa ruff tutorials/ --fix' +code-quality = { depends-on = [ + "check-pyproject", + "lint-py", + "format-py", + "format-non-py", +] } + +# Notebook management tasks +scripts-to-notebooks = 'jupytext tutorials/*.py --from py:percent --to ipynb' +stripout-notebooks = 'nbstripout tutorials/*.ipynb' +tweak-notebooks = 'python tools/tweak_notebooks.py tutorials/' +make-notebooks = { depends-on = [ + "scripts-to-notebooks", + "stripout-notebooks", + "tweak-notebooks", +] } +remove-notebooks = 'rm -f tutorials/*.ipynb' +run-notebooks = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v' + +# Documentation tasks +add-assets-to-docs = "tools/add_assets_to_docs.sh" +move-notebooks-to-docs = "mv tutorials/*.ipynb docs/tutorials/" +create-mkdocs-yml = "python tools/create_mkdocs_yml.py" +serve-docs = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs serve --dirty' +build-docs = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs build' +cleanup-docs = "tools/cleanup_docs.sh" +setup-docs = { depends-on = [ + "create-mkdocs-yml", + "add-assets-to-docs", + "make-notebooks", + "move-notebooks-to-docs", +] } + +# Other tasks +pre-commit = { depends-on = ["code-quality", "test"] } +build = "python -m build --wheel --outdir dist" +update-spdx = "python tools/update_spdx.py" +install-prettier = "npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml" + +# Shortcuts +easydiffraction = "python -m easydiffraction" +list-tutorials = "python -m easydiffraction list-tutorials" +fetch-tutorials = "python -m easydiffraction fetch-tutorials" diff --git a/pixi/prod/pixi.toml b/pixi/prod/pixi.toml new file mode 100644 index 00000000..c5ac7641 --- /dev/null +++ b/pixi/prod/pixi.toml @@ -0,0 +1,25 @@ +[workspace] +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] + +[dependencies] # == [feature.default.dependencies] +python = "3.13.*" # Python version +libcblas = "*" # CBLAS library for linear algebra. Needed for pdffit2 on Windows +pip = "*" # Needed to install from PyPI +jupyterlab = "*" # JupyterLab for notebooks +pixi-kernel = "*" # IPython kernel for Jupyter + +[pypi-dependencies] +#easydiffraction = { version = "*", extras = ["dev", "visualization"] } +easydiffraction = { git = "https://github.com/easyscience/diffraction-lib.git", branch = "pixi", extras = [ + "dev", + "visualization", +] } + +[tasks] +unit-tests = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" +func-tests = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" +test-notebooks = "python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v" +easydiffraction = "python -m easydiffraction" +list-tutorials = "python -m easydiffraction list-tutorials" +fetch-tutorials = "python -m easydiffraction fetch-tutorials" diff --git a/pixi/wheel/pixi.toml b/pixi/wheel/pixi.toml new file mode 100644 index 00000000..6323f513 --- /dev/null +++ b/pixi/wheel/pixi.toml @@ -0,0 +1,26 @@ +[workspace] +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] + +[dependencies] # = [feature.default.dependencies] +libcblas = "*" +pip = "*" + +[feature.py311.dependencies] +python = "3.11.*" + +[feature.py312.dependencies] +python = "3.12.*" + +[feature.py313.dependencies] +python = "3.13.*" + +[environments] +py311-wheel = { features = ["py311"] } # = ["default", "py311"] +py312-wheel = { features = ["py312"] } # = ["default", "py312"] +py313-wheel = { features = ["py313"] } # = ["default", "py313"] + +[tasks] +easydiffraction = "python -m easydiffraction" +unit-tests = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" +func-tests = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" diff --git a/pycrysfml.md b/pycrysfml.md new file mode 100644 index 00000000..af681478 --- /dev/null +++ b/pycrysfml.md @@ -0,0 +1,26 @@ +## Temporary pycrysfml installation process (pyenv python 3.12, macOS 14, Apple Silicon): + +- Install from local wheel + ```bash + pip install deps/pycrysfml-0.1.6-py312-none-macosx_14_0_arm64.whl + ``` +- Try to import the module + ```bash + python -c "from pycrysfml import cfml_py_utilities" + ``` +- If previous step failed, check the linked libraries + ```bash + otool -L .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so + ``` +- If the library is linked to the wrong Python version, you can fix it with: + ```bash + install_name_tool -change `python3-config --prefix`/Python `python3-config --prefix`/lib/libpython3.12.dylib .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so + ``` +- Check again the linked Python library + ```bash + otool -L .venv/lib/python3.12/site-packages/pycrysfml/crysfml08lib.so + ``` +- Try to import the module again + ```bash + python -c "from pycrysfml import cfml_py_utilities" + ``` diff --git a/pyproject.toml b/pyproject.toml index a0d65abc..22760c35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,8 @@ dependencies = [ 'tabulate', # Pretty-print tabular data for terminal output 'asciichartpy', # ASCII charts for terminal output 'pooch', # Data downloader + 'typer', # Command-line interface creation + 'rich', # Rich text and beautiful formatting in the terminal 'varname', # Variable name introspection 'asteval', # An expression evaluator for Python 'scipy', # Scientific computing library @@ -53,6 +55,7 @@ dev = [ 'validate-pyproject[all]', # Validate pyproject.toml 'versioningit', # Automatic versioning from git tags 'jupytext', # Jupyter notebook text format support + 'jupyterquiz', # Quizzes in Jupyter notebooks ] docs = [ 'mkdocs', # Static site generator @@ -115,7 +118,7 @@ source = 'versioningit' # Use versioningit to manage the version [tool.versioningit.format] distance = '{base_version}+d{distance}' # example: 0.5.8+d3, 1.2.3.post4+d2 dirty = '{base_version}' # example: 0.5.8, 1.2.3.post4 -distance-dirty = '{base_version}+d{distance}' # see 1st example +distance-dirty = '{base_version}+d{distance}' # example: as in distance # Configure how versioningit detects versions from Git # - 'match' ensures it only considers tags starting with 'v' diff --git a/src/easydiffraction/__init__.py b/src/easydiffraction/__init__.py index 38f3258c..b371c23e 100644 --- a/src/easydiffraction/__init__.py +++ b/src/easydiffraction/__init__.py @@ -1,30 +1,111 @@ # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors # SPDX-License-Identifier: BSD-3-Clause -# Analysis -from easydiffraction.analysis.analysis import Analysis +from typing import TYPE_CHECKING -# Experiments -from easydiffraction.experiments.experiment import Experiment -from easydiffraction.experiments.experiments import Experiments +# This is needed for static type checkers like mypy and IDEs to recognize the imports +# without actually importing them at runtime, which helps avoid circular dependencies +# and reduces initial load time. +if TYPE_CHECKING: + # Analysis + from easydiffraction.analysis.analysis import Analysis -# Project management -from easydiffraction.project import Project -from easydiffraction.project import ProjectInfo + # Experiments + from easydiffraction.experiments.experiment import Experiment + from easydiffraction.experiments.experiments import Experiments -# Sample model -from easydiffraction.sample_models.sample_model import SampleModel -from easydiffraction.sample_models.sample_models import SampleModels + # Project management + from easydiffraction.project import Project + from easydiffraction.project import ProjectInfo -# Summary -from easydiffraction.summary import Summary + # Sample model + from easydiffraction.sample_models.sample_model import SampleModel + from easydiffraction.sample_models.sample_models import SampleModels + + # Summary + from easydiffraction.summary import Summary + + # Utils + from easydiffraction.utils.formatting import chapter + from easydiffraction.utils.formatting import paragraph + from easydiffraction.utils.formatting import section + from easydiffraction.utils.utils import download_from_repository + from easydiffraction.utils.utils import fetch_tutorials + from easydiffraction.utils.utils import get_value_from_xye_header + from easydiffraction.utils.utils import list_tutorials + from easydiffraction.utils.utils import show_version + + +# Lazy loading of submodules and classes +# This improves initial import time and reduces memory usage +# when only a subset of functionality is needed. +def __getattr__(name): + if name == 'Analysis': + from easydiffraction.analysis.analysis import Analysis + + return Analysis + elif name == 'Experiment': + from easydiffraction.experiments.experiment import Experiment + + return Experiment + elif name == 'Experiments': + from easydiffraction.experiments.experiments import Experiments + + return Experiments + elif name == 'Project': + from easydiffraction.project import Project + + return Project + elif name == 'ProjectInfo': + from easydiffraction.project import ProjectInfo + + return ProjectInfo + elif name == 'SampleModel': + from easydiffraction.sample_models.sample_model import SampleModel + + return SampleModel + elif name == 'SampleModels': + from easydiffraction.sample_models.sample_models import SampleModels + + return SampleModels + elif name == 'Summary': + from easydiffraction.summary import Summary + + return Summary + elif name == 'chapter': + from easydiffraction.utils.formatting import chapter + + return chapter + elif name == 'section': + from easydiffraction.utils.formatting import section + + return section + elif name == 'paragraph': + from easydiffraction.utils.formatting import paragraph + + return paragraph + elif name == 'download_from_repository': + from easydiffraction.utils.utils import download_from_repository + + return download_from_repository + elif name == 'fetch_tutorials': + from easydiffraction.utils.utils import fetch_tutorials + + return fetch_tutorials + elif name == 'list_tutorials': + from easydiffraction.utils.utils import list_tutorials + + return list_tutorials + elif name == 'get_value_from_xye_header': + from easydiffraction.utils.utils import get_value_from_xye_header + + return get_value_from_xye_header + elif name == 'show_version': + from easydiffraction.utils.utils import show_version + + return show_version + raise AttributeError(f"module 'easydiffraction' has no attribute {name}") -# Utils -from easydiffraction.utils.formatting import chapter -from easydiffraction.utils.formatting import paragraph -from easydiffraction.utils.formatting import section -from easydiffraction.utils.utils import download_from_repository -from easydiffraction.utils.utils import get_value_from_xye_header # Expose the public API __all__ = [ @@ -40,5 +121,8 @@ 'section', 'paragraph', 'download_from_repository', + 'fetch_tutorials', + 'list_tutorials', 'get_value_from_xye_header', + 'show_version', ] diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py new file mode 100644 index 00000000..ead25d9e --- /dev/null +++ b/src/easydiffraction/__main__.py @@ -0,0 +1,34 @@ +import sys + +# Ensure UTF-8 output on all platforms (e.g. Windows with cp1252) +if hasattr(sys.stdout, 'reconfigure'): + sys.stdout.reconfigure(encoding='utf-8') + sys.stderr.reconfigure(encoding='utf-8') + +import typer + +import easydiffraction as ed + +app = typer.Typer(add_completion=False) + + +@app.command('version') +def version(): + """Show easydiffraction version.""" + ed.show_version() + + +@app.command('list-tutorials') +def list_tutorials(): + """List available tutorial notebooks.""" + ed.list_tutorials() + + +@app.command('fetch-tutorials') +def fetch_tutorials(): + """Download and extract tutorial notebooks.""" + ed.fetch_tutorials() + + +if __name__ == '__main__': + app() diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py index f2ce220a..8a3cd958 100644 --- a/src/easydiffraction/analysis/analysis.py +++ b/src/easydiffraction/analysis/analysis.py @@ -216,7 +216,10 @@ def show_free_params(self) -> None: print(paragraph('Free parameters for both sample models (🧩 data blocks) and experiments (πŸ”¬ data blocks)')) render_table( - columns_headers=columns_headers, columns_alignment=columns_alignment, columns_data=dataframe, show_index=True + columns_headers=columns_headers, + columns_alignment=columns_alignment, + columns_data=dataframe, + show_index=True, ) def how_to_access_parameters(self) -> None: @@ -264,7 +267,10 @@ def how_to_access_parameters(self) -> None: print(paragraph('How to access parameters')) render_table( - columns_headers=columns_headers, columns_alignment=columns_alignment, columns_data=columns_data, show_index=True + columns_headers=columns_headers, + columns_alignment=columns_alignment, + columns_data=columns_data, + show_index=True, ) def show_current_calculator(self) -> None: @@ -346,7 +352,11 @@ def show_available_fit_modes(self) -> None: columns_data.append([strategy, description]) print(paragraph('Available fit modes')) - render_table(columns_headers=columns_headers, columns_alignment=columns_alignment, columns_data=columns_data) + render_table( + columns_headers=columns_headers, + columns_alignment=columns_alignment, + columns_data=columns_data, + ) def show_current_fit_mode(self) -> None: print(paragraph('Current fit mode')) @@ -388,7 +398,11 @@ def show_constraints(self) -> None: rows = [[row[header] for header in headers] for row in rows] print(paragraph('User defined constraints')) - render_table(columns_headers=headers, columns_alignment=alignments, columns_data=rows) + render_table( + columns_headers=headers, + columns_alignment=alignments, + columns_data=rows, + ) def apply_constraints(self): if not self.constraints._items: diff --git a/src/easydiffraction/analysis/calculators/calculator_crysfml.py b/src/easydiffraction/analysis/calculators/calculator_crysfml.py index fe5da0e9..c95734fe 100644 --- a/src/easydiffraction/analysis/calculators/calculator_crysfml.py +++ b/src/easydiffraction/analysis/calculators/calculator_crysfml.py @@ -18,7 +18,8 @@ try: from pycrysfml import cfml_py_utilities - print("βœ… 'pycrysfml' calculation engine is successfully imported.") + # TODO: Add the following print to debug mode + # print("βœ… 'pycrysfml' calculation engine is successfully imported.") except ImportError: # TODO: Add the following print to debug mode # print("⚠️ 'pycrysfml' module not found. This calculation engine will not be available.") diff --git a/src/easydiffraction/analysis/calculators/calculator_cryspy.py b/src/easydiffraction/analysis/calculators/calculator_cryspy.py index 40bfb887..5154daaf 100644 --- a/src/easydiffraction/analysis/calculators/calculator_cryspy.py +++ b/src/easydiffraction/analysis/calculators/calculator_cryspy.py @@ -21,7 +21,8 @@ from cryspy.H_functions_global.function_1_cryspy_objects import str_to_globaln from cryspy.procedure_rhochi.rhochi_by_dictionary import rhochi_calc_chi_sq_by_dictionary - print("βœ… 'cryspy' calculation engine is successfully imported.") + # TODO: Add the following print to debug mode + # print("βœ… 'cryspy' calculation engine is successfully imported.") except ImportError: # TODO: Add the following print to debug mode # print("⚠️ 'cryspy' module not found. This calculation engine will not be available.") diff --git a/src/easydiffraction/analysis/calculators/calculator_pdffit.py b/src/easydiffraction/analysis/calculators/calculator_pdffit.py index 342742ea..239e936c 100644 --- a/src/easydiffraction/analysis/calculators/calculator_pdffit.py +++ b/src/easydiffraction/analysis/calculators/calculator_pdffit.py @@ -17,7 +17,8 @@ from diffpy.structure.parsers.p_cif import P_cif as pdffit_cif_parser redirect_stdout(open(os.path.devnull, 'w')) # silence the C++ engine output - print("βœ… 'pdffit' calculation engine is successfully imported.") + # TODO: Add the following print to debug mode + # print("βœ… 'pdffit' calculation engine is successfully imported.") except ImportError: # TODO: Add the following print to debug mode # print("⚠️ 'pdffit' module not found. This calculation engine will not be available.") diff --git a/src/easydiffraction/utils/utils.py b/src/easydiffraction/utils/utils.py index 15713d0c..2aa4f59e 100644 --- a/src/easydiffraction/utils/utils.py +++ b/src/easydiffraction/utils/utils.py @@ -6,13 +6,21 @@ """ import importlib +import io +import json import os import re +import urllib.request +import zipfile +from importlib.metadata import PackageNotFoundError +from importlib.metadata import version from typing import List +from urllib.parse import urlparse import numpy as np import pandas as pd import pooch +from packaging.version import Version from tabulate import tabulate try: @@ -22,8 +30,25 @@ except ImportError: IPython = None +from easydiffraction.utils.formatting import error +from easydiffraction.utils.formatting import paragraph from easydiffraction.utils.formatting import warning + +def _validate_url(url: str) -> None: + """Validate that a URL uses only safe HTTP/HTTPS schemes. + + Args: + url: The URL to validate. + + Raises: + ValueError: If the URL scheme is not HTTP or HTTPS. + """ + parsed = urlparse(url) + if parsed.scheme not in ('http', 'https'): + raise ValueError(f"Unsafe URL scheme '{parsed.scheme}'. Only HTTP and HTTPS are allowed.") + + # Single source of truth for the data repository branch. # This can be overridden in CI or development environments. DATA_REPO_BRANCH = ( @@ -45,6 +70,9 @@ def download_from_repository( branch: Branch to fetch from. If None, uses DATA_REPO_BRANCH. destination: Directory to save the file into (created if missing). overwrite: Whether to overwrite the file if it already exists. Defaults to False. + + Returns: + None """ file_path = os.path.join(destination, file_name) if os.path.exists(file_path): @@ -70,6 +98,257 @@ def download_from_repository( ) +def package_version(package_name: str) -> str | None: + """ + Get the installed version string of the specified package. + + Args: + package_name (str): The name of the package to query. + + Returns: + str | None: The raw version string (may include local part, e.g., '1.2.3+abc123'), + or None if the package is not installed. + """ + try: + return version(package_name) + except PackageNotFoundError: + return None + + +def stripped_package_version(package_name: str) -> str | None: + """ + Get the installed version of the specified package, stripped of any local version part. + + Returns only the public version segment (e.g., '1.2.3' or '1.2.3.post4'), + omitting any local segment (e.g., '+d136'). + + Args: + package_name (str): The name of the package to query. + + Returns: + str | None: The public version string, or None if the package is not installed. + """ + v_str = package_version(package_name) + if v_str is None: + return None + try: + v = Version(v_str) + return str(v.public) + except Exception: + return v_str + + +def _get_release_info(tag: str | None) -> dict | None: + """ + Fetch release info from GitHub for the given tag (or latest if None). + Uses unauthenticated API by default, but includes GITHUB_TOKEN from the environment + if available to avoid rate limiting. + + Args: + tag (str | None): The tag of the release to fetch, or None for latest. + + Returns: + dict | None: The release info dictionary if retrievable, None otherwise. + """ + if tag is not None: + api_url = f'https://api.github.com/repos/easyscience/diffraction-lib/releases/tags/{tag}' + else: + api_url = 'https://api.github.com/repos/easyscience/diffraction-lib/releases/latest' + try: + _validate_url(api_url) + headers = {} + token = os.environ.get('GITHUB_TOKEN') + if token: + headers['Authorization'] = f'token {token}' + + request = urllib.request.Request(api_url, headers=headers) # noqa: S310 + with urllib.request.urlopen(request) as response: # noqa: S310 + return json.load(response) + except Exception as e: + if tag is not None: + print(error(f'Failed to fetch release info for tag {tag}: {e}')) + else: + print(error(f'Failed to fetch latest release info: {e}')) + return None + + +def _get_tutorial_asset(release_info: dict) -> dict | None: + """ + Given a release_info dict, return the 'tutorials.zip' asset dict, or None. + + Args: + release_info (dict): The release info dictionary. + + Returns: + dict | None: The asset dictionary for 'tutorials.zip' if found, None otherwise. + """ + assets = release_info.get('assets', []) + for asset in assets: + if asset.get('name') == 'tutorials.zip': + return asset + return None + + +def _sort_notebooks(notebooks: list[str]) -> list[str]: + """ + Sorts the list of notebook filenames. + + Args: + notebooks (list[str]): List of notebook filenames. + + Returns: + list[str]: Sorted list of notebook filenames. + """ + return sorted(notebooks) + + +def _extract_notebooks_from_asset(download_url: str) -> list[str]: + """ + Download the tutorials.zip from download_url and return a sorted list of .ipynb file names. + + Args: + download_url (str): URL to download the tutorials.zip asset. + + Returns: + list[str]: Sorted list of .ipynb filenames found in the archive. + """ + try: + _validate_url(download_url) + with urllib.request.urlopen(download_url) as response: # noqa: S310 + with zipfile.ZipFile(io.BytesIO(response.read())) as zip_file: + notebooks = [ + os.path.basename(name) + for name in zip_file.namelist() + if name.endswith('.ipynb') and not name.endswith('/') + ] + return _sort_notebooks(notebooks) + except Exception as e: + print(error(f"Failed to download or parse 'tutorials.zip': {e}")) + return [] + + +def fetch_tutorial_list() -> list[str]: + """ + Return a list of available tutorial notebook filenames from the GitHub release + that matches the installed version of `easydiffraction`, if possible. If the + version-specific release is unavailable, falls back to the latest release. + + This function does not fetch or display the tutorials themselves; it only lists + the notebook filenames (e.g., '01-intro.ipynb', ...) found inside the + 'tutorials.zip' asset of the appropriate GitHub release. + + Returns: + list[str]: A sorted list of tutorial notebook filenames (without directories) + extracted from the corresponding release's tutorials.zip, or an empty list + if unavailable. + """ + version_str = stripped_package_version('easydiffraction') + tag = f'v{version_str}' if version_str is not None else None + release_info = _get_release_info(tag) + # Fallback to latest if tag fetch failed and tag was attempted + if release_info is None and tag is not None: + print(error('Falling back to latest release info...')) + release_info = _get_release_info(None) + if release_info is None: + return [] + tutorial_asset = _get_tutorial_asset(release_info) + if not tutorial_asset: + print(error("'tutorials.zip' not found in the release.")) + return [] + download_url = tutorial_asset.get('browser_download_url') + if not download_url: + print(error("'browser_download_url' not found for tutorials.zip.")) + return [] + return _extract_notebooks_from_asset(download_url) + + +def list_tutorials(): + """ + List available tutorial notebooks. + + Args: + None + + Returns: + None + """ + tutorials = fetch_tutorial_list() + columns_data = [[t] for t in tutorials] + columns_alignment = ['left'] + + released_ed_version = stripped_package_version('easydiffraction') + + print(paragraph(f'πŸ“˜ Tutorials available for easydiffraction v{released_ed_version}:')) + render_table( + columns_data=columns_data, + columns_alignment=columns_alignment, + show_index=True, + ) + + +def fetch_tutorials() -> None: + """ + Download and extract the tutorials ZIP archive from the GitHub release matching the + installed version of `easydiffraction`, if available. If the version-specific release + is unavailable, falls back to the latest release. + + The archive is extracted into the current working directory and then removed. + + Args: + None + + Returns: + None + """ + version_str = stripped_package_version('easydiffraction') + tag = f'v{version_str}' if version_str is not None else None + release_info = _get_release_info(tag) + # Fallback to latest if tag fetch failed and tag was attempted + if release_info is None and tag is not None: + print(error('Falling back to latest release info...')) + release_info = _get_release_info(None) + if release_info is None: + print(error('Unable to fetch release info.')) + return + tutorial_asset = _get_tutorial_asset(release_info) + if not tutorial_asset: + print(error("'tutorials.zip' not found in the release.")) + return + file_url = tutorial_asset.get('browser_download_url') + if not file_url: + print(error("'browser_download_url' not found for tutorials.zip.")) + return + file_name = 'tutorials.zip' + # Validate URL for security + _validate_url(file_url) + + print('πŸ“₯ Downloading tutorial notebooks...') + urllib.request.urlretrieve(file_url, file_name) # noqa: S310 + + print('πŸ“¦ Extracting tutorials to "tutorials/"...') + with zipfile.ZipFile(file_name, 'r') as zip_ref: + zip_ref.extractall() + + print('🧹 Cleaning up...') + os.remove(file_name) + + print('βœ… Tutorials fetched successfully.') + + +def show_version() -> None: + """ + Print the installed version of the easydiffraction package. + + Args: + None + + Returns: + None + """ + current_ed_version = package_version('easydiffraction') + print(paragraph(f'πŸ“˜ Current easydiffraction v{current_ed_version}')) + + def is_notebook() -> bool: """ Determines if the current environment is a Jupyter Notebook. @@ -147,6 +426,10 @@ def render_table( columns_alignment (list): Corresponding text alignment for each column (e.g., 'left', 'center', 'right'). columns_headers (list): List of column headers. show_index (bool): Whether to show the index column. + display_handle: Optional display handle for updating in Jupyter. + + Returns: + None """ # Use pandas DataFrame for Jupyter Notebook rendering @@ -232,6 +515,13 @@ def make_formatter(align): def render_cif(cif_text, paragraph_title) -> None: """ Display the CIF text as a formatted table in Jupyter Notebook or terminal. + + Args: + cif_text: The CIF text to display. + paragraph_title: The title to print above the table. + + Returns: + None """ # Split into lines and replace empty ones with a ' ' # (non-breaking space) to force empty lines to be rendered in @@ -248,7 +538,10 @@ def render_cif(cif_text, paragraph_title) -> None: print(paragraph_title) # Render the table using left alignment and no headers - render_table(columns_data=columns, columns_alignment=['left']) + render_table( + columns_data=columns, + columns_alignment=['left'], + ) def tof_to_d( diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/functional_tests/__init__.py b/tests/functional_tests/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/functional_tests/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/functional_tests/fitting/__init__.py b/tests/functional_tests/fitting/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/functional_tests/fitting/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/__init__.py b/tests/unit_tests/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/analysis/__init__.py b/tests/unit_tests/analysis/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/analysis/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/analysis/calculators/__init__.py b/tests/unit_tests/analysis/calculators/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/analysis/calculators/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/analysis/collections/__init__.py b/tests/unit_tests/analysis/collections/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/analysis/collections/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/analysis/minimizers/__init__.py b/tests/unit_tests/analysis/minimizers/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/analysis/minimizers/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/core/__init__.py b/tests/unit_tests/core/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/core/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/experiments/__init__.py b/tests/unit_tests/experiments/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/experiments/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/experiments/collections/__init__.py b/tests/unit_tests/experiments/collections/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/experiments/collections/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/experiments/components/__init__.py b/tests/unit_tests/experiments/components/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/experiments/components/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/sample_models/__init__.py b/tests/unit_tests/sample_models/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/sample_models/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/sample_models/collections/__init__.py b/tests/unit_tests/sample_models/collections/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/sample_models/collections/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tests/unit_tests/sample_models/components/__init__.py b/tests/unit_tests/sample_models/components/__init__.py new file mode 100644 index 00000000..6c98b2a1 --- /dev/null +++ b/tests/unit_tests/sample_models/components/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + diff --git a/tools/prepare_docs.sh b/tools/add_assets_to_docs.sh similarity index 65% rename from tools/prepare_docs.sh rename to tools/add_assets_to_docs.sh index 19eb862f..e13eb40a 100755 --- a/tools/prepare_docs.sh +++ b/tools/add_assets_to_docs.sh @@ -1,22 +1,16 @@ -echo "\033[0;33m:::::: Add the extra files from the ../assets-docs\033[0m" +echo "πŸ“₯ Add files from ../assets-docs" cp -R ../assets-docs/docs/assets/ docs/assets/ cp -R ../assets-docs/includes/ includes/ cp -R ../assets-docs/overrides/ overrides/ -echo "\033[0;33m:::::: Add the extra files from the ../assets-branding\033[0m" +echo "πŸ“₯ Add files from ../assets-branding" mkdir -p docs/assets/images/ cp ../assets-branding/easydiffraction/hero/dark.png docs/assets/images/hero_dark.png cp ../assets-branding/easydiffraction/hero/light.png docs/assets/images/hero_light.png cp ../assets-branding/easydiffraction/logos/dark.svg docs/assets/images/logo_dark.svg cp ../assets-branding/easydiffraction/logos/light.svg docs/assets/images/logo_light.svg cp ../assets-branding/easydiffraction/icons/color.png docs/assets/images/favicon.png + mkdir -p overrides/.icons/ cp ../assets-branding/easydiffraction/icons/bw.svg overrides/.icons/easydiffraction.svg cp ../assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg - -echo "\033[0;33m:::::: Add Jupyter notebooks from the project to the docs/\033[0m" -jupytext tutorials/*.py --to ipynb -mv tutorials/*.ipynb docs/tutorials/ - -echo "\033[0;33m:::::: Create the mkdocs.yml configuration file\033[0m" -python tools/create_mkdocs-yml.py diff --git a/tools/build_docs.sh b/tools/build_docs.sh deleted file mode 100755 index c7b189a7..00000000 --- a/tools/build_docs.sh +++ /dev/null @@ -1,4 +0,0 @@ -echo "\033[0;33m:::::: Build docs (http://127.0.0.1:8000)\033[0m" -export JUPYTER_PLATFORM_DIRS=1 -export PYTHONPATH=$(pwd)/src:$PYTHONPATH -mkdocs serve diff --git a/tools/cleanup_docs.sh b/tools/cleanup_docs.sh index b220a0fb..757ec3e4 100755 --- a/tools/cleanup_docs.sh +++ b/tools/cleanup_docs.sh @@ -1,10 +1,10 @@ -echo "\033[0;33m:::::: Clean up after building documentation\033[0m" +echo "🧹 Clean up after building documentation" rm -rf site/ -rm -rf docs/assets/ +rm -rf docs/assets/javascripts +rm -rf docs/assets/stylesheets +rm -rf docs/assets/images/*.png +rm -rf docs/assets/images/*.svg rm -rf includes/ rm -rf overrides/ -rm -rf docs/examples/ -rm -rf node_modules/ +rm -rf docs/tutorials/*.ipynb rm mkdocs.yml -rm package-lock.json -rm package.json diff --git a/tools/create_mkdocs-yml.py b/tools/create_mkdocs_yml.py similarity index 100% rename from tools/create_mkdocs-yml.py rename to tools/create_mkdocs_yml.py diff --git a/tools/install_deps.sh b/tools/install_deps.sh deleted file mode 100755 index e4a86c32..00000000 --- a/tools/install_deps.sh +++ /dev/null @@ -1,2 +0,0 @@ -echo "\033[0;33m:::::: Install Python dependencies\033[0m" -pip install mkdocs mkdocs-material 'mkdocs-autorefs<1.3.0' mkdocs-jupyter mkdocs-plugin-inline-svg mkdocs-markdownextradata-plugin mkdocstrings-python pyyaml diff --git a/tools/run_notebooks.sh b/tools/run_notebooks.sh deleted file mode 100755 index c006f8ff..00000000 --- a/tools/run_notebooks.sh +++ /dev/null @@ -1,6 +0,0 @@ -echo "\033[0;33m:::::: Add src to pythonpath\033[0m" -export PYTHONPATH="${PWD}/src:${PYTHONPATH}" -echo "PYTHONPATH: ${PYTHONPATH}" - -echo "\033[0;33m:::::: Run Jupyter notebooks\033[0m" -pytest --nbmake examples/ --ignore-glob='examples/*emcee*' --nbmake-timeout=600 --color=yes -n=auto diff --git a/tools/test_scripts.py b/tools/test_scripts.py new file mode 100644 index 00000000..928e6a00 --- /dev/null +++ b/tools/test_scripts.py @@ -0,0 +1,25 @@ +"""Test runner for tutorial scripts in the 'tutorials' directory. + +This test discovers and executes all Python scripts located under the 'tutorials' +directory to ensure they run without errors. Each script is executed in isolation +using runpy to simulate running as a standalone program. +""" + +import runpy +from pathlib import Path + +import pytest + +TUTORIALS = list(Path('tutorials').rglob('*.py')) + + +@pytest.mark.parametrize('script_path', TUTORIALS) +def test_script_runs(script_path: Path): + """Execute a tutorial script and fail if it raises an exception. + + Each script is run in the context of __main__ to mimic standalone execution. + """ + try: + runpy.run_path(str(script_path), run_name='__main__') + except Exception as e: + pytest.fail(f'{script_path}\n{e}') diff --git a/tools/prepare_notebooks.py b/tools/tweak_notebooks.py similarity index 95% rename from tools/prepare_notebooks.py rename to tools/tweak_notebooks.py index 0bb5576f..1e07ff5d 100644 --- a/tools/prepare_notebooks.py +++ b/tools/tweak_notebooks.py @@ -1,10 +1,9 @@ -#!/usr/bin/env python3 """ Add a single bootstrap code cell as the very first cell to every .ipynb file found under the given path(s). Usage: - python tools/prepare_notebooks.py tutorials/ [more_paths ...] + python tools/tweak_notebooks.py tutorials/ [more_paths ...] What it does: - Inserts a new *code* cell at index 0 that checks whether the `easydiffraction` @@ -99,7 +98,7 @@ def process_notebook(path: Path) -> int: def main(argv: list[str]) -> int: if not argv: - print('Usage: python tools/prepare_notebooks.py ', file=sys.stderr) + print('Usage: python tools/tweak_notebooks.py ', file=sys.stderr) return 2 targets = list(iter_notebooks([Path(p) for p in argv])) diff --git a/tools/update_spdx-headers.py b/tools/update_spdx.py similarity index 100% rename from tools/update_spdx-headers.py rename to tools/update_spdx.py From 28c73fe5b67fd8517ace646c11dded61359af287 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Sat, 30 Aug 2025 22:56:24 +0200 Subject: [PATCH 2/2] Standardize Pixi and CI workflow configurations (#82) * Move tests directory inside the package structure * Update PyPI install command * Update workflow to trigger only on the master branch * Fix default values in delete-old-runs workflow to be strings * Update build-docs workflow to restrict branch triggers and adjust Pixi version * Update pixi lock file * Refactor test paths in workflows and update dependencies in pixi.toml files * Remove step to move tests inside the package in the publish to PyPI workflow * Add tests directory to the package distribution * Update test command paths in pixi.toml for consistency * Move pixi-kernel dependency to the pypi-dependencies section in pixi.toml * Reorganize pixi.toml files: move libcblas dependency to target section and ensure pixi-kernel is listed under pypi-dependencies * Refactor pixi.toml: standardize formatting for libcblas dependency * Update pixi.toml * Update test-package-pypi.yaml: enhance download steps for pixi configuration and tests * Remove step to move tests inside the package in the workflow * Fix formatting in test-package-pypi.yaml: adjust line endings for consistency in download steps * Rename test script commands for consistency in pixi.toml and update workflow references in test-tutorials.yaml * Update workflows: change default values to integers in delete-old-runs.yml and streamline curl command in test-package-pypi.yaml * Refactor Pixi commands for consistency across workflows and documentation * Refactor workflow scripts and documentation for consistency * Updates pixi.lock * Removes test __init__.py files * Add SPDX license headers to __main__.py --- .github/workflows/build-docs.yml | 19 +- .github/workflows/draft-release-notes.yml | 4 +- .github/workflows/test-code.yaml | 27 +- .github/workflows/test-package-pypi.yaml | 20 +- .github/workflows/test-tutorials.yaml | 12 +- .github/workflows/validate-pixi.yaml | 5 +- DEVELOPMENT.md | 18 +- docs/installation-and-setup/index.md | 4 +- pixi.lock | 1787 ++++++++--------- pixi.toml | 139 +- pixi/prod/pixi.toml | 32 +- pixi/wheel/pixi.toml | 13 +- src/easydiffraction/__main__.py | 3 + tests/__init__.py | 3 - tests/functional_tests/__init__.py | 3 - tests/functional_tests/fitting/__init__.py | 3 - tests/unit_tests/__init__.py | 3 - tests/unit_tests/analysis/__init__.py | 3 - .../analysis/calculators/__init__.py | 3 - .../analysis/collections/__init__.py | 3 - .../analysis/minimizers/__init__.py | 3 - tests/unit_tests/core/__init__.py | 3 - tests/unit_tests/experiments/__init__.py | 3 - .../experiments/collections/__init__.py | 3 - .../experiments/components/__init__.py | 3 - tests/unit_tests/sample_models/__init__.py | 3 - .../sample_models/collections/__init__.py | 3 - .../sample_models/components/__init__.py | 3 - 28 files changed, 1006 insertions(+), 1122 deletions(-) delete mode 100644 tests/__init__.py delete mode 100644 tests/functional_tests/__init__.py delete mode 100644 tests/functional_tests/fitting/__init__.py delete mode 100644 tests/unit_tests/__init__.py delete mode 100644 tests/unit_tests/analysis/__init__.py delete mode 100644 tests/unit_tests/analysis/calculators/__init__.py delete mode 100644 tests/unit_tests/analysis/collections/__init__.py delete mode 100644 tests/unit_tests/analysis/minimizers/__init__.py delete mode 100644 tests/unit_tests/core/__init__.py delete mode 100644 tests/unit_tests/experiments/__init__.py delete mode 100644 tests/unit_tests/experiments/collections/__init__.py delete mode 100644 tests/unit_tests/experiments/components/__init__.py delete mode 100644 tests/unit_tests/sample_models/__init__.py delete mode 100644 tests/unit_tests/sample_models/collections/__init__.py delete mode 100644 tests/unit_tests/sample_models/components/__init__.py diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index 3a4c49ce..77bf31b4 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -4,7 +4,7 @@ on: # Trigger the workflow on push push: # Selected branches - branches: [develop, master, docs, patch, pixi] + branches: [master, develop, docs, patch] # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' tags: - 'v*' @@ -82,7 +82,7 @@ jobs: git clone https://github.com/easyscience/assets-branding.git - name: Add files from cloned repositories - run: pixi run add-assets-to-docs + run: pixi run docs-assets # Convert python scripts in the notebooks directory to Jupyter notebooks # Strip output from the notebooks @@ -90,31 +90,26 @@ jobs: # Run the notebooks to generate the output cells using multiple cores # The notebooks are then used to build the documentation site - name: Convert tutorial scripts to notebooks - run: pixi run make-notebooks + run: pixi run notebook-prepare - name: Run notebooks - run: pixi run run-notebooks + run: pixi run notebook-exec - name: Move notebooks to docs/tutorials - run: pixi run move-notebooks-to-docs - - # The following step is needed to avoid the following message during the build: - # "Matplotlib is building the font cache; this may take a moment" - #- name: Pre-build site step - # run: pixi run python -c "import easydiffraction" + run: pixi run docs-notebooks # Create the mkdocs.yml configuration file # The file is created by merging two files: # - assets-docs/mkdocs.yml - the common configuration (theme, plugins, etc.) # - docs/mkdocs.yml - the project-specific configuration (project name, TOC, etc.) - name: Create mkdocs.yml file - run: pixi run create-mkdocs-yml + run: pixi run docs-config # Build the static files # Input: docs/ directory containing the Markdown files # Output: site/ directory containing the generated HTML files - name: Build site with MkDocs - run: pixi run build-docs + run: pixi run docs-build # Set up the Pages action to configure the static files to be deployed # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions diff --git a/.github/workflows/draft-release-notes.yml b/.github/workflows/draft-release-notes.yml index 547241aa..8c0d86af 100644 --- a/.github/workflows/draft-release-notes.yml +++ b/.github/workflows/draft-release-notes.yml @@ -6,9 +6,7 @@ name: Update release draft on: # Runs on pushes targeting the default branch (updates the real draft release) push: - branches: - - main - - master + branches: [master] jobs: draft-release-notes: diff --git a/.github/workflows/test-code.yaml b/.github/workflows/test-code.yaml index 7fb814ec..e0d61695 100644 --- a/.github/workflows/test-code.yaml +++ b/.github/workflows/test-code.yaml @@ -76,38 +76,40 @@ jobs: shell: bash run: | pixi run npm config set registry https://registry.npmjs.org/ - pixi run install-prettier + pixi run prettier-install # Check the validity of pyproject.toml - name: Check validity of pyproject.toml id: check_pyproject continue-on-error: true shell: bash - run: pixi run check-pyproject + run: pixi run pyproject-check # Check code linting with Ruff in the project root - name: Check code linting id: check_code_linting continue-on-error: true shell: bash - run: pixi run check-lint-py + run: pixi run py-lint-check - name: Suggestion to fix code linting issues (*.py files) if: steps.check_code_linting.outcome == 'failure' shell: bash - run: echo "In project root run 'pixi run lint-py' and commit changes" + run: + echo "In project root run 'pixi run py-lint-fix' and commit changes" # Check code formatting with Ruff in the project root - name: Check code formatting id: check_code_formatting continue-on-error: true shell: bash - run: pixi run check-format-py + run: pixi run py-format-check - name: Suggestion to fix code formatting issues (*.py files) if: steps.check_code_formatting.outcome == 'failure' shell: bash - run: echo "In project root run 'pixi run format-py' and commit changes" + run: + echo "In project root run 'pixi run py-format-fix' and commit changes" # Check formatting of Markdown, YAML, TOML, etc. files with Prettier in # the project root @@ -115,13 +117,14 @@ jobs: id: check_others_formatting continue-on-error: true shell: bash - run: pixi run check-format-non-py + run: pixi run nonpy-format-check - name: Suggestion to fix non-code formatting issues (*.md, *.yml, etc.) if: steps.check_others_formatting.outcome == 'failure' shell: bash run: - echo "In project root run 'pixi run format-non-py' and commit changes" + echo "In project root run 'pixi run nonpy-format-fix' and commit + changes" - name: Force fail if any of the previous steps failed if: | @@ -185,16 +188,12 @@ jobs: if: startsWith(github.ref , 'refs/tags/v') != true run: git tag --delete $(git tag) - - name: Move tests inside the package - shell: bash - run: mv tests/ src/easydiffraction/tests/ - - name: Create Python package shell: bash run: | for env in ${{ env.PIXI_ENVS }}; do echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" - pixi run -e $env build + pixi run -e $env dist-build env_prefix="${env%%-*}" echo "πŸ“¦ Moving built wheel to dist/$env_prefix/" pixi run mkdir -p dist/$env_prefix @@ -209,6 +208,7 @@ jobs: name: edl_${{ matrix.os }}_${{ runner.arch }} path: | dist/ + tests/ pixi/wheel/pixi.toml if-no-files-found: 'error' compression-level: 0 @@ -225,7 +225,6 @@ jobs: runs-on: ${{ matrix.os }} env: - PIXI_PROJECT_MANIFEST: 'pixi/wheel/pixi.toml' PIXI_ENVS: 'py311-wheel py312-wheel py313-wheel' steps: diff --git a/.github/workflows/test-package-pypi.yaml b/.github/workflows/test-package-pypi.yaml index 2b923762..7e64c5a1 100644 --- a/.github/workflows/test-package-pypi.yaml +++ b/.github/workflows/test-package-pypi.yaml @@ -30,10 +30,16 @@ jobs: cache: false post-cleanup: false - - name: Download the pixi configuration file for EasyDiffraction - run: - curl -LO - https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml + - name: Download the pixi configuration file from the master branch + run: | + curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml + + - name: Download the tests from the master branch + run: | + curl -LO https://github.com/easyscience/diffraction-lib/archive/refs/heads/master.zip + unzip master.zip "diffraction-lib-master/tests/*" -d . + mv diffraction-lib-master/tests ./tests + rm -rf master.zip diffraction-lib-master - name: Create the environment and install dependencies run: pixi install @@ -45,10 +51,10 @@ jobs: run: pixi run func-tests - name: List the available EasyDiffraction tutorials - run: pixi run list-tutorials + run: pixi run tutorials-list - name: Fetch the EasyDiffraction tutorials - run: pixi run fetch-tutorials + run: pixi run tutorials-fetch - name: Test tutorials as notebooks - run: pixi run test-notebooks + run: pixi run notebook-tests diff --git a/.github/workflows/test-tutorials.yaml b/.github/workflows/test-tutorials.yaml index 63e3cbf1..ccc0db3e 100644 --- a/.github/workflows/test-tutorials.yaml +++ b/.github/workflows/test-tutorials.yaml @@ -54,19 +54,19 @@ jobs: - name: Convert tutorial scripts to notebooks shell: bash - run: pixi run make-notebooks + run: pixi run notebook-prepare - name: Check notebooks formatting id: check_formatting continue-on-error: true shell: bash - run: pixi run check-format-notebooks + run: pixi run notebook-format-check - name: Suggestion to fix notebook formatting if: steps.check_formatting.outcome == 'failure' shell: bash run: | - echo "Run 'pixi run fix-format-notebooks' and commit changes." + echo "Run 'pixi run notebook-format-fix' and commit changes." exit 1 # Job 2: Test tutorials as Python scripts and Jupyter Notebooks @@ -97,12 +97,12 @@ jobs: - name: Test tutorials as python scripts shell: bash - run: pixi run test-scripts + run: pixi run script-tests - name: Convert tutorial scripts to notebooks shell: bash - run: pixi run make-notebooks + run: pixi run notebook-prepare - name: Test tutorials as notebooks shell: bash - run: pixi run test-notebooks + run: pixi run notebook-tests diff --git a/.github/workflows/validate-pixi.yaml b/.github/workflows/validate-pixi.yaml index c4a8fbf9..d2e1a468 100644 --- a/.github/workflows/validate-pixi.yaml +++ b/.github/workflows/validate-pixi.yaml @@ -55,8 +55,9 @@ jobs: - name: Add PyPI dependencies run: > - pixi add --pypi "easydiffraction[visualization] @ - git+https://github.com/easyscience/diffraction-lib@${{env.CI_BRANCH}}" + pixi add --pypi 'easydiffraction[dev, visualization]' --git + https://github.com/easyscience/diffraction-lib.git --branch ${{ + env.CI_BRANCH }} - name: Add a task to run EasyDiffraction from the command line run: pixi task add easydiffraction "python -m easydiffraction" diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md index 02f0b8ad..7a04f1c8 100644 --- a/DEVELOPMENT.md +++ b/DEVELOPMENT.md @@ -26,7 +26,7 @@ This is an example of a workflow that describes the development process. ``` - Install Prettier for non-Python files formatting ```bash - pixi run install-prettier + pixi run prettier-install ``` ## Making changes @@ -61,35 +61,35 @@ This is an example of a workflow that describes the development process. ``` - Test tutorials as python scripts ```bash - pixi run test-scripts + pixi run script-tests ``` - Convert tutorial scripts to notebooks ```bash - pixi run make-notebooks + pixi run notebook-prepare ``` - Test tutorials as notebooks ```bash - pixi run test-notebooks + pixi run notebook-tests ``` ## Building and checking documentation with MkDocs - Move notebooks to docs/tutorials ```bash - pixi run move-notebooks-to-docs + pixi run docs-notebooks ``` - Add extra files to build documentation (from `../assets-docs/` and `../assets-branding/` directories) ```bash - pixi run add-assets-to-docs + pixi run docs-assets ``` - Create mkdocs.yml file ```bash - pixi run create-mkdocs-yml + pixi run docs-config ``` - Build documentation ```bash - pixi run build-docs + pixi run docs-build ``` - Test the documentation locally (built in the `site/` directory). E.g., on macOS, open the site in the default browser via the terminal @@ -98,7 +98,7 @@ This is an example of a workflow that describes the development process. ``` - Clean up after checking documentation ```bash - pixi run cleanup-docs + pixi run docs-clean ``` ## Committing and pushing changes diff --git a/docs/installation-and-setup/index.md b/docs/installation-and-setup/index.md index 3b81e130..f98a3dc2 100644 --- a/docs/installation-and-setup/index.md +++ b/docs/installation-and-setup/index.md @@ -217,11 +217,11 @@ approach. === "curl" ```bash - curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml + curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml ``` === "wget" ```bash - wget https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml + wget https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml ``` - Create the environment defined in `pixi.toml` and install all necessary diff --git a/pixi.lock b/pixi.lock index 659680d7..11d1feba 100644 --- a/pixi.lock +++ b/pixi.lock @@ -43,6 +43,7 @@ environments: - 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"win-64", - "linux-64", - "osx-64", - "osx-arm64", -] # Platforms supported for lock file (pixi.lock) ########## # FEATURES @@ -15,10 +12,14 @@ platforms = [ # Default feature configuration [dependencies] # == [feature.default.dependencies] -libcblas = "*" # CBLAS library for linear algebra. Needed for pdffit2 on Windows -pip = "*" # Needed to install from PyPI -jupyterlab = "*" # JupyterLab for notebooks -pixi-kernel = "*" # IPython kernel for Jupyter +pip = "*" # Needed to install from PyPI +jupyterlab = "*" # JupyterLab for notebooks + +[target.win-64.dependencies] +libcblas = "*" # CBLAS library for linear algebra. Needed for pdffit2 on Windows + +[pypi-dependencies] # == [feature.default.pypi-dependencies] +pixi-kernel = "*" # Pixi Jupyter kernel integration # Extra features for different Python versions @@ -72,7 +73,7 @@ easydiffraction = { version = "*", extras = ["dev", "visualization"] } # non-Python files. [feature.nodejs.dependencies] -nodejs = "*" # Needed for prettier +nodejs = ">=20,<21" # Needed for prettier; pin to a stable LTS ############## # ENVIRONMENTS @@ -83,6 +84,8 @@ nodejs = "*" # Needed for prettier # The `default` environment is always included in the lock file, so there is no # need to specify it explicitly in the environments section. +default = { features = ["py313", "ed-local-editable", "nodejs"] } + py311-dev = { features = ["py311", "ed-local", "nodejs"] } py312-dev = { features = ["py312", "ed-local", "nodejs"] } py313-dev = { features = ["py313", "ed-local", "nodejs"] } @@ -91,75 +94,77 @@ py313-docs = { features = ["py313", "ed-local-with-docs"] } py313-prod = { features = ["py313", "ed-pypi"] } -default = { features = ["py313", "ed-local-editable"] } - ####### # TASKS ####### [tasks] -# Testing tasks +# πŸ§ͺ Testing Tasks unit-tests = "python -m pytest tests/unit_tests/ --color=yes -v" func-tests = "python -m pytest tests/functional_tests/ --color=yes -n auto -v" -unit-tests-package = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" -func-tests-package = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" -test-notebooks = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v' -test-scripts = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v' -test = { depends-on = ["unit-tests", "func-tests"] } - -# Check code quality tasks -check-pyproject = "python -m validate_pyproject pyproject.toml" -check-lint-py = "python -m ruff check ." -check-format-py = "python -m ruff format . --check" -check-format-non-py = "npx prettier . --list-different --config=prettierrc.toml" -check-format-notebooks = 'nbqa ruff tutorials/' - -# Fix code quality tasks -lint-py = "python -m ruff check . --fix" -format-py = "python -m ruff format ." -format-non-py = "npx prettier . --list-different --write --config=prettierrc.toml" -fix-format-notebooks = 'nbqa ruff tutorials/ --fix' +notebook-tests = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v' +script-tests = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v' + +tests = { depends-on = ["unit-tests", "func-tests"] } + +# 🧹 Code Quality + +## βœ”οΈ Checks +pyproject-check = "python -m validate_pyproject pyproject.toml" +py-lint-check = "python -m ruff check ." +py-format-check = "python -m ruff format . --check" +nonpy-format-check = "npx prettier . --list-different --config=prettierrc.toml" +notebook-format-check = 'nbqa ruff tutorials/' + +## πŸ› οΈ Fixes +py-lint-fix = "python -m ruff check . --fix" +py-format-fix = "python -m ruff format ." +nonpy-format-fix = "npx prettier . --list-different --write --config=prettierrc.toml" +notebook-format-fix = 'nbqa ruff tutorials/ --fix' + code-quality = { depends-on = [ - "check-pyproject", - "lint-py", - "format-py", - "format-non-py", + "pyproject-check", + "py-lint-fix", + "py-format-fix", + "nonpy-format-fix", + "notebook-format-fix", ] } -# Notebook management tasks -scripts-to-notebooks = 'jupytext tutorials/*.py --from py:percent --to ipynb' -stripout-notebooks = 'nbstripout tutorials/*.ipynb' -tweak-notebooks = 'python tools/tweak_notebooks.py tutorials/' -make-notebooks = { depends-on = [ - "scripts-to-notebooks", - "stripout-notebooks", - "tweak-notebooks", +# πŸ““ Notebook Management +notebook-convert = 'jupytext tutorials/*.py --from py:percent --to ipynb' +notebook-strip = 'nbstripout tutorials/*.ipynb' +notebook-tweak = 'python tools/tweak_notebooks.py tutorials/' +notebook-clean = 'rm -f tutorials/*.ipynb' +notebook-exec = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v' + +notebook-prepare = { depends-on = [ + "notebook-convert", + "notebook-strip", + "notebook-tweak", ] } -remove-notebooks = 'rm -f tutorials/*.ipynb' -run-notebooks = 'python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v' - -# Documentation tasks -add-assets-to-docs = "tools/add_assets_to_docs.sh" -move-notebooks-to-docs = "mv tutorials/*.ipynb docs/tutorials/" -create-mkdocs-yml = "python tools/create_mkdocs_yml.py" -serve-docs = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs serve --dirty' -build-docs = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs build' -cleanup-docs = "tools/cleanup_docs.sh" -setup-docs = { depends-on = [ - "create-mkdocs-yml", - "add-assets-to-docs", - "make-notebooks", - "move-notebooks-to-docs", + +# πŸ“š Documentation Tasks +docs-assets = "tools/add_assets_to_docs.sh" +docs-notebooks = "mv tutorials/*.ipynb docs/tutorials/" +docs-config = "python tools/create_mkdocs_yml.py" +docs-serve = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs serve --dirty' +docs-build = 'JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS="ignore::RuntimeWarning" python -m mkdocs build' +docs-clean = "tools/cleanup_docs.sh" +docs-setup = { depends-on = [ + "docs-config", + "docs-assets", + "notebook-prepare", + "docs-notebooks", ] } -# Other tasks -pre-commit = { depends-on = ["code-quality", "test"] } -build = "python -m build --wheel --outdir dist" -update-spdx = "python tools/update_spdx.py" -install-prettier = "npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml" +# πŸš€ Development & Build Tasks +pre-commit = { depends-on = ["code-quality", "tests"] } +dist-build = "python -m build --wheel --outdir dist" +spdx-update = "python tools/update_spdx.py" +prettier-install = "npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml" -# Shortcuts +# πŸ”— Shortcuts easydiffraction = "python -m easydiffraction" -list-tutorials = "python -m easydiffraction list-tutorials" -fetch-tutorials = "python -m easydiffraction fetch-tutorials" +tutorials-list = "python -m easydiffraction list-tutorials" +tutorials-fetch = "python -m easydiffraction fetch-tutorials" diff --git a/pixi/prod/pixi.toml b/pixi/prod/pixi.toml index c5ac7641..918a6d46 100644 --- a/pixi/prod/pixi.toml +++ b/pixi/prod/pixi.toml @@ -1,25 +1,23 @@ [workspace] -channels = ["conda-forge"] platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] +channels = ["conda-forge"] + +[dependencies] +python = "3.13.*" +pip = "*" +jupyterlab = "*" -[dependencies] # == [feature.default.dependencies] -python = "3.13.*" # Python version -libcblas = "*" # CBLAS library for linear algebra. Needed for pdffit2 on Windows -pip = "*" # Needed to install from PyPI -jupyterlab = "*" # JupyterLab for notebooks -pixi-kernel = "*" # IPython kernel for Jupyter +[target.win-64.dependencies] +libcblas = "*" [pypi-dependencies] -#easydiffraction = { version = "*", extras = ["dev", "visualization"] } -easydiffraction = { git = "https://github.com/easyscience/diffraction-lib.git", branch = "pixi", extras = [ - "dev", - "visualization", -] } +pixi-kernel = "*" +easydiffraction = { version = "*", extras = ["dev", "visualization"] } [tasks] -unit-tests = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" -func-tests = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" -test-notebooks = "python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v" +unit-tests = "python -m pytest tests/unit_tests/ --color=yes -v" +func-tests = "python -m pytest tests/functional_tests/ --color=yes -n auto -v" +notebook-tests = "python -m pytest --nbmake tutorials/ --nbmake-timeout=600 --color=yes -n auto -v" easydiffraction = "python -m easydiffraction" -list-tutorials = "python -m easydiffraction list-tutorials" -fetch-tutorials = "python -m easydiffraction fetch-tutorials" +tutorials-list = "python -m easydiffraction list-tutorials" +tutorials-fetch = "python -m easydiffraction fetch-tutorials" diff --git a/pixi/wheel/pixi.toml b/pixi/wheel/pixi.toml index 6323f513..9aa05d85 100644 --- a/pixi/wheel/pixi.toml +++ b/pixi/wheel/pixi.toml @@ -1,11 +1,16 @@ [workspace] -channels = ["conda-forge"] platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] +channels = ["conda-forge"] [dependencies] # = [feature.default.dependencies] -libcblas = "*" pip = "*" +[target.win-64.dependencies] +libcblas = "*" + +[pypi-dependencies] # == [feature.default.pypi-dependencies] +pixi-kernel = "*" + [feature.py311.dependencies] python = "3.11.*" @@ -21,6 +26,6 @@ py312-wheel = { features = ["py312"] } # = ["default", "py312"] py313-wheel = { features = ["py313"] } # = ["default", "py313"] [tasks] +unit-tests = "python -m pytest tests/unit_tests/ --color=yes -v" +func-tests = "python -m pytest tests/functional_tests/ --color=yes -n auto -v" easydiffraction = "python -m easydiffraction" -unit-tests = "python -m pytest --pyargs easydiffraction.tests.unit_tests --color=yes -v" -func-tests = "python -m pytest --pyargs easydiffraction.tests.functional_tests --color=yes -n auto -v" diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py index ead25d9e..3ced6061 100644 --- a/src/easydiffraction/__main__.py +++ b/src/easydiffraction/__main__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors +# SPDX-License-Identifier: BSD-3-Clause + import sys # Ensure UTF-8 output on all platforms (e.g. Windows with cp1252) diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/functional_tests/__init__.py b/tests/functional_tests/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/functional_tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/functional_tests/fitting/__init__.py b/tests/functional_tests/fitting/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/functional_tests/fitting/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/__init__.py b/tests/unit_tests/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/analysis/__init__.py b/tests/unit_tests/analysis/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/analysis/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/analysis/calculators/__init__.py b/tests/unit_tests/analysis/calculators/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/analysis/calculators/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/analysis/collections/__init__.py b/tests/unit_tests/analysis/collections/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/analysis/collections/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/analysis/minimizers/__init__.py b/tests/unit_tests/analysis/minimizers/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/analysis/minimizers/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/core/__init__.py b/tests/unit_tests/core/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/core/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/experiments/__init__.py b/tests/unit_tests/experiments/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/experiments/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/experiments/collections/__init__.py b/tests/unit_tests/experiments/collections/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/experiments/collections/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/experiments/components/__init__.py b/tests/unit_tests/experiments/components/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/experiments/components/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/sample_models/__init__.py b/tests/unit_tests/sample_models/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/sample_models/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/sample_models/collections/__init__.py b/tests/unit_tests/sample_models/collections/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/sample_models/collections/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause - diff --git a/tests/unit_tests/sample_models/components/__init__.py b/tests/unit_tests/sample_models/components/__init__.py deleted file mode 100644 index 6c98b2a1..00000000 --- a/tests/unit_tests/sample_models/components/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors -# SPDX-License-Identifier: BSD-3-Clause -