From 8d53ee0574c3775037f24629a4fbc0b61555d27c Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Oct 2025 08:12:10 +0200 Subject: [PATCH 1/8] Follow standard directory structure --- .github/workflows/pipeline.yml | 10 +++++----- .github/workflows/pypi.yml | 4 +--- .gitignore | 2 +- .../pyproject.toml => pyproject.toml | 0 .../src => src}/python_workflow_definition/__init__.py | 0 .../src => src}/python_workflow_definition/aiida.py | 0 .../python_workflow_definition/cwl/__init__.py | 0 .../python_workflow_definition/cwl/__main__.py | 0 .../python_workflow_definition/executorlib.py | 0 .../src => src}/python_workflow_definition/jobflow.py | 0 .../src => src}/python_workflow_definition/models.py | 0 .../src => src}/python_workflow_definition/plot.py | 0 .../python_workflow_definition/purepython.py | 0 .../python_workflow_definition/pyiron_base.py | 0 .../src => src}/python_workflow_definition/shared.py | 0 15 files changed, 7 insertions(+), 9 deletions(-) rename python_workflow_definition/pyproject.toml => pyproject.toml (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/__init__.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/aiida.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/cwl/__init__.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/cwl/__main__.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/executorlib.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/jobflow.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/models.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/plot.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/purepython.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/pyiron_base.py (100%) rename {python_workflow_definition/src => src}/python_workflow_definition/shared.py (100%) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 24afdc7..83a42ca 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -13,7 +13,7 @@ jobs: - uses: psf/black@stable with: options: "--check --diff" - src: ./python_workflow_definition/src/python_workflow_definition + src: ./src/python_workflow_definition - uses: psf/black@stable with: options: "--check --diff" @@ -35,7 +35,7 @@ jobs: - name: Pip check shell: bash -l {0} run: | - pip install --no-deps --no-build-isolation -e python_workflow_definition + pip install --no-deps --no-build-isolation -e . pip check nfdi4ing: @@ -53,7 +53,7 @@ jobs: - name: Installation and setup shell: bash -l {0} run: | - pip install --no-deps --no-build-isolation -e python_workflow_definition + pip install --no-deps --no-build-isolation -e . conda install -c conda-forge jupyter papermill verdi presto --profile-name pwd sudo apt-get install -y $(cat binder/apt.txt) @@ -92,7 +92,7 @@ jobs: shell: bash -l {0} run: | pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser - pip install --no-deps --no-build-isolation -e python_workflow_definition + pip install --no-deps --no-build-isolation -e . conda install -c conda-forge jupyter papermill verdi presto --profile-name pwd - name: Tests @@ -122,7 +122,7 @@ jobs: - name: Installation and setup shell: bash -l {0} run: | - pip install --no-deps --no-build-isolation -e python_workflow_definition + pip install --no-deps --no-build-isolation -e . conda install -c conda-forge jupyter papermill verdi presto --profile-name pwd - name: Tests diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 4e26be5..1a02cab 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -26,9 +26,7 @@ jobs: environment-file: binder/environment.yml - name: Build shell: bash -l {0} - run: | - cd python_workflow_definition - hatch build -t sdist -t wheel + run: hatch build -t sdist -t wheel - name: Publish distribution 📦 to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: diff --git a/.gitignore b/.gitignore index cdcde78..33d3384 100644 --- a/.gitignore +++ b/.gitignore @@ -178,7 +178,7 @@ cython_debug/ input_tmp.in pyiron.log pyiron_draw.png -python_workflow_definition/src/python_workflow_definition/__pycache__/ +src/python_workflow_definition/__pycache__/ test/ mini/ evcurve.png diff --git a/python_workflow_definition/pyproject.toml b/pyproject.toml similarity index 100% rename from python_workflow_definition/pyproject.toml rename to pyproject.toml diff --git a/python_workflow_definition/src/python_workflow_definition/__init__.py b/src/python_workflow_definition/__init__.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/__init__.py rename to src/python_workflow_definition/__init__.py diff --git a/python_workflow_definition/src/python_workflow_definition/aiida.py b/src/python_workflow_definition/aiida.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/aiida.py rename to src/python_workflow_definition/aiida.py diff --git a/python_workflow_definition/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/cwl/__init__.py rename to src/python_workflow_definition/cwl/__init__.py diff --git a/python_workflow_definition/src/python_workflow_definition/cwl/__main__.py b/src/python_workflow_definition/cwl/__main__.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/cwl/__main__.py rename to src/python_workflow_definition/cwl/__main__.py diff --git a/python_workflow_definition/src/python_workflow_definition/executorlib.py b/src/python_workflow_definition/executorlib.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/executorlib.py rename to src/python_workflow_definition/executorlib.py diff --git a/python_workflow_definition/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/jobflow.py rename to src/python_workflow_definition/jobflow.py diff --git a/python_workflow_definition/src/python_workflow_definition/models.py b/src/python_workflow_definition/models.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/models.py rename to src/python_workflow_definition/models.py diff --git a/python_workflow_definition/src/python_workflow_definition/plot.py b/src/python_workflow_definition/plot.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/plot.py rename to src/python_workflow_definition/plot.py diff --git a/python_workflow_definition/src/python_workflow_definition/purepython.py b/src/python_workflow_definition/purepython.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/purepython.py rename to src/python_workflow_definition/purepython.py diff --git a/python_workflow_definition/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/pyiron_base.py rename to src/python_workflow_definition/pyiron_base.py diff --git a/python_workflow_definition/src/python_workflow_definition/shared.py b/src/python_workflow_definition/shared.py similarity index 100% rename from python_workflow_definition/src/python_workflow_definition/shared.py rename to src/python_workflow_definition/shared.py From c75ab116d752999aa30c1ab7da99953ae153391f Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Oct 2025 08:15:00 +0200 Subject: [PATCH 2/8] fix license --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b760b0b..6ce5e08 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ authors = [ { name = "Marnik Bercx", email = "marnik.bercx@psi.ch" }, { name = "Christina Ertural", email = "christina.ertural@bam.de" }, ] -license = { file = "../LICENSE" } +license = { file = "LICENSE" } dependencies = [ "numpy>=1.21,<2", "pydantic>=2.7.0,<=2.11.4", From ec0f79b29dc8b1ec40b3c98ffced33c0e8f553cd Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 16:58:49 +0200 Subject: [PATCH 3/8] Update environment.yml --- binder/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/binder/environment.yml b/binder/environment.yml index a5957e1..d23eedb 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -2,6 +2,7 @@ channels: - conda-forge dependencies: - python =3.12 +- click =8.1.0 - pydantic =2.11.4 - hatch =1.14.1 - hatchling =1.27.0 From 91a640131c4f48ed4eea0267a1d7ea960e505ee9 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 17:00:54 +0200 Subject: [PATCH 4/8] Update pipeline.yml --- .github/workflows/pipeline.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 83a42ca..09aa583 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -28,7 +28,7 @@ jobs: - name: Setup Mambaforge uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.11" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -46,7 +46,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.11" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -84,7 +84,7 @@ jobs: tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.11" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -115,7 +115,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.11" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -143,7 +143,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.11" miniforge-version: latest condarc-file: .condarc environment-file: documentation/environment.yml From 4e77916579d95b7e0914c762f11d48abed90cfce Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 17:02:24 +0200 Subject: [PATCH 5/8] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index d23eedb..97e00b1 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -1,7 +1,7 @@ channels: - conda-forge dependencies: -- python =3.12 +- python =3.11 - click =8.1.0 - pydantic =2.11.4 - hatch =1.14.1 From cb7a4fab527e901039fa113a3dfe0120708ea09d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 17:33:45 +0200 Subject: [PATCH 6/8] Update pipeline.yml --- .github/workflows/pipeline.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 09aa583..83a42ca 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -28,7 +28,7 @@ jobs: - name: Setup Mambaforge uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -46,7 +46,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -84,7 +84,7 @@ jobs: tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -115,7 +115,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: binder/environment.yml @@ -143,7 +143,7 @@ jobs: run: echo -e "channels:\n - conda-forge\n" > .condarc - uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: documentation/environment.yml From 9ddb238a990bb744441c16336f0cfd376e57bb29 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 17:37:14 +0200 Subject: [PATCH 7/8] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 97e00b1..5c741ff 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge dependencies: - python =3.11 -- click =8.1.0 +- click =8.1.8 - pydantic =2.11.4 - hatch =1.14.1 - hatchling =1.27.0 From c5d0e143b731b279acd49fb6537e544c88d381cc Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 21 Oct 2025 17:37:25 +0200 Subject: [PATCH 8/8] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 5c741ff..de25b7a 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -1,7 +1,7 @@ channels: - conda-forge dependencies: -- python =3.11 +- python =3.12 - click =8.1.8 - pydantic =2.11.4 - hatch =1.14.1