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Update pyiron_workflow and executorlib #498

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Update pyiron_workflow and executorlib

Update pyiron_workflow and executorlib #498

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.github/workflows/pipeline.yml at bac5dc7
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name: Pipeline
on:
push:
branches: [ main ]
pull_request:
jobs:
black:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
with:
options: "--check --diff"
src: ./src/python_workflow_definition
- uses: psf/black@stable
with:
options: "--check --diff"
src: ./example_workflows/quantum_espresso/qe_xml_parser/src/qe_xml_parser
pip_check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: binder/environment.yml
- name: Pip check
shell: bash -l {0}
run: |
pip install --no-deps --no-build-isolation -e .
pip check
nfdi4ing:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: binder/environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
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 $(cat binder/apt.txt)
- name: Create Additional Conda Environments
shell: bash -l {0}
run: |
conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
- name: Tests
shell: bash -l {0}
run: |
cd example_workflows/nfdi/
papermill aiida.ipynb aiida_out.ipynb -k "python3"
papermill cwl.ipynb cwl_out.ipynb -k "python3"
papermill executorlib.ipynb executorlib_out.ipynb -k "python3"
papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
quantumespresso:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Setup environment
shell: bash -l {0}
run: |
echo -e "channels:\n - conda-forge\n" > .condarc
tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: binder/environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
pip install --no-deps --no-build-isolation -e .
conda install -c conda-forge jupyter papermill
verdi presto --profile-name pwd
- name: Tests
shell: bash -l {0}
run: |
export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
cp -r example_workflows/quantum_espresso/espresso .
cd example_workflows/quantum_espresso
papermill aiida.ipynb aiida_out.ipynb -k "python3"
papermill cwl.ipynb cwl_out.ipynb -k "python3"
papermill executorlib.ipynb executorlib_out.ipynb -k "python3"
papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
arithmetic:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: binder/environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
pip install --no-deps --no-build-isolation -e .
conda install -c conda-forge jupyter papermill
verdi presto --profile-name pwd
- name: Tests
shell: bash -l {0}
run: |
cd example_workflows/arithmetic
papermill aiida.ipynb aiida_out.ipynb -k "python3"
papermill cwl.ipynb cwl_out.ipynb -k "python3"
papermill executorlib.ipynb executorlib_out.ipynb -k "python3"
papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
documentation:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: documentation/environment.yml
- name: Install Jupyterbook
shell: bash -l {0}
run: |
cp documentation/_config.yml .
cp documentation/_toc.yml .
cp documentation/*.md .
jupyter-book build . --path-output public
mv public/_build/html public_html
touch public_html/.nojekyll
unittest_matrix:
runs-on: ${{ matrix.operating-system }}
strategy:
matrix:
include:
- operating-system: macos-latest
python-version: '3.12'
- operating-system: ubuntu-latest
python-version: '3.12'
- operating-system: ubuntu-latest
python-version: '3.11'
steps:
- uses: actions/checkout@v6
- name: Setup environment
shell: bash -l {0}
run: |
echo -e "channels:\n - conda-forge\n" > .condarc
sed '/- python/d' binder/environment.yml > environment.yml
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v4
with:
python-version: ${{ matrix.python-version }}
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
verdi presto --profile-name pwd
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
coverage:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Setup environment
shell: bash -l {0}
run: |
echo -e "channels:\n - conda-forge\n" > .condarc
sed '/- python/d' binder/environment.yml > environment.yml
echo '- coverage' >> environment.yml
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v4
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
verdi presto --profile-name pwd
pip install . --no-deps --no-build-isolation
coverage run
coverage xml
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
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