CI: try parallelizing notebook execution #1384
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "master" | |
| - "dev" | |
| workflow_dispatch: | |
| schedule: | |
| # every two weeks on Monday at 3 am | |
| - cron: "0 3/336 * * 1" | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Conda | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: teachopencadd | |
| environment-file: devtools/test_env.yml | |
| test: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| notebook: | |
| - teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb | |
| - teachopencadd/talktorials/T002_compound_adme/talktorial.ipynb | |
| - teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest $PYTEST_ARGS teachopencadd/talktorials/ $IGNORE | |
| #test: | |
| #name: Pytest | |
| #runs-on: ${{ matrix.cfg.os }} | |
| #strategy: | |
| #fail-fast: false | |
| #matrix: | |
| #cfg: | |
| #- os: ubuntu-latest | |
| #python-version: "3.8" | |
| #- os: ubuntu-latest | |
| #python-version: "3.9" | |
| #- os: macos-latest | |
| #python-version: "3.8" | |
| #- os: windows-latest | |
| #python-version: "3.8" | |
| #env: | |
| #PYVER: ${{ matrix.cfg.python-version }} | |
| #PACKAGE: teachopencadd | |
| #steps: | |
| #- uses: actions/checkout@v3 | |
| #- uses: conda-incubator/setup-miniconda@v2 | |
| #with: | |
| #python-version: ${{ matrix.cfg.python-version }} | |
| #miniforge-variant: Mambaforge | |
| #miniforge-version: latest | |
| #activate-environment: teachopencadd | |
| #environment-file: devtools/test_env.yml | |
| #- name: Additional info about the build | |
| #shell: bash | |
| #run: | | |
| #uname -a | |
| #df -h | |
| #ulimit -a | |
| #- name: Install package | |
| #shell: bash -l {0} | |
| #run: | | |
| #pip install . --no-deps -vv | |
| #- name: Environment Information | |
| #shell: bash -l {0} | |
| #run: | | |
| #conda info --all | |
| #conda list | |
| #- name: Test CLI | |
| #shell: bash -l {0} | |
| #run: | | |
| #teachopencadd -h | |
| #pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/ | |
| #- name: Run tests | |
| #shell: bash -l {0} | |
| #run: | | |
| #PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2" | |
| #PYTEST_IGNORE_T001="--ignore=teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb" | |
| #PYTEST_IGNORE_T018="--ignore=teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb" | |
| #PYTEST_IGNORE_T019="--ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb" | |
| #PYTEST_IGNORE_T020="--ignore=teachopencadd/talktorials/T020_md_analysis/talktorial.ipynb" | |
| #PYTEST_IGNORE_T035="--ignore=teachopencadd/talktorials/T035_graph_neural_networks/talktorial.ipynb" | |
| #PYTEST_IGNORE_T036="--ignore=teachopencadd/talktorials/T036_e3_equivariant_gnn/talktorial.ipynb" | |
| #PYTEST_IGNORE_T038="--ignore=teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/talktorial.ipynb" | |
| #IGNORE="$PYTEST_IGNORE_T001" | |
| #if [ "$RUNNER_OS" == "Windows" ]; then | |
| ## Ignore T019 under Windows, see https://github.com/volkamerlab/teachopencadd/issues/313 | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T019" | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T035" | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T036" | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T038" | |
| #fi | |
| #if [ "$RUNNER_OS" == "Linux" ]; then | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T018" # see 385 | |
| #fi | |
| #if [ "$RUNNER_OS" == "macOS" ]; then | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T018" # see 385 | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T019" | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T035" # may cause kernel dying in pytest | |
| #IGNORE="$IGNORE $PYTEST_IGNORE_T036" # may cause kernel dying in pytest | |
| #fi | |
| #pytest $PYTEST_ARGS teachopencadd/talktorials/ $IGNORE | |
| #format: | |
| #name: Black | |
| #runs-on: ubuntu-latest | |
| #steps: | |
| #- uses: actions/checkout@v3 | |
| #- uses: actions/setup-python@v3 | |
| #- name: Install format dependencies | |
| #run: python -m pip install black-nb shyaml | |
| #- name: Run black-nb | |
| #run: | | |
| #black-nb -l 99 --check teachopencadd/talktorials/T*/talktorial.ipynb | |
| #readmes: | |
| #name: READMEs | |
| #runs-on: ubuntu-latest | |
| #steps: | |
| #- uses: actions/checkout@v3 | |
| #- uses: actions/setup-python@v3 | |
| #- name: Install nbformat | |
| #run: python -m pip install nbformat shyaml | |
| #- name: Check READMEs are up-to-date | |
| #run: | | |
| #for path in teachopencadd/talktorials/T*/talktorial.ipynb; do | |
| #python devtools/regenerate_readmes.py --output README.md $path | |
| #done | |
| ## If the script above introduced changes (it shouldn't!), git diff will have output and an error code | |
| #git diff --exit-code |