CI: trigger on experimental branch #1386
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| - "ci-experiments" | |
| pull_request: | |
| branches: | |
| - "master" | |
| - "dev" | |
| workflow_dispatch: | |
| schedule: | |
| # every two weeks on Monday at 3 am | |
| - cron: "0 3/336 * * 1" | |
| jobs: | |
| test: | |
| name: Pytest | |
| runs-on: ${{ matrix.cfg.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| cfg: | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| - os: macos-latest | |
| python-version: "3.9" | |
| - os: windows-latest | |
| python-version: "3.9" | |
| env: | |
| PYVER: ${{ matrix.cfg.python-version }} | |
| PACKAGE: teachopencadd | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Conda | |
| 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 ${PACKAGE}/tests/ | |
| - name: Find changed notebooks | |
| id: find_changed | |
| run: | | |
| # Find changed notebooks in the last commit | |
| changed_files=$(git diff --name-only ${{ github.sha }}^ ${{ github.sha }} | grep 'talktorial.ipynb$' || true) | |
| echo "Changed notebooks: $changed_files" | |
| echo "::set-output name=changed_notebooks::$changed_files" | |
| - name: Setup environment variables | |
| 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 | |
| - name: Test changed notebooks | |
| if: steps.find_changed.outputs.changed_notebooks != '' | |
| run: | | |
| pytest $PYTEST_ARGS ${{ steps.find_changed.outputs.changed_notebooks }} $IGNORE | |
| - name: Test all notebooks | |
| if: github.event_name == 'schedule' | |
| shell: bash -l {0} | |
| run: | | |
| 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 |