push: refs/heads/ci-update #1344
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| name: CI | |
| run-name: "${{ github.event_name }}: ${{ github.ref }}" | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - "master" | |
| schedule: | |
| - cron: "0 3 * * 1" # weekly on Monday | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macOS-latest, ubuntu-latest] | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| env: | |
| CI_OS: ${{ matrix.os }} | |
| PYVER: ${{ matrix.python-version }} | |
| PACKAGE: "opencadd" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: 'Setup conda environment' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| create-args: python=${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| micromamba-version: latest | |
| generate-run-shell: true | |
| init-shell: bash | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - defaults | |
| - bioconda | |
| # TODO: Remove this step when patched theseus makes it to CF | |
| - name: Build patched mmligner | |
| shell: micromamba-shell {0} | |
| run: | | |
| micromamba install conda-build | |
| conda build devtools/conda-recipes/mmligner/ | |
| - name: Install package | |
| shell: micromamba-shell {0} | |
| run: | | |
| micromamba install -c local mmligner pip | |
| python -m pip install . --no-deps | |
| micromamba list | |
| - name: Run tests | |
| shell: micromamba-shell {0} | |
| run: | | |
| pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/ | |
| - name: CodeCov | |
| if: github.event_name == 'push' && github.ref_name == 'master' | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| yml: ./.codecov.yml | |
| ############# | |
| lint-format: | |
| runs-on: ubuntu-latest | |
| env: | |
| PACKAGE: "opencadd" | |
| steps: | |
| - name: Checkout the code | |
| uses: actions/checkout@v4 | |
| - name: 'Setup Python' | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install linter and formatter | |
| run: | | |
| python -m pip install pylint black | |
| - name: Run pylint | |
| run: pylint $PACKAGE/ | |
| - name: Run black check | |
| if: always() | |
| run: black --check -l 99 $PACKAGE/ |