Biopython update #1348
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| #!/bin/bash | |
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "master" | |
| schedule: | |
| # Run a cron job once weekly on Monday | |
| - cron: "0 3 * * 1" | |
| 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@v3 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: test | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| channels: conda-forge,defaults,bioconda | |
| # TODO: Remove this step when patched theseus makes it to CF | |
| - name: Build patched mmligner | |
| shell: bash -l {0} | |
| run: | | |
| conda activate base | |
| conda install conda-build | |
| conda build devtools/conda-recipes/mmligner/ | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c local mmligner pip | |
| python -m pip install . --no-deps | |
| conda list | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/ | |
| - name: CodeCov | |
| 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: | |
| CI_OS: ubuntu-latest | |
| PACKAGE: "opencadd" | |
| PYVER: "3.8" | |
| steps: | |
| - name: Checkout the code | |
| uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.8" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: test | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| channels: conda-forge,defaults,bioconda | |
| - name: Install linter and formatter | |
| shell: bash -l {0} | |
| run: | | |
| conda install -y pylint black | |
| - name: Run pylint | |
| shell: bash -l {0} | |
| run: | | |
| pylint $PACKAGE/ | |
| - name: Run black check | |
| shell: bash -l {0} | |
| if: always() | |
| run: | | |
| black --check -l 99 $PACKAGE/ |