fix #116 - commas needed #435
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| name: CI | |
| on: [push,pull_request,workflow_dispatch] | |
| jobs: | |
| test_mac: | |
| name: "Python ${{ matrix.python-version }}" | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [macos-13] #macos-latest/macos-14 is M1 - porechop-abi etc don't have M1 package builds, so fails CI | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: "actions/checkout@v3" | |
| with: | |
| fetch-depth: 0 | |
| # Setup env | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: hybracterENV | |
| environment-file: build/environment.yaml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| - name: "Setup hybracter on ${{ matrix.os }} for Python ${{ matrix.python-version }}" | |
| shell: bash -l {0} | |
| run: | | |
| conda install python=${{ matrix.python-version }} | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: "Run tests on ${{ matrix.os }} for Python ${{ matrix.python-version }}" | |
| shell: bash -l {0} | |
| run: | | |
| export TERM=linux | |
| pip install pytest | |
| pytest --run_mac . | |
| test_ubuntu: | |
| name: "Python ${{ matrix.python-version }}" | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: "actions/checkout@v3" | |
| with: | |
| fetch-depth: 0 | |
| # Setup env | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: hybracterENV | |
| environment-file: build/environment.yaml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| channel-priority: strict | |
| channels: conda-forge,bioconda,defaults,anaconda | |
| auto-update-conda: true | |
| - name: "Setup hybracter on ${{ matrix.os }} for Python ${{ matrix.python-version }}" | |
| shell: bash -l {0} | |
| run: | | |
| conda install python=${{ matrix.python-version }} | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: "Run tests and generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}" | |
| shell: bash -l {0} | |
| run: | | |
| export TERM=linux | |
| pip install pytest pytest-cov | |
| pytest --cov=./ --cov-report xml --cov-report lcov --cov-append | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |