describe the filtering criteria in SAM/BAM/BAMPE parser #177
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: MACS3 CI Mac OS | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '**.md' | |
| - 'ChangeLog' | |
| - '.github/workflows/**' | |
| - '!.github/workflows/build-and-test-MACS3-macos.yml' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '**.md' | |
| - 'ChangeLog' | |
| - '.github/workflows/**' | |
| - '!.github/workflows/build-and-test-MACS3-macos.yml' | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [macos-13] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| runs-on: ${{ matrix.os }} | |
| name: Build on ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| steps: | |
| - name: Checkout MACS | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'true' | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| # This path is specific to Ubuntu | |
| path: ~/.cache/pip | |
| # Look to see if there is a cache hit for the corresponding requirements file | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| ${{ runner.os }}- | |
| - name: Setup venv | |
| run: | | |
| # create venv | |
| python3 -m venv macs3venv | |
| - name: Install dependencies | |
| run: | | |
| # make sure pip is the lastest | |
| source macs3venv/bin/activate | |
| python3 -m pip install --upgrade pip | |
| python3 -m pip install pytest | |
| if [ -f requirements.txt ]; then python3 -m pip install --upgrade -r requirements.txt; fi | |
| - name: Install MACS | |
| run: | | |
| # we use pip install instead of old fashion setup.py install | |
| source macs3venv/bin/activate | |
| python3 -m pip install . | |
| - name: Output versions of installed libraries | |
| run: | | |
| source macs3venv/bin/activate | |
| python3 -m pip freeze | |
| - name: Test with pytest | |
| run: | | |
| source macs3venv/bin/activate | |
| pytest --runxfail && cd test && ./cmdlinetest macs3 | |
| - name: Build sdist | |
| run: | | |
| source macs3venv/bin/activate | |
| python3 setup.py sdist | |
| - name: Archive sdist | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: | | |
| dist/*.tar.gz | |