Decode BAM sequence with less code. Dispatch function at dynamic link time rather than at run time. #587
Workflow file for this run
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| lint: | |
| # Run for PRs only if they come from a forked repo (avoids duplicate runs) | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| timeout-minutes: 10 | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| toxenv: [flake8, black, mypy, docs] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install tox | |
| run: python -m pip install tox | |
| - name: Run tox ${{ matrix.toxenv }} | |
| run: tox -e ${{ matrix.toxenv }} | |
| build: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # required for setuptools_scm | |
| - name: Build sdist and temporary wheel | |
| run: pipx run build | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/*.tar.gz | |
| test: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| timeout-minutes: 10 | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| include: | |
| - os: macos-13 | |
| python-version: "3.10" | |
| - os: macos-14 | |
| python-version: "3.10" | |
| - os: windows-latest | |
| python-version: "3.10" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install tox | |
| run: python -m pip install tox | |
| - name: Test | |
| run: tox -e py | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| wheels: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| needs: [lint, test] | |
| timeout-minutes: 15 | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-13, macos-14] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # required for setuptools_scm | |
| - name: Build wheels | |
| uses: pypa/[email protected] | |
| env: | |
| CIBW_BUILD: "cp*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64" | |
| CIBW_SKIP: "cp37-*" | |
| CIBW_TEST_SKIP: "cp38-macosx_*:arm64" | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-${{ matrix.os }} | |
| path: wheelhouse/*.whl | |
| publish: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| needs: [build, wheels] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/ | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: wheels-* | |
| path: dist/ | |
| merge-multiple: true | |
| - name: Publish to PyPI | |
| uses: pypa/[email protected] | |
| with: | |
| password: ${{ secrets.pypi_password }} | |
| #password: ${{ secrets.test_pypi_password }} | |
| #repository_url: https://test.pypi.org/legacy/ |