Use readinto in FastaReader if supported by the file-like object
#17
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| name: Test | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| test_linux: | |
| name: Test (Linux) | |
| runs-on: ubuntu-22.04 | |
| env: | |
| OS: Linux | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # - python-version: 3.7 | |
| # python-release: v3.7 | |
| # python-impl: CPython | |
| # - python-version: 3.8 | |
| # python-release: v3.8 | |
| # python-impl: CPython | |
| # - python-version: 3.9 | |
| # python-release: v3.9 | |
| # python-impl: CPython | |
| # - python-version: '3.10' | |
| # python-release: v3.10 | |
| # python-impl: CPython | |
| # - python-version: 3.11 | |
| # python-release: v3.11 | |
| # python-impl: CPython | |
| - python-version: 3.12 | |
| python-release: v3.12 | |
| python-impl: CPython | |
| # - python-version: pypy-3.6 | |
| # python-release: v3.6 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.7 | |
| # python-release: v3.7 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.8 | |
| # python-release: v3.8 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.9 | |
| # python-release: v3.9 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.10 | |
| # python-release: v3.10 | |
| # python-impl: PyPy | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Update pip | |
| run: python -m pip install -U pip | |
| - name: Install Python requirements | |
| run: python -m pip install -r .github/workflows/requirements.txt | |
| - name: Cache build folder | |
| uses: actions/cache@v4 | |
| with: | |
| path: build | |
| key: ${{ runner.os }} | |
| - name: Build Cython extensions in debug mode | |
| run: python -m pip install -v . -C cmake.build-type=Debug | |
| - name: Test with coverage | |
| run: python -m coverage run -m unittest discover -vv | |
| - name: Upload to Codecov | |
| if: matrix.python-impl == 'CPython' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }} | |
| name: test-python-${{ matrix.python-version }} | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| # test_osx: | |
| # name: Test (OSX) | |
| # runs-on: macos-12 | |
| # env: | |
| # OS: OSX | |
| # strategy: | |
| # fail-fast: false | |
| # matrix: | |
| # include: | |
| # - python-version: 3.7 | |
| # python-release: v3.7 | |
| # python-impl: CPython | |
| # - python-version: 3.8 | |
| # python-release: v3.8 | |
| # python-impl: CPython | |
| # - python-version: 3.9 | |
| # python-release: v3.9 | |
| # python-impl: CPython | |
| # - python-version: '3.10' | |
| # python-release: v3.10 | |
| # python-impl: CPython | |
| # - python-version: '3.11' | |
| # python-release: v3.11 | |
| # python-impl: CPython | |
| # - python-version: '3.12' | |
| # python-release: v3.12 | |
| # python-impl: CPython | |
| # - python-version: pypy-3.7 | |
| # python-release: v3.7 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.8 | |
| # python-release: v3.8 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.9 | |
| # python-release: v3.9 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.10 | |
| # python-release: v3.10 | |
| # python-impl: PyPy | |
| # steps: | |
| # - name: Checkout code | |
| # uses: actions/checkout@v4 | |
| # with: | |
| # submodules: true | |
| # - name: Setup Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Setup deployment target | |
| # shell: bash | |
| # if: ${{ startsWith(matrix.python-version, 'pypy') || matrix.python-version == '3.11' || matrix.python-version == '3.12' }} | |
| # run: echo "MACOSX_DEPLOYMENT_TARGET=10.12" >> $GITHUB_ENV | |
| # - name: Update pip | |
| # run: python -m pip install -U pip | |
| # - name: Install Python requirements | |
| # run: python -m pip install -r .github/workflows/requirements.txt | |
| # - name: Build Cython extensions in debug mode | |
| # run: python -m pip install -vv . --no-build-isolation -C cmake.build-type=Debug | |
| # - name: Test with coverage | |
| # run: python -m coverage run -m unittest discover -vv | |
| # - name: Upload to Codecov | |
| # if: matrix.python-impl == 'CPython' | |
| # uses: codecov/codecov-action@v4 | |
| # with: | |
| # flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }} | |
| # name: test-python-${{ matrix.python-version }} | |
| # fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # test_windows: | |
| # name: Test (Windows) | |
| # runs-on: windows-latest | |
| # env: | |
| # OS: Windows | |
| # strategy: | |
| # fail-fast: false | |
| # matrix: | |
| # include: | |
| # - python-version: 3.6 | |
| # python-release: v3.6 | |
| # python-impl: CPython | |
| # - python-version: 3.7 | |
| # python-release: v3.7 | |
| # python-impl: CPython | |
| # - python-version: 3.8 | |
| # python-release: v3.8 | |
| # python-impl: CPython | |
| # - python-version: 3.9 | |
| # python-release: v3.9 | |
| # python-impl: CPython | |
| # - python-version: '3.10' | |
| # python-release: v3.10 | |
| # python-impl: CPython | |
| # - python-version: '3.11' | |
| # python-release: v3.11 | |
| # python-impl: CPython | |
| # - python-version: '3.12' | |
| # python-release: v3.12 | |
| # python-impl: CPython | |
| # - python-version: pypy-3.7 | |
| # python-release: v3.7 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.8 | |
| # python-release: v3.8 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.9 | |
| # python-release: v3.9 | |
| # python-impl: PyPy | |
| # - python-version: pypy-3.10 | |
| # python-release: v3.10 | |
| # python-impl: PyPy | |
| # steps: | |
| # - name: Checkout code | |
| # uses: actions/checkout@v4 | |
| # with: | |
| # submodules: true | |
| # - name: Setup Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # architecture: x64 | |
| # - name: Update pip | |
| # run: python -m pip install -U pip | |
| # - name: Install Python requirements | |
| # run: python -m pip install -r .github/workflows/requirements.txt | |
| # - name: Build Cython extensions in debug mode | |
| # run: python -m pip install -vv . --no-build-isolation -C cmake.build-type=Debug | |
| # - name: Test with coverage | |
| # run: python -m coverage run -m unittest discover -vv |