Fix SequenceFile.__init__ crashing on opening SSI indices for gzip-…
#835
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| name: Test | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| test_linux_x86: | |
| name: Test (Linux) | |
| runs-on: ubuntu-latest | |
| env: | |
| OS: Linux | |
| strategy: | |
| matrix: | |
| include: | |
| - 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: '3.13' | |
| python-release: 'v3.13' | |
| python-impl: CPython | |
| - python-version: '3.14' | |
| python-release: 'v3.14' | |
| python-impl: CPython | |
| - 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: Show Python build environment | |
| run: python -m sysconfig | |
| - name: Update pip | |
| run: python -m pip install -U pip wheel setuptools | |
| - name: Install Python requirements | |
| run: python -m pip install -r .github/workflows/requirements.txt | |
| - name: Build C extension | |
| run: pip install -vv -e . --no-build-isolation | |
| - name: Install test requirements | |
| run: python -m pip install -r src/pyhmmer/tests/requirements.txt | |
| - name: Test without coverage | |
| run: python -m unittest pyhmmer.tests -vv | |
| #- name: Upload to Codecov | |
| # if: matrix.python-impl == 'CPython' | |
| # uses: codecov/codecov-action@v3 | |
| # with: | |
| # flags: ${{ matrix.python-release }} | |
| # env_vars: OS | |
| # name: test-python-${{ matrix.python-version }} | |
| # fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # verbose: true | |
| # # test_linux_arm64: | |
| # # name: Test (Linux, arm64) | |
| # # runs-on: ubuntu-22.04-arm | |
| # # strategy: | |
| # # matrix: | |
| # # python-tag: | |
| # # - cp310-manylinux_aarch64 | |
| # # - cp311-manylinux_aarch64 | |
| # # steps: | |
| # # - uses: actions/checkout@v4 | |
| # # with: | |
| # # submodules: true | |
| # # - name: Build manylinux wheels | |
| # # uses: pypa/cibuildwheel@v2.16.5 | |
| # # env: | |
| # # CIBW_ARCHS: aarch64 | |
| # # CIBW_BUILD: ${{ matrix.python-tag }} | |
| # # CIBW_BUILD_VERBOSITY: 2 | |
| # # CIBW_BEFORE_BUILD: pip install cython | |
| # # CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv | |
| # # CIBW_TEST_REQUIRES: importlib-resources | |
| # # with: | |
| # # output-dir: dist | |
| # # - uses: actions/upload-artifact@v3 | |
| # # with: | |
| # # name: wheels | |
| # # path: dist/* | |
| test_osx_x86: | |
| name: Test (OSX) | |
| runs-on: macos-latest | |
| env: | |
| OS: OSX | |
| strategy: | |
| matrix: | |
| include: | |
| - 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: '3.13' | |
| python-release: 'v3.13' | |
| python-impl: CPython | |
| - python-version: '3.14' | |
| python-release: 'v3.14' | |
| python-impl: CPython | |
| - 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: Show Python build environment | |
| run: python -m sysconfig | |
| - name: Update pip | |
| run: python -m pip install -U pip wheel setuptools | |
| - name: Install Python requirements | |
| run: python -m pip install -r .github/workflows/requirements.txt | |
| - name: Build C extension | |
| run: pip install -vv -e . --no-build-isolation | |
| - name: Install test requirements | |
| run: python -m pip install -r src/pyhmmer/tests/requirements.txt | |
| if: matrix.python-impl == 'CPython' | |
| - name: Test without coverage | |
| run: python -m unittest pyhmmer.tests -vv | |
| # - name: Upload to Codecov | |
| # uses: codecov/codecov-action@v4 | |
| # if: matrix.python-impl == 'CPython' | |
| # with: | |
| # flags: ${{ matrix.python-release }} | |
| # env_vars: OS | |
| # name: test-python-${{ matrix.python-version }} | |
| # fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # codecov_curl_args: "--globoff" | |
| # verbose: true | |
| test_win32_x86: | |
| name: Test (Windows) | |
| runs-on: windows-2019 | |
| env: | |
| OS: Windows | |
| strategy: | |
| matrix: | |
| include: | |
| - 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: '3.13' | |
| python-release: 'v3.13' | |
| python-impl: CPython | |
| - python-version: '3.14' | |
| python-release: 'v3.14' | |
| python-impl: CPython | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Set up MinGW | |
| uses: egor-tensin/setup-mingw@v3 | |
| id: setup | |
| with: | |
| platform: x64 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show Python build environment | |
| run: python -m sysconfig | |
| - name: Update pip | |
| run: python -m pip install -U pip wheel setuptools | |
| - name: Install Python requirements | |
| run: python -m pip install -r .github/workflows/requirements.txt | |
| - name: Build C extension | |
| run: pip install -vv . --no-build-isolation | |
| env: | |
| CC: "${{ steps.setup.outputs.gcc }}" | |
| CMAKE_GENERATOR: Ninja | |
| CMAKE_GENERATOR_PLATFORM: "" | |
| - name: Install test requirements | |
| run: python -m pip install -r src/pyhmmer/tests/requirements.txt | |
| - name: Test without coverage | |
| run: python -m unittest pyhmmer.tests -vv | |
| #- name: Upload to Codecov | |
| # if: matrix.python-impl == 'CPython' | |
| # uses: codecov/codecov-action@v3 | |
| # with: | |
| # flags: ${{ matrix.python-release }} | |
| # env_vars: OS | |
| # name: test-python-${{ matrix.python-version }} | |
| # fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # verbose: true |