Attempt fixing segmentation fault on MacOS in GitHub Actions #550
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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: 3.7 | |
| # 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 | |
| # steps: | |
| # - name: Checkout code | |
| # uses: actions/checkout@v2 | |
| # with: | |
| # submodules: true | |
| # - name: Cache Python requirements | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: ~/.cache/pip | |
| # key: ${{ runner.os }}-pip-${{ matrix.python-version }} | |
| # restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }} | |
| # - name: Setup Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v2 | |
| # 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: python setup.py build_ext --inplace --debug -j0 | |
| # - name: Install test requirements | |
| # run: python -m pip install -r pyhmmer/tests/requirements.txt | |
| # - 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@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-latest | |
| # strategy: | |
| # matrix: | |
| # python-tag: | |
| # - cp310-manylinux_aarch64 | |
| # - cp311-manylinux_aarch64 | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # with: | |
| # submodules: true | |
| # - name: Set up QEMU | |
| # id: qemu | |
| # uses: docker/setup-qemu-action@v2 | |
| # with: | |
| # platforms: all | |
| # - name: Build manylinux wheels | |
| # uses: pypa/cibuildwheel@v2.11.3 | |
| # 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 | |
| _PYTHON_HOST_PLATFORM: macosx-10.9-x86_64 | |
| strategy: | |
| 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 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Cache Python requirements | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ matrix.python-version }} | |
| restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }} | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show Python build environment | |
| run: arch -x86_64 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: arch -x86_64 python setup.py build_ext --inplace --debug | |
| - name: Install test requirements | |
| run: python -m pip install -r pyhmmer/tests/requirements.txt | |
| if: matrix.python-impl == 'CPython' | |
| # - name: Test Plan7 Background | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_background | |
| # - name: Test Plan7 Block | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_block | |
| # - name: Test Plan7 Builder | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_builder | |
| # - name: Test Plan7 Hit | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hit | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_checksum | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_composition | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_copy | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_eq | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_insert_emissions | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_command_line | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_name | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_accession | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_description | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_consensus | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_set_consensus | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_set_consensus_error | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write_empty | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write_error | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_renormalize | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_scale | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_zero | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_pickle | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_no_cutoffs | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_cutoffs | |
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_cutoffs_pickle | |
| # - name: Test Plan7 HMMFile | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hmmfile | |
| # - name: Test Plan7 OptimizedProfile | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_optimizedprofile | |
| # - name: Test Plan7 Pipeline | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_pipeline | |
| # - name: Test Plan7 Profile | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_profile | |
| # - name: Test Plan7 TopHits | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tophits | |
| # - name: Test Plan7 TraceAligner | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tracealigner | |
| # - name: Test Plan7 Traces | |
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_traces | |
| # - name: Test HMMER | |
| # run: python -m unittest -vv pyhmmer.tests.test_hmmer | |
| # run: python -m coverage run -m unittest discover -vv | |
| # - name: Upload to Codecov | |
| # uses: codecov/codecov-action@v3 | |
| # 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 |