capture and print test_scripts output for debugging CI-testing #3 #252
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python [3.7,3.8,3.9,3.10,3.11,3.12] MacOs | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| workflow_dispatch: | |
| env: | |
| BEZIER_NO_EXTENSION: true | |
| OPENBLAS_NUM_THREADS: 1 | |
| MKL_NUM_THREADS : 1 | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest] | |
| python-version: [3.7, 3.8, 3.9, '3.10', '3.11','3.12'] | |
| # Proposed workaround for legacy versions, see | |
| # https://github.com/actions/setup-python/issues/856 and | |
| # https://github.com/actions/runner-images/issues/9770#issuecomment-2085623315 | |
| exclude: # Python < v3.8 does not support Apple Silicon ARM64. | |
| - python-version: "3.7" | |
| os: macos-latest | |
| include: # So run those legacy versions on Intel CPUs. | |
| - python-version: "3.7" | |
| os: macos-13 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conditionally set up Conda for Python 3.7 | |
| if: ${{ matrix.python-version == '3.7' }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| ### Python 3.7 block | |
| - name: Conditionally set up conda for Python 3.7 | |
| if: ${{ matrix.python-version == '3.7' }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| - name: If Python is 3.7 install openmm via conda | |
| if: ${{ matrix.python-version == '3.7' }} | |
| run: conda install openmm -c conda-forge -y | |
| shell: bash | |
| - name: If Python is 3.7 install dependencies in conda base environment | |
| if: ${{ matrix.python-version == '3.7' }} | |
| run: | | |
| conda run --live-stream -n base python -m pip install --upgrade pip | |
| conda run --live-stream -n base pip install pytest pytest-cov pytest-xdist | |
| shell: bash | |
| - name: If Python is 3.7 install package in conda base environment | |
| if: ${{ matrix.python-version == '3.7' }} | |
| run: | | |
| conda run --live-stream -n base pip install --upgrade pip | |
| conda run --live-stream -n base pip install --upgrade setuptools | |
| conda run --live-stream -n base pip install -e . | |
| conda run --live-stream -n base pip freeze | |
| shell: bash | |
| - name: If Python is 3.7 test with pytest and coverage Linux 8 threads in conda base environment | |
| if: ${{ matrix.python-version == '3.7' }} | |
| run: | | |
| echo -e '[run]\nomit = *dihedrals.py,*contact_matrix.py' > .coveragerc | |
| conda run --live-stream --live-stream -n base pytest -n 8 -v -s --cov=./ --cov-report=xml --disable-warnings --cov-config=.coveragerc | |
| shell: bash | |
| #### End Python 3.7 block | |
| - name: If Python != 3.7 install dependencies normally | |
| if: ${{ matrix.python-version != '3.7' }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest pytest-cov pytest-xdist | |
| - name: If Python != 3.7 install package normaly | |
| if: ${{ matrix.python-version != '3.7' }} | |
| run: | | |
| pip install --upgrade pip | |
| pip install --upgrade setuptools | |
| pip install -e . | |
| pip freeze | |
| - name: If Python != 3.7 test with pytest and coverage Linux 8 threads normally | |
| if: ${{ matrix.python-version != '3.7' }} | |
| run: | | |
| echo -e '[run]\nomit = *dihedrals.py,*contact_matrix.py' > .coveragerc | |
| pytest -k test_mdc_neighborhood -vs --cov=./ --cov-report=xml --disable-warnings --cov-config=.coveragerc | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| #directory: ./coverage/reports/ | |
| flags: unittests | |
| env_vars: OS,PYTHON | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| #path_to_write_report: ./coverage/codecov_report.gz | |