Merge pull request #250 from Becksteinlab/update-pandas-testing #208
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| name: CI | |
| on: | |
| # run every Sunday at 4:44 UTC | |
| schedule: | |
| - cron: "44 4 * * 0" | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "main" | |
| concurrency: | |
| group: "${{ github.ref }}-${{ github.head_ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macOS-latest] | |
| python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11"] | |
| gromacs-version: ["2021.1"] | |
| # Test other GROMACS versions selectively on a recent Python. | |
| # On macOS only test one GROMACS version and two Python versions | |
| # to keep the testing matrix manageable. | |
| exclude: | |
| - os: macOS-latest | |
| python-version: "3.6" | |
| - os: macOS-latest | |
| python-version: "3.7" | |
| - os: macOS-latest | |
| python-version: "3.8" | |
| - os: macOS-latest | |
| python-version: "3.9" | |
| - os: macOS-latest | |
| python-version: "3.10" | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "2.7" | |
| gromacs-version: "4.6.5" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| gromacs-version: "4.6.5" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| gromacs-version: "2018.6" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| gromacs-version: "2019.1" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| gromacs-version: "2020.6" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| gromacs-version: "2022.4" | |
| env: | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: setup miniconda (Python ${{ matrix.python-version }}) | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| auto-update-conda: true | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| show-channel-urls: true | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| - name: Python version ${{ matrix.python-version }} | |
| shell: bash -l {0} | |
| run: | | |
| python -c "import sys; print(sys.version)" | |
| - name: Install package dependencies | |
| shell: bash -l {0} | |
| run: | | |
| mamba install six numpy scipy matplotlib-base pandas numkit | |
| - name: Install pytest and plugins | |
| shell: bash -l {0} | |
| run: | | |
| mamba install pytest pytest-pep8 pytest-cov codecov | |
| - name: Install GROMACS (${{ matrix.gromacs-version }}) | |
| shell: bash -l {0} | |
| run: | | |
| mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --no-deps . | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./tests | |
| - name: Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |