Use MDTraj dssp #366
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: test package | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| env: | |
| VERMOUTH_TEST_DSSP: mkdssp | |
| SKIP_GENERATE_AUTHORS: 1 | |
| SKIP_WRITE_GIT_CHANGELOG: 1 | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| py_version: ["3.8", "3.9", "3.10", "3.11"] | |
| include: | |
| - py_version: "3.8" | |
| WITH_CODECOV: true | |
| - py_version: "3.9" | |
| WITH_CODECOV: true | |
| - py_version: "3.10" | |
| WITH_CODECOV: true | |
| - py_version: "3.11" | |
| WITH_CODECOV: true | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.py_version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.py_version }} | |
| cache: pip | |
| cache-dependency-path: | | |
| **/setup.cfg | |
| **/requirements-*.txt | |
| **/pyproject.toml | |
| - name: Install dependencies part I | |
| run: | | |
| sudo apt-get install dssp | |
| pip install --upgrade setuptools pip | |
| - name: Install package and requirements | |
| run: | | |
| pip install --upgrade . | |
| pip install -r requirements-tests.txt | |
| - name: Run pytest with codecoverage | |
| run: pytest vermouth --cov=vermouth --cov-report=xml --hypothesis-show-statistics | |
| - if: ${{ matrix.WITH_CODECOV }} | |
| name: Upload coverage codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| cache: pip | |
| cache-dependency-path: | | |
| **/setup.cfg | |
| **/requirements-*.txt | |
| **/pyproject.toml | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade setuptools pip | |
| pip install --upgrade . | |
| pip install -r requirements-tests.txt | |
| - name: Run pylint | |
| run: | | |
| pylint --disable=fixme --fail-under=8.0 vermouth | |
| pylint --disable=fixme --fail-under=9.0 bin/martinize2 | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| cache: pip | |
| cache-dependency-path: | | |
| **/setup.cfg | |
| **/requirements-*.txt | |
| **/pyproject.toml | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade setuptools pip | |
| pip install --upgrade . | |
| pip install -r requirements-docs.txt | |
| - name: Run docs | |
| run: | | |
| mkdir -p doc/source/_static | |
| sphinx-build -EnW -b html doc/source/ doc/build/html |