Add Persistence #110
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| name: GH Actions CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| # Weekly tests at midnight on Sundays: | |
| - cron: "0 0 * * 0" | |
| concurrency: | |
| group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| main-tests: | |
| if: github.repository == 'yuxuanzhuang/ggmolvis' | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| mdanalysis-version: ["latest", "develop"] | |
| molecular-nodes-version: ["main", "v4.2.9", "v4.2.10"] | |
| python-version: ["3.11"] | |
| exclude: | |
| # Temporarily skip Windows with "latest" MDAnalysis version | |
| - os: windows-latest | |
| mdanalysis-version: "latest" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Set MolecularNodes version | |
| run: | | |
| cp devtools/conda-envs/test_env.yaml devtools/conda-envs/test_env_temp.yaml | |
| perl -pi -e "s/v4.2.9/${{ matrix.molecular-nodes-version }}/g" devtools/conda-envs/test_env_temp.yaml | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env_temp.yaml | |
| add-pip-as-python-dependency: true | |
| miniforge-variant: Miniforge3 | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| activate-environment: ggmolvis-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: ${{ matrix.mdanalysis-version }} | |
| install-tests: true | |
| installer: mamba | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -n 2 -v --cov=ggmolvis --cov-report=xml --color=yes ggmolvis/tests/ || true | |
| exit_code=$? | |
| if [ $exit_code -eq 139 ]; then | |
| echo "Segmentation fault occurred. Ignoring and continuing CI." | |
| exit 0 | |
| elif [ $exit_code -ne 0 ]; then | |
| echo "Tests failed with exit code $exit_code." | |
| exit $exit_code | |
| fi | |
| - name: codecov | |
| if: github.repository == 'yuxuanzhuang/ggmolvis' && github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| pylint_check: | |
| if: "github.repository == 'yuxuanzhuang/ggmolvis'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint mdanalysis | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint ggmolvis | |
| pypi_check: | |
| if: "github.repository == 'yuxuanzhuang/ggmolvis'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| pip install pipx twine | |
| - name: Build package | |
| run: | | |
| python -m pipx run build --sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/ggmolvis-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/ggmolvis-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION | |
| build_docs: | |
| if: "github.repository == 'yuxuanzhuang/ggmolvis'" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 15 | |
| env: | |
| CYTHON_TRACE_NOGIL: 1 | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.11" | |
| environment-file: docs/requirements.yaml | |
| add-pip-as-python-dependency: true | |
| miniforge-variant: Miniforge3 | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| activate-environment: ggmolvis-docs | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: build docs with sphinx | |
| # if: github.event_name == 'pull_request' | |
| continue-on-error: true | |
| run: | | |
| sphinx-build --keep-going ./docs/source ./docs/_build/html || true | |
| - name: Setup SSH | |
| uses: webfactory/[email protected] | |
| with: | |
| ssh-private-key: ${{ secrets.DEPLOY_KEY_PRIVATE }} | |
| - name: Clone Pages Repo using SSH | |
| run: | | |
| # Set folder name based on event type | |
| if [[ "${{ github.event_name }}" == "pull_request" ]]; then | |
| export FOLDER_NAME="main" | |
| else | |
| export FOLDER_NAME="latest" | |
| fi | |
| # Get version and branch details | |
| python devtools/write_version.py || true | |
| export VERSION=$(cat VERSION.txt) | |
| echo "VERSION: $VERSION" | |
| BRANCH="${GITHUB_REF#refs/heads/}" | |
| echo "Branch: $BRANCH" | |
| # Move built docs into versioned folder | |
| cd docs/_build/html | |
| mkdir -p ../${VERSION} | |
| mv * ../${VERSION} | |
| mv ../${VERSION} $VERSION | |
| # Get Git revision hash | |
| REV=$(git rev-parse --short HEAD) | |
| echo "Git Revision: $REV" | |
| # Initialize and configure Git | |
| git init | |
| git config user.name "GitHub Actions" | |
| git config user.email "[email protected]" | |
| git remote add upstream "[email protected]:yuxuanzhuang/ggmolvis.github.io.git" | |
| git fetch --depth 50 upstream gh-pages | |
| git reset upstream/gh-pages | |
| # Create redirects and copies | |
| mkdir -p ${FOLDER_NAME} | |
| cp -r ${VERSION}/* ${FOLDER_NAME}/ | |
| touch .nojekyll | |
| cp ../../../devtools/index.html . | |
| # Add changes to Git | |
| git add -A ${VERSION}/ | |
| git add -A ${FOLDER_NAME}/ | |
| git add .nojekyll *.html index.html | |
| # Add additional directories if they exist | |
| for dirname in dev stable documentation_pages; do | |
| if [ -d "$dirname" ]; then | |
| git add "$dirname" | |
| fi | |
| done | |
| # Check for uncommitted changes and commit | |
| git diff-index --quiet HEAD -- || \ | |
| git commit -m "Rebuilt HTML docs for version ${VERSION} from branch ${BRANCH} with Sphinx at ${REV}" | |
| # Push changes to upstream gh-pages branch | |
| git push -q upstream HEAD:gh-pages |