Allow bonds etc to be additively guessed when present (#4761) #6220
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| name: GH Actions CI | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| pull_request: | |
| branches: | |
| - develop | |
| workflow_dispatch: | |
| concurrency: | |
| # Probably overly cautious group naming. | |
| # Commits to develop will cancel each other, but PRs will only cancel | |
| # commits within the same PR | |
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| main_tests: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, ] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| full-deps: [true, ] | |
| codecov: [true, ] | |
| include: | |
| - name: python_313 | |
| os: ubuntu-latest | |
| python-version: "3.13" | |
| full-deps: false | |
| codecov: true | |
| - name: macOS_monterey_py311 | |
| os: macOS-12 | |
| python-version: "3.12" | |
| full-deps: true | |
| codecov: true | |
| - name: macOS_14_arm64_py312 | |
| os: macOS-14 | |
| python-version: "3.12" | |
| full-deps: false | |
| codecov: true | |
| - name: numpy_min | |
| os: ubuntu-latest | |
| python-version: "3.10" | |
| full-deps: false | |
| codecov: true | |
| numpy: numpy=1.23.2 | |
| - name: asv_check | |
| os: ubuntu-latest | |
| python-version: "3.10" | |
| full-deps: true | |
| codecov: false | |
| extra-pip-deps: asv | |
| env: | |
| CYTHON_TRACE_NOGIL: 1 | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: setup_os | |
| uses: ./.github/actions/setup-os | |
| with: | |
| os-type: ${{ matrix.os }} | |
| - name: setup_micromamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: mda | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pip | |
| # using jaime's shim to avoid pulling down the cudatoolkit | |
| condarc: | | |
| channels: | |
| - jaimergp/label/unsupported-cudatoolkit-shim | |
| - conda-forge | |
| - bioconda | |
| - name: install_deps | |
| uses: ./.github/actions/setup-deps | |
| with: | |
| micromamba: true | |
| full-deps: ${{ matrix.full-deps }} | |
| # disable GSD because it occasionally introduce hanging in testing #4209 | |
| gsd: '' | |
| # in most cases will just default to empty, i.e. pick up max version from other deps | |
| numpy: ${{ matrix.numpy }} | |
| extra-pip-deps: ${{ matrix.extra-pip-deps }} | |
| - name: build_srcs | |
| uses: ./.github/actions/build-src | |
| with: | |
| build-tests: true | |
| build-docs: false | |
| # The standard mdanalysis deployment is to build with the | |
| # oldest supported numpy version and then use whatever new | |
| # numpy version we want at runtime. To do this we ensure | |
| # that we use build isolation | |
| isolation: true | |
| - name: check_deps | |
| run: | | |
| micromamba list | |
| pip list | |
| - name: run_tests | |
| if: contains(matrix.name, 'asv_check') != true | |
| run: | | |
| PYTEST_FLAGS="--disable-pytest-warnings --durations=50" | |
| if [ ${{ matrix.codecov }} = "true" ]; then | |
| PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml" | |
| fi | |
| echo $PYTEST_FLAGS | |
| pytest -n logical --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS | |
| - name: run_asv | |
| if: contains(matrix.name, 'asv_check') | |
| run: | | |
| cd benchmarks | |
| time python -m asv check -E existing | |
| - name: codecov | |
| if: matrix.codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True | |
| build_docs: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 15 | |
| env: | |
| CYTHON_TRACE_NOGIL: 1 | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: setup_micromamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: mda | |
| create-args: >- | |
| python=3.10 | |
| pip | |
| # using jaime's shim to avoid pulling down the cudatoolkit | |
| condarc: | | |
| channels: | |
| - jaimergp/label/unsupported-cudatoolkit-shim | |
| - conda-forge | |
| - bioconda | |
| - name: install_deps | |
| uses: ./.github/actions/setup-deps | |
| with: | |
| micromamba: true | |
| full-deps: true | |
| gsd: '' | |
| extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils" | |
| extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0" | |
| - name: build_srcs | |
| uses: ./.github/actions/build-src | |
| with: | |
| build-tests: true | |
| build-docs: true | |
| isolation: true | |
| - name: doctests | |
| if: github.event_name == 'pull_request' | |
| continue-on-error: true | |
| run: | | |
| cd package && sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html | |
| - name: deploy_docs | |
| if: github.event_name != 'pull_request' | |
| env: | |
| GH_USER: github-actions | |
| GH_EMAIL: "github-action@users.noreply.github.com" | |
| GH_REPOSITORY: "github.com/${{ github.repository }}.git" | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| URL: https://docs.mdanalysis.org | |
| run: | | |
| # set up environment variables | |
| # cannot execute bash to make variables in env section | |
| # export URL for the Python script $UPDATE_JSON | |
| export URL | |
| export VERSION=$(cd package/MDAnalysis; python -c 'import version; print(version.__version__)') | |
| UPDATE_JSON=$(pwd)/maintainer/update_json_stubs_sitemap.py | |
| BRANCH="${GITHUB_REF#refs/heads/}" | |
| # the below turns off non-blocking as it causes large writes to stdout to fail | |
| # (see https://github.com/travis-ci/travis-ci/issues/4704) | |
| # commented out as this is not a problem with gh-actions | |
| # python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);' | |
| cd package/doc/html/ | |
| # move docs into version subfolder | |
| mkdir ../${VERSION} && mv * ../${VERSION} && mv ../${VERSION} $VERSION | |
| # set up git | |
| REV=$(git rev-parse --short HEAD) | |
| git init | |
| git config user.name $GH_USER | |
| git config user.email $GH_EMAIL | |
| git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}" | |
| git fetch --depth 50 upstream $BRANCH gh-pages | |
| git reset upstream/gh-pages | |
| # redirects and copies | |
| mkdir latest | |
| python $UPDATE_JSON | |
| touch . | |
| touch .nojekyll | |
| git add -A ${VERSION}/ | |
| git add .nojekyll versions.json *.xml *.html index.html latest | |
| for dirname in dev stable documentation_pages ; do | |
| if [ -d $dirname ]; then git add $dirname; fi | |
| done | |
| # check for anything to commit | |
| # https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes | |
| git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs for version ${VERSION} from branch ${BRANCH} with sphinx at ${REV}" | |
| git push -q upstream HEAD:gh-pages | |
| sdist_check_and_build: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: install_deps | |
| run: | | |
| python -m pip install -U pip pipx wheel build | |
| python -m pip install twine "readme-renderer>=34.0" pytest-xdist pytest-timeout | |
| - name: build_package_sdist | |
| run: | | |
| pipx run build --sdist --outdir dist package | |
| - name: build_testsuite_sdist | |
| run: | | |
| pipx run build --sdist --outdir dist testsuite | |
| - name: check_package_build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/mdanalysis-*.tar.gz | head -n1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysis-*.tar.gz found"; exit 1; } | |
| twine check $DISTRIBUTION | |
| - name: check_testsuite_build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/mdanalysistests-*.tar.gz | head -n1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysisTests-*.tar.gz found"; exit 1; } | |
| twine check $DISTRIBUTION | |
| - name: install sdist | |
| working-directory: ./dist | |
| run: | | |
| ls -a . | |
| python -m pip install mdanalysis-*.tar.gz | |
| python -m pip install mdanalysistests-*.tar.gz | |
| - name: check install | |
| run: pip list | |
| - name: run tests | |
| working-directory: ./dist | |
| run: python -m pytest --timeout=200 -n logical --pyargs MDAnalysisTests |