Fixed okwarning block warning #974
Workflow file for this run
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| name: mda_gh_ci | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| tags: | |
| - "release-*" | |
| pull_request: | |
| branches: | |
| - develop | |
| schedule: | |
| # 3 am Tuesdays and Fridays | |
| - cron: "0 3 * * 2,5" | |
| 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 }}-${{ github.workflow }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| SPHINX_DIR: "doc/" | |
| HTML_DIR: "doc/build/html" | |
| jobs: | |
| build_docs: | |
| runs-on: ubuntu-latest | |
| env: | |
| CYTHON_TRACE_NOGIL: 1 | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| - name: setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| environment-name: mda-user-guide | |
| cache-environment: true | |
| cache-downloads: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| - name: install_deps | |
| run: | | |
| jupyter-nbextension enable nglview --py --sys-prefix | |
| - name: install_released_mda | |
| # If it's a release, pick up the latest version of MDAnalysis/Tests and deploy that | |
| if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/release')) | |
| run: python -m pip install MDAnalysis MDAnalysisTests -U --force-reinstall | |
| - name: build_docs | |
| run: | | |
| make -C ${SPHINX_DIR} html | |
| - name: deploy_docs | |
| if: github.event_name != 'pull_request' | |
| env: | |
| GH_USER: github-actions | |
| GH_EMAIL: "[email protected]" | |
| GH_REPOSITORY: "github.com/${{ github.repository }}.git" | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| URL: https://userguide.mdanalysis.org | |
| run: | | |
| # set up environment variables | |
| # cannot execute bash to make variables in env section | |
| # export URL for the Python script $UPDATE_JSON | |
| export URL | |
| export VERSION=$(python -c "import MDAnalysis; print(MDAnalysis.__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 ${{ env.HTML_DIR }} | |
| # move docs into version subfolder | |
| mkdir ../${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 ; do | |
| if [ -d $dirname ]; then git add $dirname; fi | |
| done | |
| # add redirect html files if they're generated | |
| if [ "$(ls *.html | wc -l)" -ge "1" ]; then | |
| # get list of directories and files present in the latest version | |
| cd $VERSION && mdfiles=$(ls -d *) && cd - | |
| for item in $mdfiles ; do | |
| # if the directory/file exists in top level, add it | |
| if [[ -f $item ]] || [[ -d $item ]]; then git add $item; fi | |
| done | |
| fi | |
| # 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 |