gh-ci.yaml

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: "github-action@users.noreply.github.com"
        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