notebook-pr.yaml

name: notebook-pr

on: 
  pull_request:
    branches: main
    paths: '**/*.ipynb'

env:
  NB_KERNEL: python
  ORG: neuromatch
  NMA_REPO: nasa-open-science
  NMA_MAIN_BRANCH: main

jobs:

  process-notebooks:

    runs-on: ubuntu-latest
    steps:

      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          fetch-depth: 0
          ref: ${{ github.head_ref }}

      - name: Get commit message
        run: |
          readonly local msg=$(git log -1 --pretty=format:"%s")
          echo "COMMIT_MESSAGE=$msg" >> $GITHUB_ENV

      - name: Set up Python
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        uses: actions/setup-python@v4
        with:
          python-version: 3.9

      - name: Install CI tools
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        run: |
          BRANCH=`python -c 'import os, re; m = re.search(r"nmaci:([\w-]+)", os.environ["COMMIT_MESSAGE"]); print("main" if m is None else m.group(1))'`
          # NOTE: might enventually change this back if we integrate changes
          wget https://github.com/neuromatch/nmaci/archive/refs/heads/$BRANCH.tar.gz
          tar -xzf $BRANCH.tar.gz
          pip install --upgrade pip
          pip install -r nmaci-$BRANCH/requirements.txt
          mv nmaci-$BRANCH/scripts/ ci/
          rm -r nmaci-$BRANCH
          echo ci/ >> .gitignore

      - name: Install dependencies
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        run: |
          python -m pip install --upgrade pip wheel
          pip install -r requirements.txt
          pip install jupyter_client==7.3.5  # downgrade jupyter-client to fix hangs

      - name: Install XKCD fonts
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        run: |
          sudo apt-get update -yq
          wget http://archive.ubuntu.com/ubuntu/pool/universe/f/fonts-humor-sans/fonts-humor-sans_1.0-4_all.deb
          sudo dpkg -i --force-all fonts-humor-sans_1.0-4_all.deb <<< 'yes'
          sudo apt install -fy
          rm -f $HOME/.matplotlib/fontList.cache

      - name: Get changed files
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        id: changed-files
        uses: tj-actions/changed-files@v35
        
      - name: List all changed files
        run: |
          for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
            echo "$file was changed."
          done

      - name: Process notebooks
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        id: process_notebooks
        run: |
          branch=${{ github.event.pull_request.head.ref }}
          nbs=`python ci/select_notebooks.py ${{ steps.changed-files.outputs.all_changed_files }}`
          if ${{ contains(env.COMMIT_MESSAGE, 'ci:check') }}; then
            execflag="--check-execution";
          else
            execflag="--execute";
          fi
          python ci/process_notebooks.py $nbs $execflag
          python ci/verify_exercises.py $nbs --c "$COMMIT_MESSAGE"
          python ci/make_pr_comment.py $nbs --branch $branch --o comment.txt

      # - name: Add PR comment
      #   if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
      #   uses: machine-learning-apps/pr-comment@1.0.0
      #   env:
      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      #   with:
      #     path: comment.txt

      - name: Update READMEs
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
        run: python ci/generate_tutorial_readmes.py

      - name: Remove unreferenced derivatives
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci') && success()"
        run: |
          python ci/find_unreferenced_content.py > to_remove.txt
          if [ -s to_remove.txt ]; then git rm --pathspec-from-file=to_remove.txt; fi

      - name: Commit post-processed files
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci') && success()"
        run: |
          git config --local user.email "action@github.com"
          git config --local user.name "GitHub Action"
          git add '**/*.ipynb'
          git add '**/static/*.png'
          # git add '**/solutions/*.py'
          git add '**/README.md'
          git diff-index --quiet HEAD || git commit -m "Process tutorial notebooks"

      - name: Push post-processed files
        if: "!contains(env.COMMIT_MESSAGE, 'skip ci') && success()"
        uses: ad-m/github-push-action@v0.6.0
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ github.head_ref }}