Fix linking in jdaviz for NIRISS notebook #173
Workflow file for this run
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| name: Build HTML on merge | |
| on: | |
| pull_request_target: | |
| types: [closed] | |
| paths: | |
| - '**.ipynb' | |
| env: | |
| CASJOBS_PW: ${{ secrets.CASJOBS_PW }} | |
| CASJOBS_USERID: ${{ secrets.CASJOBS_USERID }} | |
| jobs: | |
| prepare_matrix: | |
| if: github.event.pull_request.merged == true | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - id: set-matrix | |
| run: | | |
| files=$(git diff --name-only ${{ github.event.pull_request.base.sha }}...${{ github.event.pull_request.head.sha }} '*.ipynb') | |
| #files_json=$(echo $files | jq -R -s -c 'split("\n")[:-1]') | |
| files_json=$(echo "$files" | jq -R -s -c 'split("\n")[:-1]') | |
| echo "::set-output name=matrix::${files_json}" | |
| execute-notebooks: | |
| if: github.event.pull_request.merged == true | |
| needs: prepare_matrix | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| notebook: ${{fromJson(needs.prepare_matrix.outputs.matrix)}} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ vars.PYTHON_VERSION }} | |
| - name: Install Dependencies (if requirements.txt exists) and Execute Notebook | |
| run: | | |
| notebook="${{ matrix.notebook }}" | |
| dir=$(dirname "$notebook") | |
| if [ -f "$dir/requirements.txt" ]; then | |
| pip install -r "$dir/requirements.txt" | |
| fi | |
| pip install notebook | |
| jupyter nbconvert --to notebook --execute --inplace "$notebook" | |
| - name: Commit modified file on current branch | |
| run: | | |
| git config user.name 'CI Bot' | |
| git config user.email '[email protected]' | |
| git add "${{ matrix.notebook }}" | |
| git commit -m "Storing executed notebook ${{ matrix.notebook }}" | |
| - name: Checkout only the file to the target branch | |
| run: | | |
| git fetch | |
| git pull | |
| git checkout -f gh-storage | |
| git checkout @{-1} "${{ matrix.notebook }}" | |
| - name: Commit and push modifications to target branch | |
| run: | | |
| git commit -m "Storing executed notebook ${{ matrix.notebook }}" | |
| MAX_RETRIES=5 | |
| RETRY_DELAY=10s | |
| for i in $(seq 1 $MAX_RETRIES); do | |
| git push origin gh-storage --force && break || { | |
| echo "Push $i failed... waiting $RETRY_DELAY" | |
| sleep $RETRY_DELAY | |
| } | |
| done | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| generate_html: | |
| if: github.event.pull_request.merged == true | |
| needs: execute-notebooks | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ vars.PYTHON_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ vars.PYTHON_VERSION }} | |
| - name: Install dependencies | |
| run: | | |
| pip install ghp-import | |
| pip install jupyter-book==v0.15.1 | |
| pip install myst-nb | |
| pip install astroid | |
| pip install nbval | |
| #pip install bs4 | |
| #pip install lxml | |
| ## test to bypass the jupyter-book lower version | |
| pip install jsonschema==4.6.0 | |
| PATH="${PATH}:${HOME}/.local/bin" | |
| - name: Build HTML | |
| run: | | |
| git fetch | |
| git checkout origin/gh-storage -- notebooks/ | |
| jupyter-book build . | |
| - name: Execute JDAVIZ placeholder substitution | |
| run: | | |
| cp jdaviz_placeholder_new.png _build/html | |
| chmod +x placeholder.sh | |
| ./placeholder.sh | |
| # Push the book's HTML to github-pages | |
| - name: GitHub Pages action | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./_build/html |