Manual Full Archive Execute-Store-Generate HTML #10
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| name: Manual Execute and Merge Notebooks | |
| on: [workflow_dispatch] | |
| jobs: | |
| find_notebooks: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| notebook_list: ${{ steps.find.outputs.notebook_list }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Find notebook files | |
| id: find | |
| run: | | |
| notebook_files=$(find notebooks -name "*.ipynb" | jq -R -s -c 'split("\n")[:-1]') | |
| #echo "::set-output name=notebook_list::$notebook_files" | |
| echo "notebook_list=$notebook_files" >>$GITHUB_OUTPUT | |
| execute_notebooks: | |
| needs: find_notebooks | |
| runs-on: ubuntu-latest | |
| outputs: | |
| executed_notebooks: ${{ steps.execute.outputs.executed_notebooks }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| notebook: ${{fromJson(needs.find_notebooks.outputs.notebook_list)}} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| export PYDEVD_DISABLE_FILE_VALIDATION=1 | |
| python -m pip install --upgrade pip | |
| pip install -r pre-requirements.txt | |
| pip install -r requirements.txt | |
| pip install pytest | |
| pip install nbval | |
| pip install nbconvert | |
| - name: Execute notebook | |
| id: execute | |
| run: | | |
| if [ "${{ matrix.notebook }}" != "notebooks/preimaging/preimaging_01_mirage.ipynb" ]; then | |
| if ! jupyter nbconvert --to notebook --execute --inplace ${{ matrix.notebook }}; then | |
| python .github/scripts/insert_failure_message.py ${{ matrix.notebook }} | |
| fi | |
| fi | |
| - name: Archive executed notebooks | |
| run: | | |
| if [ "${{ matrix.notebook }}" != "notebooks/preimaging/preimaging_01_mirage.ipynb" ]; then | |
| git config pull.rebase false | |
| git config --global user.name "GitHub Actions" | |
| git config --global user.email "[email protected]" | |
| git checkout -b gh-storage | |
| git add ${{ matrix.notebook }} | |
| git commit -m 'Added executed notebook ${{ matrix.notebook }}' | |
| ATTEMPTS_LEFT=3 | |
| until [ $ATTEMPTS_LEFT -lt 1 ] | |
| do | |
| git pull origin gh-storage -s recursive -X ours --allow-unrelated-histories | |
| git push origin gh-storage 2>&1 | tee output.log | |
| if grep -q "Updates were rejected because the remote contains work" output.log; then | |
| echo "Push failed due to conflicting remote changes. Remaining attempts: $ATTEMPTS_LEFT" | |
| let "ATTEMPTS_LEFT--" | |
| sleep 5 | |
| else | |
| break | |
| fi | |
| done | |
| fi | |
| generate_html: | |
| needs: execute_notebooks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| pip install jupyter-book | |
| - 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 | |
| # ./placeholder.sh | |
| # Push the book's HTML to github-pages | |
| - name: GitHub Pages action | |
| uses: peaceiris/[email protected] | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./_build/html |