All Days Improvement #24
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| 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/[email protected] | |
| # 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 "[email protected]" | |
| 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/[email protected] | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: ${{ github.head_ref }} |