Check Python Notebooks #56
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| name: Check Python Notebooks | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: '0 0 * * 0' # Runs once a week on Sunday at midnight | |
| concurrency: | |
| group: test-python-notebooks-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test-python-notebooks: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # Removed: {windows-latest, macos-latest} as they were taking too long. Consider adding back in the future | |
| os: [ubuntu-latest] | |
| directory: [PM1, PM2, PM3, PM4, PM5, CM1, CM2, CM3, AC1, AC2, T] | |
| steps: | |
| - name: Checkout repository | |
| if: "! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: ${{ github.event_name == 'pull_request' && 2 || 0 }} | |
| - name: Find changed notebooks in PR | |
| if: github.event_name == 'pull_request' | |
| id: find_notebooks_pr | |
| run: | | |
| # git fetch origin ${{ github.event.pull_request.base.ref }} ${{ github.event.pull_request.head.ref }} | |
| # git diff --name-only origin/${{ github.event.pull_request.base.ref }}...origin/${{ github.event.pull_request.head.ref }} > changed_files.txt | |
| git diff --name-only -r HEAD^1 HEAD > changed_files.txt | |
| grep -E '\.ipynb$|\.py$|\.github/workflows/python-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt | |
| - name: Find changed notebooks in Push | |
| if: github.event_name == 'push' | |
| id: find_notebooks_push | |
| run: | | |
| git diff --name-only ${{ github.event.before }} ${{ github.event.after }} > changed_files.txt | |
| grep -E '\.ipynb$|\.py$|\.github/workflows/python-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt | |
| - name: Check if any notebooks changed in PR or Push | |
| if: (github.event_name == 'push') || (github.event_name == 'pull_request') | |
| id: check_notebooks | |
| run: | | |
| cat changed_notebooks.txt | |
| if grep -q -E '^${{ matrix.directory }}/[^/]+\.ipynb$|^${{ matrix.directory }}/.*\.py$|\.github/workflows/python-notebooks.yml$' changed_notebooks.txt; then | |
| echo "notebooks_changed=true" >> $GITHUB_ENV | |
| else | |
| echo "notebooks_changed=false" >> $GITHUB_ENV | |
| echo "No Python notebooks or python scripts changed in folder ${{ matrix.directory }} in this PR." | |
| fi | |
| - name: Set notebooks changed to true for schedule (or other ways of triggering the job) | |
| if: "! ((github.event_name == 'push') || (github.event_name == 'pull_request'))" | |
| id: set_check_notebooks_true | |
| run: | | |
| # we run all folders if it is the weekly scheduled run to | |
| # check if something broke due to changes in dependencies | |
| echo "notebooks_changed=true" >> $GITHUB_ENV | |
| - name: Install git | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sudo apt-get update | |
| sudo apt-get install -y git | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| brew install git | |
| elif [ "$RUNNER_OS" == "Windows" ]; then | |
| choco install git -y --no-progress || powershell -Command "Start-Sleep -Seconds 30; choco install git -y --no-progress" | |
| fi | |
| shell: bash | |
| - name: Install libgraphviz-dev if folder is CM3 | |
| if: "(env.notebooks_changed == 'true') && (matrix.directory == 'CM3' && matrix.os == 'ubuntu-latest')" | |
| run: sudo apt-get install -y libgraphviz-dev | |
| shell: bash | |
| - name: Install R if folder is CM3 | |
| if: "(env.notebooks_changed == 'true') && (matrix.directory == 'CM3' && matrix.os == 'ubuntu-latest')" | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y r-base | |
| shell: bash | |
| - name: Set up Python | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' # Use Python 3.10 | |
| - name: Install dependencies | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip install jupyter nbconvert flake8 flake8-nb ipython nbstripout | |
| shell: bash | |
| - name: Strip outputs from .ipynb files | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| run: | | |
| for notebook in ${{ matrix.directory }}/*.ipynb; do | |
| nbstripout "$notebook" | |
| done | |
| - name: Run Flake8 linting on notebooks | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| id: lint | |
| run: | | |
| mkdir -p linting_logs | |
| flake8_errors=0 | |
| for notebook in ${{ matrix.directory }}/*.ipynb; do | |
| [ "$(basename "$notebook")" = "python-dosearch.ipynb" ] && continue | |
| flake8-nb --config=.flake8 "$notebook" > "linting_logs/$(basename "$notebook" .ipynb)_linting.txt" 2>&1 || flake8_errors=$((flake8_errors+1)) | |
| done | |
| echo "flake8_errors=$flake8_errors" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Convert Jupyter notebooks to Python scripts | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| id: convert | |
| run: | | |
| mkdir -p converted_scripts | |
| for notebook in ${{ matrix.directory }}/*.ipynb; do | |
| [ -e "$notebook" ] || continue | |
| [ "$(basename "$notebook")" = "DoubleML_and_Feature_Engineering_with_BERT.ipynb" ] && continue | |
| jupyter nbconvert --to script "$notebook" --output-dir converted_scripts | |
| done | |
| shell: bash | |
| - name: Run converted Python scripts with IPython | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| id: execute | |
| run: | | |
| mkdir -p logs | |
| script_errors=0 | |
| for script in converted_scripts/*.py; do | |
| [ -e "$script" ] || continue | |
| echo "Running $script" | |
| ipython "$script" > "logs/$(basename "$script" .py).txt" 2>&1 || script_errors=$((script_errors+1)) | |
| done | |
| echo "script_errors=$script_errors" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Aggregate and report errors and warnings | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| run: | | |
| echo "Aggregating errors and warnings..." | |
| grep -E "Traceback|Error:|Exception:|ModuleNotFoundError|FutureWarning|TypeError" logs/*.txt linting_logs/*.txt > logs/errors_and_warnings.txt || true | |
| echo "Errors and Warnings:" | |
| cat logs/errors_and_warnings.txt | |
| shell: bash | |
| - name: Upload linting logs | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linting-logs-${{ matrix.directory }}-${{ matrix.os }} | |
| path: linting_logs | |
| - name: Upload execution logs | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: execution-logs-${{ matrix.directory }}-${{ matrix.os }} | |
| path: logs | |
| - name: Send failure mail | |
| if: "((github.event_name == 'schedule') && (env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')) && (env.flake8_errors != '0' || env.script_errors != '0')))" | |
| uses: dawidd6/action-send-mail@v3 | |
| with: | |
| # Required mail server address if not connection_url: | |
| server_address: smtp.gmail.com | |
| # Server port, default 25: | |
| server_port: 465 | |
| # Optional whether this connection use TLS (default is true if server_port is 465) | |
| secure: true | |
| # Optional (recommended) mail server username: | |
| username: ${{secrets.MAIL_USERNAME}} | |
| # Optional (recommended) mail server password: | |
| password: ${{secrets.MAIL_PASSWORD}} | |
| # Required mail subject: | |
| subject: FAILURE Python (${{matrix.directory}}) test Github Action job failed! | |
| # Required recipients' addresses: | |
| to: [email protected] | |
| # Required sender full name (address can be skipped): | |
| from: GA-MetricsML-Notebooks <[email protected]> | |
| # Optional plain body: | |
| body: Python notebook tests of directory ${{matrix.directory}} in Git repo ${{github.repository}} failed!! | |
| ignore_cert: true | |
| - name: Check for errors | |
| if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')) && (env.flake8_errors != '0' || env.script_errors != '0'))" | |
| run: exit 1 | |
| - name: Send success mail | |
| if: "((github.event_name == 'schedule') && (env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))))" | |
| uses: dawidd6/action-send-mail@v3 | |
| with: | |
| # Required mail server address if not connection_url: | |
| server_address: smtp.gmail.com | |
| # Server port, default 25: | |
| server_port: 465 | |
| # Optional whether this connection use TLS (default is true if server_port is 465) | |
| secure: true | |
| # Optional (recommended) mail server username: | |
| username: ${{secrets.MAIL_USERNAME}} | |
| # Optional (recommended) mail server password: | |
| password: ${{secrets.MAIL_PASSWORD}} | |
| # Required mail subject: | |
| subject: SUCCESS Python (${{matrix.directory}}) test Github Action job succeeded! | |
| # Required recipients' addresses: | |
| to: [email protected] | |
| # Required sender full name (address can be skipped): | |
| from: GA-MetricsML-Notebooks <[email protected]> | |
| # Optional plain body: | |
| body: Python notebook tests of directory ${{matrix.directory}} in Git repo ${{github.repository}} succedded. | |
| ignore_cert: true | |
| # - name: Check out the branch for pull request | |
| # if: "(github.event_name == 'pull_request') && (env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| # run: | | |
| # git fetch --all | |
| # git checkout ${{ github.event.pull_request.head.ref }} | |
| # - name: Check if there are any changes (e.g. stripped outputs) | |
| # if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')))" | |
| # id: verify_diff | |
| # run: | | |
| # git pull | |
| # git diff --quiet ${{ matrix.directory }}/*.ipynb || echo "changed=true" >> $GITHUB_OUTPUT | |
| # - name: Commit and push stripped .ipynb files | |
| # if: "(env.notebooks_changed == 'true') && (! (matrix.directory == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))) && (steps.verify_diff.outputs.changed == 'true')" | |
| # run: | | |
| # git config --global user.name 'github-actions[bot]' | |
| # git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| # git pull | |
| # git add ${{ matrix.directory }}/*.ipynb | |
| # git commit -m 'Strip outputs from .ipynb files in ${{ matrix.directory }} [skip ci]' | |
| # git push --force-with-lease | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |