Merge branch 'main' of https://github.com/CausalAIBook/MetricsMLNoteb… #95
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| name: Run Jupyter Notebooks | |
| on: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: '0 0 * * 0' # Runs once a week on Sunday at midnight | |
| concurrency: | |
| group: run-notebooks-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run-notebooks: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| folder: [PM1, PM2, PM3, PM4, PM5, CM1, CM2, CM3, AC1, AC2] | |
| steps: | |
| - name: Checkout repository | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| uses: actions/checkout@v2 | |
| - name: Install git | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| run: | | |
| if [ "$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: matrix.folder == 'CM3' && matrix.os == 'ubuntu-latest' | |
| run: sudo apt-get install -y libgraphviz-dev | |
| shell: bash | |
| - name: Install R if folder is CM3 | |
| if: matrix.folder == 'CM3' && matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y r-base | |
| shell: bash | |
| - name: Set up Python | |
| if: "! (matrix.folder == '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: "! (matrix.folder == '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 | |
| shell: bash | |
| - name: Run Flake8 linting on notebooks | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| id: lint | |
| run: | | |
| mkdir -p linting_logs | |
| flake8_errors=0 | |
| for notebook in ${{ matrix.folder }}/*.ipynb; do | |
| [ "$(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: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| id: convert | |
| run: | | |
| mkdir -p converted_scripts | |
| for notebook in ${{ matrix.folder }}/*.ipynb; do | |
| [ -e "$notebook" ] || continue | |
| jupyter nbconvert --to script "$notebook" --output-dir converted_scripts | |
| done | |
| shell: bash | |
| - name: Run converted Python scripts with IPython | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| id: execute | |
| run: | | |
| mkdir -p logs | |
| script_errors=0 | |
| for script in converted_scripts/*.py; do | |
| [ -e "$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" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Aggregate and report errors and warnings | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| run: | | |
| echo "Aggregating errors and warnings..." | |
| grep -E "Traceback|Error:|Exception:|ModuleNotFoundError|FutureWarning|TypeError" logs/*.txt linting_logs/*.txt > logs/errors_and_warnings.txt || true | |
| echo "Errors and Warnings:" | |
| cat logs/errors_and_warnings.txt | |
| shell: bash | |
| - name: Upload linting logs | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: linting-logs-${{ matrix.folder }} | |
| path: linting_logs | |
| - name: Upload execution logs | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: execution-logs-${{ matrix.folder }} | |
| path: logs | |
| - name: Check for errors | |
| if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest')) && (env.flake8_errors != '0' || env.script_errors != '0')" | |
| run: exit 1 |