deprecated images #103
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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: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: [ubuntu-latest, windows-latest, macos-latest] | |
folder: [PM1, PM2, PM3, PM4, PM5, CM1, CM2, CM3, AC1, AC2, T] | |
steps: | |
- name: Checkout repository | |
if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
uses: actions/checkout@v2 | |
- name: Install git | |
if: "! (matrix.folder == 'CM3' && (matrix.os == 'windows-latest' || matrix.os == 'macos-latest'))" | |
run: | | |
if [ "$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 |