fix notebook #22
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name: "[test] test siibra-paper notebooks" | |
on: | |
push: | |
branches: ["main", "refactor_attr"] | |
pull_request: | |
branches: ["*"] | |
jobs: | |
test_tutorials: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install -U . | |
pip install matplotlib jupyter | |
sudo apt-get install -y pandoc texlive-xetex | |
- name: Run notebooks with nbmake | |
run: | | |
error_flag=0 | |
for notebook in $(find ./paper_notebooks -type f) | |
do | |
echo "jupyter execute $notebook --allow-errors --inplace" | |
jupyter execute $notebook --allow-errors --inplace | |
# All error cells | |
ERROR_CELLS=$(jq -r '[.cells[].outputs[] | select( .output_type == "error" )]' $notebook) | |
# Set error flag | |
echo $ERROR_CELLS | jq 'length' | |
if [[ $(echo $ERROR_CELLS | jq 'length') -gt "0" ]] | |
then | |
echo "Setting error flag." | |
error_flag=1 | |
fi | |
# Print error messages | |
echo $ERROR_CELLS | jq -rc '.[]' $notebook \ | |
| while IFS= read -r line | |
do | |
echo $line | jq -rc '.traceback | join("")' | |
done | |
echo "jupyter nbconvert --to pdf $notebook" | |
jupyter nbconvert --to pdf $notebook | |
done | |
if [[ ! $error_flag -eq "0" ]] | |
then | |
exit 1 | |
fi | |
- if: always() | |
name: Archive code coverage results | |
uses: actions/upload-artifact@v4 | |
with: | |
name: Notebook PDFs | |
path: | | |
paper_notebooks/*.pdf | |
paper_notebooks/*.ipynb |