remove query from tabular recipe, update DFAccessor to take row as well #27
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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 | |
| echo "Trying to print tracebacks & set error flag where appropriate" | |
| jq -c '.cells[]' $notebook | while IFS= read -r line | |
| do | |
| echo "-------------------------------" | |
| outputs=$(echo $line | jq '.outputs') | |
| # sometimes outputs is null (non code block?) | |
| if [[ $outputs == "null" ]] | |
| then | |
| echo "Non code block. Skipping..." | |
| continue | |
| fi | |
| error_length=$(echo $line | jq '[.outputs[] | select( .output_type == "error" )] | length') | |
| # if outputs has no errors, then continue | |
| if [[ $error_length -eq 0 ]] | |
| then | |
| echo "No Error. Skipping" | |
| continue | |
| fi | |
| error_flag=1 | |
| echo $line | jq -r '.outputs[] | select( .output_type == "error" ) | .traceback | join("")' | |
| done | |
| echo "jupyter nbconvert --to pdf $notebook" | |
| jupyter nbconvert --to pdf $notebook | |
| done | |
| echo "End of evaluation $error_flag" | |
| if [[ "$error_flag" != "0" ]] | |
| then | |
| echo "Trying to exit 1" | |
| 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 |