Add automated notebook testing with Papermill

[drbenvincent]

Summary

• guard nbclient widget output to avoid display_id assertion errors
• clear notebook outputs before injection and use unique injection ids
• add optional --parallel execution flag and document runner behavior
• update interrogate badge from pre-commit

Test Plan

• pre-commit run --all-files

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📚 Documentation preview 📚: https://causalpy--602.org.readthedocs.build/en/602/

[Copilot]

Pull request overview

This PR introduces automated testing for Jupyter notebooks in CI using Papermill. The implementation includes a runner script that mocks PyMC's MCMC sampling with faster prior predictive sampling to validate notebooks execute without errors.

Key changes:

• New notebook runner script with filtering capabilities for different notebook types
• Mock PyMC sampling implementation that replaces expensive MCMC with prior predictive sampling (10 draws)
• GitHub Actions workflow that runs notebooks in parallel across three categories (PyMC, sklearn, and other notebooks)

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
scripts/run_notebooks/runner.py	Main script for executing notebooks with Papermill, includes filtering and logging
scripts/run_notebooks/injected.py	Mock implementation of pm.sample that uses prior predictive sampling
scripts/run_notebooks/README.md	Documentation for the notebook runner usage and CI integration
.github/workflows/test_notebook.yml	GitHub Actions workflow for parallel notebook testing
pyproject.toml	Adds papermill to test dependencies
docs/source/_static/interrogate_badge.svg	Updates documentation coverage badge from 96.3% to 96.0%

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.35%. Comparing base (fed2b5c) to head (dede24d).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #602   +/-   ##
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  Coverage   94.35%   94.35%           
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  Files          44       44           
  Lines        7517     7517           
  Branches      456      456           
=======================================
  Hits         7093     7093           
  Misses        262      262           
  Partials      162      162           

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[drbenvincent]

passing!

@NathanielF See skip_notebooks.yaml. I had to bypass testing some of yours for reasons explained in the file. Those reasons are probably fixable in a follow up PR.

[drbenvincent]

bugbot review

[cursor]

PR Summary

Introduces CI to validate docs notebooks execute without errors.

• Adds .github/workflows/test_notebook.yml to run notebooks in parallel splits on Python 3.12
• New scripts/run_notebooks/ utilities: runner.py (Papermill execution with temporary notebooks), injected.py (mocks pm.sample with prior draws and minimal sample_stats), skip_notebooks.yml (notebooks excluded from CI), and a brief README.md
• Updates docs/source/_static/interrogate_badge.svg from 96.3% to 96.0%

^{Written by Cursor Bugbot for commit c15a229. This will update automatically on new commits. Configure here.}

[cursor]

✅ Bugbot reviewed your changes and found no bugs!

[drbenvincent]

TODO: don't use papermill. Use nbmake or nbconvert

Papermill has good support for the trick where we change sampling behaviour to sample from the prior for ultra fast evaluation