Sync main into pymc6_and_pymcmarketing1_migration (2026-09-26)

[daimon-pymclabs]

Merges main into the migration branch so it is up to date before the 1.0.0rc1 PR. Brings in the 8 commits on main that the branch lacked, including #1213 (markdown tables for pymarkdown 0.9.40, merged today), #1181 (SEO/AEO), and CI/pre-commit bot updates.

Please merge with a merge commit, not squash, so git records main as merged and the final PR into main doesn't re-conflict.

Conflict resolutions:

• .pre-commit-config.yaml: kept the branch's removal of the mypy hook (mypy is configured twice, the two configurations disagree, and neither gates anything #1127, typecheck runs via make typecheck); took main's rev bumps.
• ARCHITECTURE.md: kept the branch's Key Conventions rows, with main's | --- | --- | separator style.
• scripts/generate_gallery.py: kept the branch's explanatory comment.
• inverse-propensity-pymc.ipynb: kept the branch's re-executed notebook, which already had main's title change.
• synthetic-control-pymc.ipynb: kept the branch's re-executed notebook and added main's intro paragraph to the title cell.

Also fixes two branch-only markdown lint failures that pymarkdown 0.9.40 now catches (README.md emphasis style, scripts/migration_baseline/REPORT_TEMPLATE.md table separator). prek run --all-files passes locally.

🤖 Generated with Claude Code

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[cursor]

PR Summary

Low Risk
Documentation, notebook markdown, and pre-commit hook version changes only; no causal inference or API code paths are modified in the diff.

Overview
This PR syncs main into the PyMC 6 migration branch and aligns the tree with pymarkdown v0.9.40 (from #1213 on main).

Tooling: .pre-commit-config.yaml bumps the pymarkdown hook from v0.9.39 to v0.9.40.

Markdown lint compliance: Many docs, skills, agent resources, and README/ARCHITECTURE/CONTRIBUTING tables switch separator rows to the spaced form | --- | --- | instead of compact |---|---| headers. CONTRIBUTING.md fixes two internal anchor links to lowercase GitHub-style slugs. README.md changes runtime-notes emphasis from *first* to _first_ for the linter.

Content from main: docs/source/notebooks/synthetic-control-pymc.ipynb adds the introductory paragraph to the title markdown cell (on top of the branch’s re-executed outputs). docs/source/knowledgebase/design_notation.md gets the same table formatting pass for quasi-experimental notation tables.

Conflict resolutions described in the PR (mypy hook removal, ARCHITECTURE conventions, gallery script comment, other notebooks) are not all visible in the truncated diff snippet but are part of the merge intent. No Python package runtime behavior changes appear in the shown diff.

^{Reviewed by Cursor Bugbot for commit 9cda5c1. Bugbot is set up for automated code reviews on this repo. Configure here.}

[read-the-docs-community]

Documentation build overview

📚 causalpy | 🛠️ Build #34778835 | 📁 Comparing 9cda5c1 against latest (89f18de)

  🔍 Preview build  

397 files changed · + 126 added · ± 251 modified · - 20 deleted

+ Added

• release_notes.html
• _modules/causalpy/custom_exceptions.html
• _modules/causalpy/input_data.html
• _modules/causalpy/reporting.html
• _modules/causalpy/utils.html
• api/generated/causalpy.checks.operating_characteristics.html
• api/generated/causalpy.checks.placebo_in_space.PlaceboInSpace.plot_mspe_ratio.html
• api/generated/causalpy.checks.placebo_in_time.PlaceboInTime.plot_calibration.html
• api/generated/causalpy.experiments.base.BaseExperiment.build.html
• api/generated/causalpy.experiments.base.BaseExperiment.sample_prior_predictive.html
• and 116 more...

± Modified

• genindex.html
• index.html
• py-modindex.html
• _modules/index.html
• api/index.html
• knowledgebase/causal_written_resources.html
• knowledgebase/custom_pymc_models.html
• knowledgebase/glossary.html
• knowledgebase/prediction-contract.html
• knowledgebase/quasi_dags.html
• and 241 more...

- Deleted

• api/generated/causalpy.checks.placebo_in_time.AssuranceResult.html
• api/generated/causalpy.experiments.base.BaseExperiment.get_plot_data.html
• api/generated/causalpy.experiments.diff_in_diff.DifferenceInDifferences.algorithm.html
• api/generated/causalpy.experiments.diff_in_diff.DifferenceInDifferences.get_plot_data.html
• api/generated/causalpy.experiments.instrumental_variable.InstrumentalVariable.algorithm.html
• api/generated/causalpy.experiments.instrumental_variable.InstrumentalVariable.get_plot_data.html
• api/generated/causalpy.experiments.interrupted_time_series.InterruptedTimeSeries.algorithm.html
• api/generated/causalpy.experiments.inverse_propensity_weighting.InversePropensityWeighting.algorithm.html
• api/generated/causalpy.experiments.inverse_propensity_weighting.InversePropensityWeighting.get_plot_data.html
• api/generated/causalpy.experiments.panel_regression.PanelRegression.algorithm.html
• and 10 more...

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.14%. Comparing base (86342b0) to head (9cda5c1).

Additional details and impacted files

@@                         Coverage Diff                         @@
##           pymc6_and_pymcmarketing1_migration    #1214   +/-   ##
===================================================================
  Coverage                               97.14%   97.14%           
===================================================================
  Files                                     130      130           
  Lines                                   24033    24033           
  Branches                                 1349     1349           
===================================================================
  Hits                                    23348    23348           
  Misses                                    477      477           
  Partials                                  208      208           

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.