docs: examples nav reorg, notebook refresh, and corrplot rendering fixes - #34
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…de test count The flat "Examples" gallery/toctree section (17 unrelated notebooks) is split into 6 scoped categories (Benchmarks & Case Studies, Discovery Features, CI Tests, Effects/Queries/Forecasting, Data Handling & Visualization, Integrations & Extending) via separate captioned toctree blocks, matching the existing Tutorials/CEDAR/GRACE section pattern. Each renders as its own collapsible group in the sidebar nav. Adds examples/custom_ci_test.ipynb, mirroring custom_algorithm.ipynb's structure: a worked @register_ci_test example (Spearman partial correlation) that fills a real gap — docs/ci_tests.md documents the custom-CI-test mechanism but had no companion notebook, unlike custom_algorithm. Replaces hardcoded "8 CI tests" / "eight GPU-accelerated CI tests" wording in docs/index.md, README.md, docs/getting_started/index.md, and the ci_test_comparison gallery tooltip with qualitative language, since the exact count drifts every time a test is added/renamed and was already stale in spirit (4 separate places to keep in sync).
…e front page - corrplot: add diag='glyph' so directed matrices render a real diagonal instead of a correlation matrix's trivial 1.0; fix grid border clipping (right/bottom edges vanished); honour colorbar=False for every glyph method, which supersedes #31 - rerun weather_benchmark, custom_ci_test and plotting notebooks so the stored outputs match the current code - front-page "Last updated" now derives from the build date via {sub-ref}`today` rather than being hand-edited - examples gallery: "Getting Started Tutorial" -> "Getting Started" - add a feature_selection thumbnail Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Dependency Review✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.Scanned FilesNone |
markdownlint MD024 is configured with siblings_only, and [Unreleased] had two "### Fixed" sections under it. Folds the banner-link entry into the existing Fixed block. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
… CSS Appending a rule to docs/_static/css/custom.css pulled the whole pre-existing file into super-linter's stylelint pass (it only scans changed files), surfacing 60 unrelated errors. Use the bootstrap utilities the pydata theme already ships instead, leaving custom.css untouched. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Groups the examples gallery into categories, adds a custom CI test notebook, and fixes three rendering issues in
corrplot.Library changes (
causalts/plotting/corrplot.py)diag='glyph'(new) — renders the diagonal as an ordinary cell using the same method and colormap. Needed for directed matrices, where the diagonal is real self-AR data rather than a correlation matrix's trivial 1.0. Significance markers and CI overlays still skip the diagonal._draw_griddrew the border withaxhline/axvlineat exactly the axis limits, so half of each boundary line fell outside the clip box and the right and bottom edges vanished. Now interior lines plus an unclipped borderRectangle.colorbar=Falsefix — was ignored formethodin{"color", "shade"}, silently overriding an explicit argument. Supersedes Honour colorbar=False for colour-only corrplot glyphs #31, whose fix and tests are included here.Docs
custom_ci_test.ipynb— a worked@register_ci_testexample mirroringcustom_algorithm.ipynb.{sub-ref}`todayinstead of being hand-edited.feature_selectionthumbnail.Notebooks
weather_benchmark,custom_ci_testandplottingre-executed so stored outputs match the current code.weather_benchmarkalso moves its heatmaps tocorrplotand adds a CEDAR bootstrap persistence figure.Caveat on the weather_benchmark comparison
§8b reports CDNOTS+ 0.667 vs CEDAR 0.545 on cross-station edges, but the two arms use different alphas (CDNOTS+
0.05, CEDARalpha_cond1/2=0.01). At a matched0.01the ordering reverses. Recall is identical (0.500) — CDNOTS+ differs only on precision. This is caveated in the notebook and should not be read as "CDNOTS+ beats CEDAR". Headline F1 is also dominated by 16 free self-AR edges; only 6 of 38 are cross-station, soexclude_self_loops=Trueis the number to read.Verification
pytest tests/test_plotting.py— 14 passed (5 new)black --check,isort --check,flake8— cleancodespell— clean on all changed filessphinx-build— succeeds at the 237-warning baseline🤖 Generated with Claude Code