[timtreis]

Client documentation site for https://spatialdata-db.readthedocs.io (RTD project spatialdata-db).

Merge order: after #24 (RTD config; its commit is at the base of this branch) and after #25 (the docs describe the catalog-latest default and the fixed Catalog(version=...)).

What's in it:

• Theme: scverse sphinx_book_theme with the DB's identity — site colour tokens for dark and light (follows the OS), SpatialData-DB wordmark + logo/favicon, header icons to the DB site / GitHub / Lamin, DB-coloured code highlighting (light-mode tokens darkened to ≥4.5:1 contrast).
• Landing: live dataset count, git install line, a 5-line quickstart that loads the smallest Visium lung store (~10 MB), cards to the guides and API.
• Introduction: spatial assays (one card per technology incl. legacy Spatial Transcriptomics, live counts + example links, any new technology listed generically) and a user-level "how the DB works" page (releases, validation/tiers, licenses, storage, versioning and drift — no byte-retention promise).
• Guides: find & load, cohorts & reproducibility, ML / TaskAdapter (notebooks pre-executed against the live DB, small stores, outputs committed; RTD doesn't execute), CLI & MCP agents.
• Reference: autosummary of sddb.__all__, CLI reference generated by Typer, MCP tools table, catalog-columns table generated from the schema, changelog. Tests fail if an export, CLI command or MCP tool goes undocumented.
• Cite & license page + CITATION.cff (software; DB paper forthcoming).
• Build-time stats come from the live catalog; if it's unreachable the pages render without numbers and the build stays green.
• CI docs job (sphinx-build -W), gated in check.
• Website links use one SITE_URL (currently https://spatialdata-db-web.pages.dev, since spatialdata-db.com isn't wired yet).
• Also: README install line → git install; SpatialDataCohort.verify docstring corrected; gene-index size in CLI help (~260 MB).

tutorials/ is folded into the guides and removed.

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[read-the-docs-community]

Documentation build overview

📚 spatialdata-db | 🛠️ Build #35229522 | 📁 Comparing 14962fc against latest (893a32d)

  🔍 Preview build  

27 files changed · + 22 added · ± 3 modified · - 2 deleted

+ Added

• changelog.html
• cite-and-license.html
• guides/cli-and-agents.html
• guides/cohorts.html
• guides/find-and-load.html
• guides/ml.html
• intro/assays.html
• intro/db-stack.html
• reference/api.html
• reference/catalog-columns.html
• and 12 more...

± Modified

• genindex.html
• index.html
• search.html

- Deleted

• tutorials/cohorts.html
• tutorials/query_and_load.html

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.15%. Comparing base (64fadf0) to head (14962fc).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #26      +/-   ##
==========================================
+ Coverage   92.05%   92.15%   +0.10%     
==========================================
  Files          18       18              
  Lines        1460     1466       +6     
==========================================
+ Hits         1344     1351       +7     
+ Misses        116      115       -1     

☔ 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.