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P10: Nature figure standards — palette, Altair theme, DAG colors #49

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kert commented 2026-03-21 17:57:59 +00:00
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Summary

  • Add Nature Research figure guide citation to bib store (key 9ASETLJ4)
  • Create styles/nature.py — accessible 8-colour palette (Paul Tol bright), Altair theme, matplotlib rcParams, Cytoscape helpers
  • Retrofit all ~30 Altair charts in notebooks/acodb_explorer.py to use Nature theme
  • Update src/aco/dag.py to import shared palette from styles/nature.py

Nature specs implemented

  • Sans-serif (Helvetica/Arial), 5-7pt body, 8pt bold titles
  • No gridlines, axis lines + tick marks mandatory
  • Accessible colorblind-safe palette
  • RGB colour space, 450 DPI

Closes #45, closes #46, refs #47

Test plan

  • All 11,766 tests pass
  • ruff lint + format clean
  • marimo check passes
  • Visual review of charts in notebook
## Summary - Add Nature Research figure guide citation to bib store (key `9ASETLJ4`) - Create `styles/nature.py` — accessible 8-colour palette (Paul Tol bright), Altair theme, matplotlib rcParams, Cytoscape helpers - Retrofit all ~30 Altair charts in `notebooks/acodb_explorer.py` to use Nature theme - Update `src/aco/dag.py` to import shared palette from `styles/nature.py` ## Nature specs implemented - Sans-serif (Helvetica/Arial), 5-7pt body, 8pt bold titles - No gridlines, axis lines + tick marks mandatory - Accessible colorblind-safe palette - RGB colour space, 450 DPI Closes #45, closes #46, refs #47 ## Test plan - [x] All 11,766 tests pass - [x] ruff lint + format clean - [x] marimo check passes - [ ] Visual review of charts in notebook
kert added this to the P10: Figure Standards — Nature-conformant chart styling milestone 2026-03-21 17:57:59 +00:00
kert added 1 commit 2026-03-21 17:57:59 +00:00
add Nature figure standards: palette, Altair theme, DAG colors
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33701365be 
Create styles/nature.py with accessible 8-colour palette (Paul Tol
bright scheme), Altair theme registration, matplotlib rcParams, and
Cytoscape style helpers — all conforming to Nature Research figure
specifications (bib citation 9ASETLJ4).

Retrofit acodb_explorer.py: replace all hardcoded set2/hex colors
with PALETTE references, enable the Nature Altair theme on import.

Update src/aco/dag.py to import schema colors from the shared
styles/nature.py module instead of maintaining a separate Tableau 10
palette.

fix #45, fix #46, refs #47
kert added 1 commit 2026-03-21 18:08:05 +00:00
fix notebook runtime: add altair/pandas deps, fix table ref, fix sys.path
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cfeb09eff4 
- Add altair and pandas as dev dependencies so notebooks run as scripts
- Fix sys.path for styles/ to resolve relative to __file__, not CWD
- Fix broken table ref: chronic_conditions_long → cms_chronic_conditions_long
- Update pre-commit hook: lint only staged files, run notebooks as scripts

refs #45
kert closed this pull request 2026-03-21 18:38:15 +00:00
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Reference: homelab/stack#49
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