Restore narrative flow in colouring guide#75
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Pull request overview
Reorders the docs/colouring.rst guide to prioritize a “show first code example earlier” narrative, moving API-reference-heavy details out of the intro and adding a brief cross-reference for trajectory/per-frame colouring.
Changes:
- Removes the early, API-reference-style discussion of
set_atom_data/del_atom_data/clear_2d_atom_dataworkflows from the intro. - Consolidates “partial/sparse data” guidance into a single section placed immediately after categorical data.
- Adds a short “Per-frame colouring” section that points readers to the
animationsguide for deeper trajectory examples.
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Summary
The colouring guide had accumulated API-reference material (three-method listing, 2-D consistency rules, recovery workflows, read-only mapping note) between the intro and the first code example. A reader wanting to colour atoms by charge had to wade through
clear_2d_atom_databefore seeing their first snippet.Restores the original narrative flow: continuous data, categorical data, partial/sparse data, custom functions, layers, polyhedra. Moves the 2-D trajectory content to a brief cross-reference to the animations docs (which already cover per-frame colouring in detail). API-reference material is already in the docstrings rendered via
:members:in api.rst.