cosanlab / cosanlab/nltools

Consolidate the tutorials to eight notebooks

Open
#505 5 comments 0 reactions 0 assignees View on GitHub
docs recovery
Dominant language
Python
Stars
130
Forks
48
Avg merge
6h 42m
Merged PRs (30d)
34

Description

## Rulings

> User decisions 2026-09-11. Target set, eight marimo notebooks in two groups. Data
> operations (3): BrainData (loading, indexing, arithmetic, saving, plotting, NeuroVault, and
> a masks-and-ROIs section that includes brain space and resolution), DesignMatrix,
> Adjacency. Analysis (5): univariate GLM (the real eight-subject workflow; the simulated
> per-subject port becomes its opening), prediction (decoding, classification and ROC,
> encoding, spatial scales), similarity and RSA, functional alignment with decomposition as a
> closing section, intersubject correlation. No Roc or Simulator tutorials: users meet them
> through the class methods and the reference. Sources: the twelve v0.5.1 ports under
> data-operations/ and analysis/, and the seven 0.6.0 notebooks under basics/ and workflows/;
> the duplication audit lists the overlaps and what each source uniquely covers. Each target
> notebook is built from its sources, keeps every unique section the audit lists, states each
> caveat once, stays trimmed (aim under 400 lines), runs clean under the stderr gate, and
> caches fits in .tutorial-cache. Delete the source notebooks, update docs/tutorials/index.md
> (one line per notebook, the community links live here only), zensical.toml nav, the
> tutorials-check/tutorials-run tasks and CLAUDE.md. Gate: uv run poe tutorials, uv run poe
> docs-build, uv run poe ok, then prose review and unslop.

> User decisions 2026-09-08 (the consolidation decision this target came from): port-first
> (all twelve v0.5.1 examples one-to-one as marimo notebooks in the two original groups, then
> prune and merge in a second pass); document decompose/component_viewer, upload_neurovault,
> Simulator, and restore the v0.5.1 README community links.

> Amended 2026-09-12: the lineage labelling of the nav groups is done by the docs re-cut,
> which re-cuts the nav first; this slice starts from the labelled nav and goes straight to
> building the eight notebooks.

Also fold in the tutorial items from #489: an "open in molab" button per tutorial, and
suppressible UserWarnings so the rendered pages are clean.

Blocked by: #506
Blocks: #507

Contributor guide

Open the contributing guide

Research direction

Start from the labelled nav and the twelve v0.5.1 sources under data-operations/ and analysis/ plus the seven 0.6.0 notebooks under basics/ and workflows/. Review the duplication audit, then build the eight target notebooks, update docs/tutorials/index.md, zensical.toml, the tutorials-check/tutorials-run tasks, and CLAUDE.md. Done means the sources are deleted, the tutorials cache fits, and uv run poe tutorials, uv run poe docs-build, and uv run poe ok pass, followed by prose review and unslop.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
documentation
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
25/100

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