docs: sync 2.1 migration guide + batch/collect API refs - #772
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The capstone doc for cellpy 2.1 (Stage 4), describing what shipped now that
Epics A-E have all landed.
- new `docs/getting_started/migration_v2.0_to_2.1.md`: every Epic E removal
with old->new mappings (headers->schema, ICA shims, plotting knobs +
dropped seaborn/bokeh backends, batch_tools->cellpy.batch/collect,
prms.*->cellpy.config with c.mass kept), the batch symbol map +
iterate_batches/process_batch recipes, and the collectors cross-cell
cycle-narrowing bug-fix before/after.
- wire it into the Zensical nav ("Coming from cellpy 2.0") and cross-link it
from the 1.x->2.x guide.
- HISTORY.md: a 2.1 (Stage 4) release-notes block under Unreleased.
All cited APIs verified against the code (CellpyCell.vacant, summary_plot
backend=/x_range=, cellpy.collect.collect_*, cellpy.batch load/from_db/
from_journal/combine_summaries, cellpy.config.override).
Closes #720.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
(cherry picked from commit 53fc2d4)
) The 2.1 batch/collect redesign lived in `cellpy.batch` / `cellpy.collect` but the API reference only documented the `cellpy.utils.*` re-export shims. - new `docs/api/batch.md` (`cellpy.batch` + facade / journal / aggregate) and `docs/api/collect.md` (`cellpy.collect` + summary / curves / ica / collection), wired into the Zensical nav and the "Where to look" table. - `utils.md`: relabel the batch/collectors sections as shims that re-export the new packages, pointing at the new pages. Docstring-generated (mkdocstrings), so it tracks the code. Verified with the CI docs build (`zensical build --clean`): **No issues found**, 0 warnings — all referenced modules resolve and links are intact. Closes #719. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com> (cherry picked from commit b6119e2)
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…able mkdocstrings cannot collect modules that are absent from the docs branch. Bring the package trees from master so the #756 API pages build. Co-authored-by: Cursor <cursoragent@cursor.com>
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Summary
masterintov2-docs-stablefor the 2.1 ship (Release v2.1 #768):cellpy.batch/cellpy.collectAPI reference (G2: docstring-driven API-reference cleanup #719 / docs: API reference for cellpy.batch and cellpy.collect (G2, #719) #756)Skipped #754 (marimo integrate into master) — marimo was withdrawn on this docs branch.
Test plan
v2-docs-stablelooks saneRefs #768
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