docs: API reference for cellpy.batch and cellpy.collect (G2, #719) - #756
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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>
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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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* docs: add 2.0->2.1 migration guide + release notes (G3, #720) (#755) 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) * docs: API reference for cellpy.batch and cellpy.collect (G2, #719) (#756) 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) * docs: ship cellpy.batch/collect sources for API autodoc on v2-docs-stable 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> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com> Co-authored-by: Cursor <cursoragent@cursor.com>
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The API-reference slice of Epic G. Closes #719.
Gap
The 2.1 batch/collect redesign lives in
cellpy.batch/cellpy.collect, butdocs/api/only documented thecellpy.utils.*re-export shims — the new primary surfaces had no reference pages.What
docs/api/batch.md—cellpy.batch(entry points) +facade/journal/aggregate.docs/api/collect.md—cellpy.collect(collectors) +summary/curves/ica/collection.utils.md: relabel the batch/collectors sections as shims that re-export the new packages, with pointers.The pages are docstring-generated (mkdocstrings), so they track the code. Schema (
cellpy.parameters.cell_schema) and ICA/plotting were already covered; no dead references remain indocs/api/.Verification
Ran the CI docs build locally —
uvx --with mkdocstrings-python zensical build --clean: "No issues found", 0 warnings. All referenced modules resolve and links are intact.Closes #719.
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