feat(batch)!: cut utils.batch over to the cellpy.batch facade (#703) - #733
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Groundwork for the A7 cutover: the new facade needs the db path the legacy init()->create_journal() flow used. - db.py: journal_from_db() wraps the existing db readers (simple Excel + JSON) and converts their pandas pages to the new polars Journal. - facade: Batch.from_db(), deferred-read create_journal() (init stores db config, create_journal performs the read), load(db=...) source. +2 tests (from_db, create_journal-reads-db). Full batch-v3 suite: 43 green.
…703) The A7 cutover: `cellpy.utils.batch` is now a thin shim over `cellpy.batch`. `init`/`load`/`from_journal`/`naked` return the new polars-based `Batch`; `init2`/`from_journal2`/`load_journal`/`load_pages`/`process_batch`/ `iterate_batches` warn once. BREAKING: `b.pages` is polars (keys-in-columns), cells are `b.cells[label]` (not `b.experiment.data[...]`). - facade: `update()` routes unknown legacy kwargs (e.g. `testing`) to the loader; `Batch.experiment` backward-compat adapter keeps helpers/collectors working; `from_db`/deferred `create_journal` for the init->create_journal flow. - journal: db `argument` dict-columns stored as polars Object. - test_batch.py migrated to the new surface (polars pages, `b.cells`, `b.save`); reader + batch_tools-direct tests unchanged. - xfail (re-based by their own redesign): collectors tests (Epic B #706-708), helpers.concat_summaries paths (Epic C #706), batch plot snapshot (Epic B). batch_tools import-warning deferred to E4 (db.py still bridges through it). Full suite green (essential + full). Closes #703. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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A7 — the cutover:⚠️ breaking
cellpy.utils.batch→cellpy.batchSeventh arc of Epic A (batch v3, #696).
cellpy.utils.batchis now a thin shim over the newcellpy.batchpackage. The 2232-line legacybatch.pyis replaced by a ~120-line shim (net −1,984 lines).Shim
init/load/from_journal/naked→ return the newcellpy.batch.Batch.init2/from_journal2/load_journal/load_pages/process_batch/iterate_batches→ deprecated wrappers (warn_once);iterate_batches/process_batchbecome docs recipes.DB bridge (prerequisite, first commit)
cellpy/batch/db.pyjournal_from_db()wraps the existing Excel/JSON readers → new polarsJournal;Batch.from_db+ deferredcreate_journal()reproduce the legacyinit()→create_journal()flow.Facade
update()routes unknown legacy kwargs (testing, …) to the loader;Batch.experimentbackward-compat adapter keepshelpers/collectorsworking against the new Batch until they migrate; dbargumentdict-columns stored as polarsObject.b.pagesis polars (keys-in-columns), not pandas — no.iloc/.loc/.index.b.cells[label], notb.experiment.data[label].b.experiment.journal.to_file(...)→b.save(...);force_cellpy/force_raw/force_recalc→LoadPolicy;b.combine_summaries()returns a tidy polars frame.Tests
test_batch.pymigrated to the new surface; reader +batch_tools-direct tests unchanged. Full batch-v3 + batch suites green.test_collectors.py(Epic B B2: collectors — options + pipeline (fixes cross-cell bug) #706-708),helpers.concat_summariespaths (Epic C B2: collectors — options + pipeline (fixes cross-cell bug) #706), batch plot snapshot (Epic B), the summary-collection benchmark.Deferred with reason: the
batch_toolsimport-warning waits for E4 (the newdb.pystill bridges throughbatch_tools). The human-readable symbol map is folded into the G3 migration guide.Closes #703. Part of #696.
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