Port the DB-journal path natively into cellpy.batch (E4 part 1, #716) - #748
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`journal_from_db` (backing `Batch.from_db`) delegated the entire database parse to `LabJournal.from_db()` in `utils/batch_tools/batch_journals.py` (~1134 lines) via `batch_tools/engines.py` (~412 lines). That was the last live consumer of `batch_tools/` from the new `cellpy.batch` stack. This reimplements the DB-journal path natively: - new `cellpy/batch/_dbengine.py`: `simple_db_engine` + `_create_pages_dict` + `_query` (from engines.py) and `find_files` / `fix_groups` / `make_unique_groups` / `create_labels` / `create_factory` (from batch_helpers.py), plus `make_db_reader` (the reader construction that was in `LabJournal.__init__`). The db readers themselves (`dbreader`, `json_dbreader`) are unchanged and still own db access. - `cellpy/batch/db.py` orchestrates from_db natively (reader → select_batch → simple_db_engine → polars Journal); no more `LabJournal` import. `batch_tools/` is now unused by production code (only its own tests still reference it directly). Its deletion + test migration follows in part 2. Verified: the full `Batch.from_db` path (simple Excel reader) plus the create_journal/deferred-db flow pass (test_batch_v3_facade.py), and the whole batch suite stays green (test_batch.py, 50 passed). Part of #716. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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With the DB-journal path ported natively (part 1, #748), nothing in production imports `cellpy/utils/batch_tools/` any more. Remove it (~4300 lines: the farm/barn Do-er machinery, LabJournal, engines, batch_helpers, exporters, dumpers, analyzers, reporters, sqlite_from_excel_db) and migrate the tests that still referenced it directly: - test_batch.py: repoint `engines.simple_db_engine` / `engines._query` / `batch_helpers.find_files` to `cellpy.batch._dbengine`; import `get_headers_journal` from `cellpy.parameters.internal_settings`; delete the tests bound to the removed machinery (CyclingExperiment, CSVExporter/dumpers, LabJournal-direct construction, the `batch_plotters`-removed probe). - test_batch_helpers_nulldata.py: deleted (tested the removed `batch_helpers.join_summaries` farm/barn path). - test_dbreader.py: drop the skip-only excel->sqlite test (used the removed `sqlite_from_excel_db`). `cellpy.utils.batch` / `cellpy.utils.collectors` stay as permanent re-export shims (they never imported batch_tools). Stale docstring pointers updated. Verified: test_batch.py + test_dbreader.py + test_batch_v3_facade.py = 57 passed, 1 skipped, 5 xfailed; full suite collects (1463 tests, no import errors). Closes #716. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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Part 1 of E4 (#716): the native DB-journal port. This is the substantive feature work the issue flagged as "a real feature port, comparable to C2, not a mechanical deletion."
Why
cellpy.batch.db.journal_from_db(which backsBatch.from_db) delegated the entire database parse toLabJournal.from_db()inutils/batch_tools/batch_journals.py(~1134 lines), driven bybatch_tools/engines.py(~412 lines). That was the last live consumer ofbatch_tools/from the newcellpy.batchstack — sobatch_tools/could not be deleted until the DB-journal path was reimplemented natively.What
cellpy/batch/_dbengine.py— native port of the piecesfrom_dbactually needs:simple_db_engine+_create_pages_dict+_query(fromengines.py)find_files/fix_groups/make_unique_groups/create_labels/create_factory(frombatch_helpers.py)make_db_reader— the reader construction that lived inLabJournal.__init__cellpy.readers.dbreader,cellpy.readers.json_dbreader) are unchanged and still own db access.cellpy/batch/db.py— orchestratesfrom_dbnatively (reader →select_batch→simple_db_engine→ polarsJournal); no moreLabJournalimport.After this,
batch_tools/is unused by production code — only its own tests still reference it directly.Verification
test_batch_v3_facade.py— the fullBatch.from_db("simple_excel_reader")path and the deferred-_dbcreate_journal()flow both pass (9 passed).test_batch.py+ facade + helpers = 50 passed, 1 skipped, 5 xfailed.Follow-up (part 2)
Delete
cellpy/utils/batch_tools/and migrate the 3 tests that still import it directly (test_batch.py,test_batch_helpers_nulldata.py,test_dbreader.py), keepingcellpy.utils.batch/cellpy.utils.collectorsas re-export shims. That PR will close #716.Part of #716.
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