[guijacquemet]

This is PP-2 of the v0.4.0 plan (preprocessing-design-v0.4.md, revision 4, §8). It removes features and is breaking. PP-0 (#65) is merged, and main is merged into this branch (17fcb2e).

Summary

• convert_tiffs and zarr_export are removed:
  • OME-Zarr copies in <output>/ome_zarr, OmeZarrWriter, ConversionSettings, ConversionEstimate, estimate_conversion, ome_zarr_relative_path and _CopyStaging.
  • run_experiment(convert_tiffs=, conversion=) and RunResult.converted.
  • The CLI options --convert-tiff, --chunk-size, --compression, --compression-level and --pyramid-levels.
  • The notebook's "(Optional) Image conversion" card.
  • _staged_outputs/_publish_outputs lose their copy handling.
• Manifest: settings.convert_tiffs, settings.conversion and files[].ome_zarr_path are no longer written.
  • An older manifest that holds them is still read, and its rows are kept, since they were the TIFF's own.
  • Copies such a run left on disk are not touched.
• free_space moves to _io, for the disk check of PP-11's OME-TIFF conversion.
• The deprecated stand-ins are removed: _moved.py, the csv_io, dtypes, histogram, normalization, pooling and records modules, and the package __getattr__. Tests now import from morphobricks_normalization.
• check_declared_axes and declared_axes_transposed are removed, not deprecated (audit M7): they read a Y/X swap transposed, which v0.4 forbids. Their tests are removed; the axis check covers the rules.
• Baseline: shrinks by 14 entries; the # noqa: ANN count goes from 63 to 57.
• Docs:
  • contract §9 (removed keys), §10 (replaced by a removal note) and §16;
  • user guide (install, step 3, CLI table, outputs, messages);
  • plan §12 Q46 (and Q45 amended);
  • AGENTS.md and README.

Review fix (ecfc5af)

AGENTS.md's decisions log (Q12, Q15, P1) and its testing note, and the plan's OME-Zarr and large-plane passages, still described the conversion and the stand-ins as current. They are now marked as history.

Notes for review

• About 3.5k lines are removed, mostly zarr_export.py, its 1,000-line test file and the notebook card.
• Pickles: PhysicalSizes objects pickled under the old module path morphobricks_preprocessing.zarr_export no longer unpickle. Its test was removed.
• OME-Zarr input is unchanged: zarr_input, labels, and the unknown_scale reading.
• Other bricks still use removed names on their main (to migrate in their v0.4 PRs; not edited here):
  • CellPatcher: check_declared_axes and declared_axes_transposed;
  • MorphoFeature: axes.check_declared_axes and declared_axes_transposed;
  • MorphoRelate: the same two, and zarr_export.OmeZarrWriter in a test;
  • fiberfeatures: the same two.

Tests

• New file tests/test_removed_in_v040.py (25 tests): removed names and modules are gone; the run and the CLI refuse the conversion options; a v0.3 manifest with conversion keys is still read and its rows kept; free_space. On old main it fails at collection (_io does not exist).
• Full gate as CI on ecfc5af (ruff check, ruff format --check, tools/check.py --rules, pytest with .[dev,notebook,zarr]):
  • Python 3.13 with zarr 3: 1343 passed, 1 skipped (root ignores file modes).
  • Python 3.11 with zarr 2.18: 1325 passed, 19 skipped (that root skip plus 18 OME-NGFF 0.5 tests that need zarr 3).

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Generated by Claude Code

[guijacquemet]

Independent review: approved after a merge of main and one docs commit.

Checked

• Removals are complete:
  • The removed public names are ConversionEstimate, ConversionSettings, OmeZarrWriter, estimate_conversion, ome_zarr_relative_path, check_declared_axes and declared_axes_transposed, plus the 21 moved names.
  • The removed modules are _moved, csv_io, dtypes, histogram, normalization, pooling, records and zarr_export.
  • I compared the package's __all__ and submodules on main and on this branch.
  • No code, test or notebook still refers to them, outside the removal notes and test_removed_in_v040.py.
• run.py:
  • The non-conversion path is unchanged.
  • _publish_outputs keeps the same rollback for the table, design and manifest.
  • An old manifest's ome_zarr_path and conversion are ignored. Its rows are kept, which is right because the copies held the source values.
• Breaking change documented: plan Q46, contract §9/§10/§16, the user guide and README.

Fixed

• 17fcb2e merges main (PP-0). The baseline conflict keeps main's identical-bodies sizes of 0 and drops the entries this PR made unnecessary.
• ecfc5af: AGENTS.md's decisions log (Q12, Q15, P1), its testing note, and plan.md's OME-Zarr and large-plane passages still described the conversion and the stand-ins as current. They are now marked as history.

Other bricks, origin/main, read-only. These uses of removed names must migrate:

• CellPatcher 2c0a533:
  • src/cellpatcher/io.py:778 imports both axis functions;
  • tests/test_declared_axes.py:43,49;
  • docs in orchestration.py and types.py, and the notebook CHANGELOG.md.
• MorphoFeature 9951a58:
  • src/morphofeature/fov_files.py:72 (axes.check_declared_axes, declared_axes_transposed);
  • docs in run_config.py:467 and README.md:147;
  • tests/test_run_config.py:324.
• MorphoRelate ea19bb0:
  • src/morphorelate/io/tiff.py:18 (both axis functions);
  • tests/test_three_commands.py:17 (zarr_export.OmeZarrWriter);
  • docs in docs/input_contract.md, CHANGELOG.md and tests/test_io_tiff.py.
• fiberfeatures 362f1ba:
  • src/fiberfeatures/batch.py:16-19,291,294,309 (both axis functions);
  • docs in AGENTS.md, CHANGELOG.md and tests/test_batch.py.
• MorphoObjects, MorphoEmbed, MorphoCoverage and normalization have none.

Gate on ecfc5af: ruff check and format clean, --rules clean.

• 3.13 with zarr 3.4.2: 1343 passed, 1 skipped (root ignores file modes).
• 3.11 with zarr 2.18.7: 1325 passed, 19 skipped (that one plus 18 OME-NGFF 0.5 tests that need zarr 3).
• CI is green on all 7 jobs.

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Generated by Claude Code