[guijacquemet]

This is PP-3 of the v0.4.0 plan (preprocessing-design-v0.4.md revision 4, §8; plan-structure audit §5). It only moves code: no behaviour change. Review it with git diff --color-moved.

It is stacked on PP-2 (#66), which is stacked on PP-0 (#65, based on main). Merge order: #65, #66, then this PR.

Summary

run.py (895 lines after PP-2) becomes the package morphobricks_preprocessing/run/:

• preflight.py: Preflight, SamplePlane, preflight, sample_planes, _exclusion_issues, _normalise
• pipeline.py: run_experiment
• result.py: RunResult
• reuse.py: _load_previous, _describe_histogram
• rows.py: _read_file, _bin_count, _range_issues, _pixel_issues, _row_order
• publish.py: _staged_outputs, _publish_outputs, _OutputRollbackError
• __init__.py: keeps the module docstring and re-exports the public names, so from morphobricks_preprocessing.run import … and morphobricks_preprocessing.run_experiment work as before.

Other changes:

• Layers: each new module declares its layer in pyproject.toml. result.py is pure, pipeline.py is orchestration, and the rest are io.
• Tests: they now patch the submodule that uses a name, for example run.rows.iter_xyc_planes or run.pipeline.file_sha256, instead of run.<name>. No assertion changed.
• tools/check.py --rename OLD=NEW: a new option that re-keys the baseline entries of moved code, so a move does not count as a new violation. It never adds or raises an entry, and --update-baseline then drops what the move removed.
• AGENTS.md: the module map and the testing notes are updated.

Notes for review

• run_experiment is still 300+ lines (complexity 73). Cutting it below 60 lines is PP-7's job.
• Each new module is under 400 lines.

Tests

• No new tests (moves only); every existing test passes unchanged in substance.
• Full gate as CI (ruff check, ruff format --check, tools/check.py --rules, pytest with .[dev,notebook,zarr]):
  • Python 3.13 with zarr 3: 1339 passed, 1 skipped (running as root ignores file modes).
  • Python 3.11 with zarr 2.18: 1321 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, no fix needed beyond the merge of main (3e60007). Status: everything below is verified, and merging is the only step left.

Move only, verified

• I compared the ASTs of every top-level def, class and assignment in the old run.py (PP-2 head ecfc5af) with the run/ package. All 20 are identical, docstrings included. The only new item is __all__ in run/__init__.py.
• git diff --color-moved=zebra --color-moved-ws=allow-indentation-change: every non-moved added line is an import, a module docstring or the re-export.
• Baseline: the five function entries are re-keyed with the same sizes, and the run.py file entry drops.
• Tests only change patch targets to the submodules (run.rows.iter_xyc_planes, run.pipeline.*, global os/shutil). No assertion changed.
• Old import paths:
  • morphobricks_preprocessing.run still exports Preflight, RunResult, SamplePlane, preflight, run_experiment and sample_planes. That covers MorphoRelate's from morphobricks_preprocessing.run import Preflight, preflight, the only use in the other bricks.
  • Names that were only incidentally importable from the old module (e.g. OUTPUT_FILENAME, private helpers) are gone. Nothing in this repo or the bricks used them.
• Logger names become morphobricks_preprocessing.run.<module>. The CLI and the notebook attach their handlers to the package logger, so nothing is lost.

Merge of main (3e60007): the one AGENTS.md conflict keeps PP-3's testing note (run.rows.iter_xyc_planes).

Gate on 3e60007: 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.

Follow-up: --rename can re-key any baseline entry to any path. Shrink-only is enforced only against the code, so baseline diffs need a reviewer's eye, or a CI check against origin/main's baseline.

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Generated by Claude Code