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PP-3: split run.py into the run package (move only) - #109

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claude/pp-3-split-run
Nov 1, 2026
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PP-3: split run.py into the run package (move only)#109
guijacquemet merged 3 commits into
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claude/pp-3-split-run

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@guijacquemet guijacquemet commented Nov 1, 2026

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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).

Generated by Claude Code

claude added 2 commits November 1, 2026 12:03
@claude
PP-3: split run.py into the run package, moving code only
ef070f7 
Spec revision 4, section 8 PP-3 (plan-structure audit, section 5). No
behaviour change: every function and class is moved as it was, reviewable
with git diff --color-moved.

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

Tests now patch the submodule that uses a name: run.rows.iter_xyc_planes,
run.pipeline.file_sha256 and the like.

tools/check.py --rename OLD=NEW re-keys the baseline entries of moved code;
it never adds or raises one. Each new module has a declared layer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WX6rdMV1r5jUPUR94kxV5a
@claude
Merge PP-2 (restacked on the new main) into PP-3
6efe206 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WX6rdMV1r5jUPUR94kxV5a
@guijacquemet guijacquemet mentioned this pull request Nov 1, 2026
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@guijacquemet
guijacquemet changed the base branch from claude/pp-2-removals to main November 1, 2026 17:21
@claude
Merge main (PP-2 merged, with its review fixes) into PP-3
3e60007 
The AGENTS.md testing note keeps PP-3's wording: spy on `run.rows.iter_xyc_planes`, the
submodule that uses the name.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WX6rdMV1r5jUPUR94kxV5a
@guijacquemet Claude

guijacquemet commented Nov 1, 2026

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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.

Generated by Claude Code

@guijacquemet
guijacquemet marked this pull request as ready for review November 1, 2026 17:26
@guijacquemet
guijacquemet merged commit c16e757 into main Nov 1, 2026
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@guijacquemet guijacquemet mentioned this pull request Nov 13, 2026
Merged
@guijacquemet
guijacquemet deleted the claude/pp-3-split-run branch November 14, 2026 08:20
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@guijacquemet @claude