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Pin morphobricks-normalization v0.4.0 (position_id required) - #268
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Part 2 of #262: PlaneRecord.position_id is required and keyword-only, a blank position_id in a CSV row is refused, and schema v1-3 tables are refused. - tests pass position_id= wherever a PlaneRecord is built - run/steps.py: remove the dead fill-in of blank position ids - test_run: a table without position ids is refused and rebuilt - run/rows.py: position is str - README example, AGENTS.md and CHANGELOG note the new pin - pyproject.toml: @v0.3.4 -> @v0.4.0 Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01G3qp9AxjpGPw9xfWAUJNqc
Keeps both CHANGELOG entries (normalization v0.4.0 pin, three-cell notebook). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01G3qp9AxjpGPw9xfWAUJNqc
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Fixes #262
Part 2 of #262 (part 1 was #265). Moves the normalization pin from
@v0.3.4to@v0.4.0(tagc9522636a66dab0f6e9e907079a4d5f46a8d0a6c). That release is breaking:PlaneRecord.position_idis required and keyword-only, a blankposition_idin a CSV row is refused withCsvFormatError, and schema v1-3 tables are refused.Changes (the issue's checklist)
position_id=wherever aPlaneRecordis built:simulation.py,test_intensity.py,test_report.py,test_unchecked_channels.py,test_notebook_debt.py,test_histogram_goldens.py(the successor oftest_schema_v2_equivalence.py).run/steps.py: the dead fill-inreplace(r, position_id=...)is removed.tests/test_run.py:test_table_without_position_ids_is_filled_without_readingbecomes..._is_refused_and_rebuilt. It blanks the column, andrun/reuse.pyturns the reader'sCsvFormatErrorinto a full rebuild ("the earlier histogram table could not be read"). The test checks that every image is read again and that the rebuilt table is byte-identical to the original.run/rows.py:position: str | Nonebecomesstr.PlaneRecord(...)example getsposition_id=.pyproject.tomlpin v0.3.4 to v0.4.0 (the only place the URL appears). README and AGENTS.md text that states the pin is updated. CHANGELOG has an Unreleased note. No test states the pin.Also:
tools/code_rules_baseline.jsonlowers thetests/test_run.pyline baseline from 860 to 859 (the rewritten test is shorter).Not touched, as requested:
notebooks/MorphoBricks_Preprocessing.ipynbandRELEASE_REF. TheRELEASE_REFinstall still pins normalization v0.3.4, which is unchanged and fine.Evidence
make_described_runon main (normalization 0.3.4) and on this branch (0.4.0).plane_histograms.csvis byte-identical for all seven (SHA-256 equal, e.g. v030d7a0081...4876, 53476 bytes).python tools/check.pypasses: ruff check, ruff format --check, 5148 passed, 4 skipped, code rules at baseline. The skips are four platform skips (test_cli_log.py:166,test_folder_rules.py:199and:230for case-sensitive file systems;test_discovery.py:665for running as root).Generated by Claude Code