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Refuse images in a folder that also holds subfolders - #46
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Owner decision (October 2026): a folder holding both image files and subfolders is an error in discovery, not a warning, as in every other brick (CellPatcher already refuses it). The code stays tiff_outside_leaf (OME-Zarr images included); its severity becomes error, so check/run block and nothing is written. It is no longer counted as a skipped item in the CLI report or the notebook tiles. Contract §1/§8, user guide, plan and AGENTS updated. Regression tests test_images_beside_subfolders_are_an_error and test_a_run_with_images_beside_subfolders_writes_nothing (both fail on main). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VbytvBRB9CmKQ5AAkhEFcv
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VbytvBRB9CmKQ5AAkhEFcv
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Merged main (#45) in with no conflicts. Generated by Claude Code |
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Summary
discovery.py: images (TIFF or OME-Zarr) in a folder that also has subfolders are now an error instead of a warning. The issue code staystiff_outside_leaf, so code that reads issue codes keeps working. With an error,checkandrunstop and write nothing. The new message says a folder holds either images or subfolders, never both.report.py,notebook_ui.py: these images are no longer counted under "skipped" items, because they now block the run.Decisions
Owner decision (October 2026), passed on by the coordinator: every MorphoBricks brick refuses a mixed folder, and CellPatcher already does, so its images are never dropped with only a warning. Excluding the paths does not clear this error, just as with other folder-structure errors (
folder_too_deep).Tests
test_images_beside_subfolders_are_an_errorreplaces the old warning test.test_a_run_with_images_beside_subfolders_writes_nothingis new. Both fail on main.pytest: 1122 passed, 1 skipped (test_discovery.py:472, root ignores file modes).ruff check .andruff format --check .are clean.Generated by Claude Code