im_info: add DROPPABLE_KEYS + presets + remove_marked_intermediates (Slice 1 of #245)#250
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…Slice 1 of #245) Foundation for per-output intermediate retention. Adds module-level ``DROPPABLE_KEYS`` (the 14-key universe of toggleable outputs: 12 image-like intermediates + ``adjacency_maps`` + the special ``im_path``), three preset constants (``KEEP_EVERYTHING_PRESET``, ``MASKS_AND_CSVS_PRESET``, ``CSVS_ONLY_PRESET``), and a new method ``ImInfo.remove_marked_intermediates(drop_keys)`` that validates the input against ``DROPPABLE_KEYS`` and deletes only the marked files (silently skipping any that were never produced). Legacy ``ImInfo.remove_intermediates()`` is refactored into a one-line shim calling ``remove_marked_intermediates(drop_keys=DROPPABLE_KEYS)``; the two pre-existing pinned tests (``test_remove_intermediates_preserves_csv_files``, ``test_remove_intermediates_deletes_canonical_im_path``) continue to pass unchanged. 11 new tests in ``tests/test_verifier_iminfo.py`` (section H.1) pin: ``DROPPABLE_KEYS`` membership exact (no CSVs); each preset's membership; per-key drop semantics; empty drop set is a no-op; unknown / CSV keys raise ``AssertionError``; missing files are silently skipped; ``im_path`` resolves correctly; legacy shim matches the new method. ADR 0014 documents the API-shape decision (``frozenset[str]`` over a structured dataclass). Closes #246 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This was referenced May 12, 2026
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… Qt importorskip + wiki close-out (#245) (#254) CI fixes for the per-output retention slices (PRs #250-#253): 1. **Windows mmap-release** in ``ImInfo.remove_marked_intermediates``. The post-rewrite method tried to ``os.remove(im_path)`` while ``self.im`` still held the tifffile memmap, triggering ``PermissionError [WinError 32] The process cannot access the file because it is being used by another process`` on Windows CI. Fix: drop ``self.im`` (and ``gc.collect()``) at the start of the method — the existing pattern documented at ``_release_iminfo_memmap`` in ``test_verifier_iminfo.py``. Always-release is the cheapest and safest default; any pipeline intermediate could be memmap'd by a stage that's still alive in the process. Callers who use ``info.im`` after cleanup get ``None`` (correct — the file may be gone). 2. **Ubuntu headless Qt** ImportError on ``libEGL.so.1`` for ``test_napari_settings.py``. ``qtpy.QtWidgets`` transitively pulls Qt's display libs even for the dataclass-only tests (``SettingsConfig`` lives in the same module). Fix: module-level ``pytest.importorskip("qtpy.QtWidgets")`` so the entire file skips cleanly on systems without Qt's display libs. Tests pass normally where Qt loads. Phase 5 wiki close-out for PRD #245: - ``wiki/glossary.md`` — new ``DROPPABLE_KEYS`` entry pointing to [[decisions/0014-intermediates-policy-frozenset]]. - ``wiki/pipeline.md`` Gotchas — new bullet for the per-output cleanup mechanism: end-of-pipeline-only, only-on-success (inherits the existing "no try/except around stages" gotcha), ``cleanup_drop_keys`` kwarg surface. - ``wiki/im-info.md`` test-coverage line — updated to call out ``remove_marked_intermediates`` + ``DROPPABLE_KEYS`` / preset-constants alongside the legacy ``remove_intermediates`` shim. Test count bumped (~57 → ~68). - ``wiki/now.md`` — "Active work" cleared; "Recently shipped" entry summarizes the four-slice chain, the API surface, the failure semantics, the test count delta (715 → 748 non-perf), and the new ADR. Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
nellie.im_info:DROPPABLE_KEYS(the 14-key universe),KEEP_EVERYTHING_PRESET,MASKS_AND_CSVS_PRESET,CSVS_ONLY_PRESET.ImInfo.remove_marked_intermediates(drop_keys: frozenset[str])— validates againstDROPPABLE_KEYS, deletes only the marked files, silently skips missing ones.ImInfo.remove_intermediates()into a one-line shim calling the new method withDROPPABLE_KEYS. Both pre-existing pinned tests pass unchanged.tests/test_verifier_iminfo.py(section H.1) pin the contract.wiki/decisions/0014-intermediates-policy-frozenset.md.Closes #246. Foundation for Slices 2/3 of #245.
Test plan
uv run pytest tests/test_verifier_iminfo.py -q— 68 passed (was 57, 11 new)DROPPABLE_KEYSmembership matches_create_output_paths(every non-CSV key plusim_path)remove_intermediates()semantics preserved end-to-end🤖 Generated with Claude Code