napari/settings: replace single checkbox with per-output retention group + presets (Slice 3 of #245)#252
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…oup + presets (Slice 3 of #245) Replaces the legacy "Remove intermediate files" checkbox with a new ``IntermediateRetentionGroup`` widget composed of: - A preset radio row at top (Keep everything / Masks + CSVs only / CSVs only / Custom). Custom is auto-selected when the per-output selection diverges from any named preset; not user-clickable. - Eight stage-grouped subgroups (Filter, Label, Network, Markers, Tracking, Voxel reassignment, Hierarchy, Pipeline input) holding one checkbox per key in ``DROPPABLE_KEYS``. Checkbox semantics: **checked = drop**. Each checkbox carries a tooltip describing the source stage and downstream consumers (re-run implications). Selecting a named preset radio sets the per-output checkboxes to match the preset's drop set. Toggling any individual checkbox flips the radio to "Custom"; toggling back to the preset's exact drop set re-selects the preset. ``SettingsConfig`` schema change: ``remove_intermediates: bool`` → ``cleanup_drop_keys: frozenset[str]``. ``to_config`` reads the widget's ``drop_keys()``; ``apply_config`` calls ``set_drop_keys(...)`` which also syncs the preset radio. 17 new tests in ``tests/test_napari_settings.py`` pin: default state ("Keep everything", empty drop set); checkbox count and membership; tooltips present; preset → drop-set mapping (×3); ``set_drop_keys`` round-trip (×3); preset radio reflects loaded drop set (named + Custom); checkbox toggle after preset switches to Custom (and back); unknown / CSV keys rejected; ``SettingsConfig`` field schema and round-trip. Note: ``nellie_processor.py`` still references the now-removed ``remove_intermediates_checkbox``; that attribute lookup will fail at runtime in ``run_feature_export`` until Slice 4 (#249) re-wires it. No tests exercise that path so the regression suite stays green (715 passed). Closes #248 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This was referenced May 12, 2026
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Summary
IntermediateRetentionGroupwidget (innellie_napari/nellie_settings.py) replaces the single "Remove intermediate files" checkbox: 4-radio preset row + 8 stage-grouped subgroups holding 14 checkboxes (one per key inDROPPABLE_KEYS).SettingsConfigschema:remove_intermediates: bool→cleanup_drop_keys: frozenset[str].to_config/apply_configupdated.tests/test_napari_settings.pypin the contract via the publicdrop_keys()/set_drop_keys(...)API.nellie_processor.py) still reads the now-removedremove_intermediates_checkboxattribute. Slice 4 (#249) re-wires it. No test exercises that path, so the suite stays green.Closes #248. Builds on #246 (Slice 1).
Test plan
uv run pytest tests/test_napari_settings.py tests/test_run_cleanup.py tests/test_verifier_iminfo.py -q— 90 passeduv run pytest -q --ignore=tests/test_*_perf.py— 715 passed, 0 regressions🤖 Generated with Claude Code