RunInputs.resolve_request: the shared request resolver (contract v1, v0.5.1) - #256

Target v0.5.1 (the first change after PP-C, merged in main cf69fd5). Implements MorphoBricks-Spec ADR 0002 (AR1-AR11, merged in Spec main 63e567e; checked against 9a03d89). Design: MorphoFeature claude/restart-doc, docs/restart/designs/resolver-design-2026-11-10.md; Stage 2 plan row PP-0.

Summary (by module)

• run_inputs_request.py (pure): the resolver contract's types and rules. RESOLVER_VERSION = 1; Request(channel_ids, masks, planes, capabilities, device), MaskRequest(mask_id, role, binary_mask_policy), Capabilities(rgb_support, volume_support); ResolvedRequest(selections, refusals, coverage, provenance) with FovSelection, MaskSelection, PlaneSelection, Refusal, RepeatCoverage, Provenance; VolumeNotSupportedError (A_VOLUME_NOT_SUPPORTED); the pure rules (scope_refusal "present in k of n acquisitions", coverage full / partial / unavailable, plane_selections, the mask, RGB and volume refusals, check_request).
• run_inputs_resolve.py (io): the ResolvingInputs mixin, a base of RunInputs: resolve_request(request) reads the manifest, the published description (SHA-checked) and mask_representation.json once, classifies, and returns the immutable result. A refused request has no selections; every applicable refusal is reported together. It reads no pixel, runs no kernel, writes nothing, converts no mask (a recorded binary_mask_policy is returned as MaskSelection.conversion for the route's shared labeller, CellPatcher's), checks only the device's spelling, and imports no brick, CellPatcher or provider module.
• fov_identity.py: FovIdentity.image_type (the unit's declared type) for the RGB check. Fov is unchanged (PP-1 adds Fov.image_type).
• run_inputs.py: one import, one base class. __init__.py: the new names exported. pyproject.toml: the two layer declarations. docs/contract.md §9.1 and §16, CHANGELOG.md Unreleased (v0.5.1) "PP-0".

After PP-C (this update)

• Merged main cf69fd5 (no textual conflicts). The CHANGELOG entry had landed in the 0.5.0 section; it is now its own "PP-0" section of Unreleased (v0.5.1).
• Trimmed (AR10): the resolver's undescribed-run branch (description() is None → plain RunInputsError) and its test are removed, with the or () / str() fallbacks for undescribed Fovs. Every run the resolver sees is described: RunInputs.open refuses one without morphobricks.toml with A_DESCRIPTION_REQUIRED (tested in the resolver suite).

Adversarial review against AR1-AR11 (findings and fixes)

1. Provenance defaulted silently (experiment_description or {}, sha256 → "", digests → ()): now read strictly from the manifest's record, which every version-4 manifest carries.
2. A request with a list was recorded mutable. Request(["DNA"]) was resolved and recorded as given in Provenance.request and in every FovSelection.channel_ids, so the "immutable" result could change after the fact and was unhashable; Request("DNA") was read as the channels D, N, A; a truthy non-bool capability (rgb_support=1, "no") granted support. All are now ValueErrors (malformed request, not a refusal), with tests.
3. The import test missed transitive imports and skimage. The AST scan covers only the two modules' own imports, and the sys.modules check sliced off skimage with scipy. A new test imports the resolver in a fresh interpreter and bars every brick, CellPatcher, provider, torch and skimage module (scipy is preprocessing's own dependency).
4. Gaps closed with tests: A_MASK_UNCHECKED for 1 of 4 files (only "4 of 4" was tested); a description changed since the run is refused, not resolved; device spellings CUDA and cuda:0 refused.
5. Checked and sound, no change: classification only (AR1, AR7); no writes, no pixel read (monkeypatched asarray, read_plane, read_mask); refusals all reported in contract order with "k of n" from the run's images (masks: of the recorded files); per-FOV channel_indices by canonical ID (v13 plus a reordered-channel test; a real mixed-layout run cannot be written yet, preprocessing processes one layout per experiment); mask policy returned, not applied (AR5); volume_support refusing by default, a one-slice volume equal to the plane selection (AR3/AR8); device spelling checked and recorded, availability left to the consumer (AR9); RESOLVER_VERSION = 1; provenance = description SHA-256 + section digests + request.
6. Noted, not changed (PP-C's behaviour): a morphobricks.toml deleted after RunInputs.open gives description()'s plain RunInputsError ("is gone: the run recorded a description"), not A_DESCRIPTION_REQUIRED.

Tests

python tools/check.py on a fresh clone (Python 3.13, Linux, .[dev,notebook,zarr]): ruff check . clean; ruff format --check . 411 files already formatted; code rules against the baseline: pass; pytest: 5015 passed, 4 skipped (all environment skips: three "this file system tells names apart by case", one "running with permissions that ignore file modes"; none in a Spec module). Spec modules (tests/test_spec_*.py): 1708 passed, 0 skipped; test_spec_resolve_request.py 43 tests (registered in spec_gate.EXPECTED_MODULES).

Fixes nothing yet (#200 and fiberfeatures #195 are fixed by the consuming PRs); prepares P24, P27, P28, SI1.

https://claude.ai/code/session_01G3qp9AxjpGPw9xfWAUJNqc

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