Physical R_* checks of an experiment description (Stage 1, PR 8)

AGENTS.md

@@ -107,6 +107,9 @@ src/morphobricks_preprocessing/
   description.py        the model (Description, Condition, Channel, Repeat, Member, Unit, Mask)
                     built from a reader-accepted document; description_from_bytes -> DescriptionError
   description_write.py  the canonical writer (Spec experiment-v1 9.1) and section digests (9.3)
+  physical_check.py the physical R_* checks of a description against the folder and image headers
+                    (units found/declared, homogeneity, header evidence, image type, mask types
+                    declared); layout_groups (header-named layouts are batch-confirmable, Q3)
   description_reconcile.py reconcile(published, observed): units unchanged/new/removed by exact folder
                     labels, N35 reopening (confirmed_on kept), stated renames (FolderRename),
                     confirm_repeat; description_removal.py candidate (the draft), removal_questions

CHANGELOG.md

@@ -8,6 +8,20 @@ are in [docs/plan.md](docs/plan.md) §12. Upgrading from v0.3: see the
 
 ## Unreleased
 
+- **Physical `R_*` checks of an experiment description (Stage 1, PR 8; stacked on the
+  discovery and header additions, which provide the raw header names).** New module
+  `physical_check`: `check_physical(description, discovery, metadata, ...)` reports
+  `R_UNIT_NOT_FOUND`, `R_UNIT_NOT_DECLARED`, `R_UNIT_NOT_HOMOGENEOUS` (names the FOV, path and C
+  index; it replaces the count and header checks of its unit), `R_CHANNEL_COUNT_MISMATCH`,
+  `R_HEADER_CONTRADICTION` (raw names, NFC of both sides, no trimming, no case folding),
+  `R_IMAGE_TYPE_CONTRADICTS_HEADER` (both directions, header only; OME-Zarr states no colour
+  interpretation and is recorded as not header-verified) and `R_MASK_TYPE_NOT_DECLARED`. Pixels
+  are never read and no mask representation is defaulted or inferred. Homogeneity compares the
+  axes with `T` left out, so time-lapses of different lengths are one layout. An image whose
+  channel count the header does not state (a plain stack without confirmed roles) or whose header
+  cannot be read is listed in `unchecked`, not passed. `layout_groups` groups units by identical
+  layout; only groups whose channels are all header-named are batch-confirmable. Not used by any
+  run, notebook or CLI command yet.
 - **Reconciliation of the published description with the folder (Stage 1, PR 9; conformance
   P07, P08, P15, P33).** New modules `description_reconcile`, `description_removal` and
   `reconcile_observe`. Each unit is `unchanged`, `new` or `removed`, matched only by its exact

pyproject.toml

@@ -176,6 +176,7 @@ baseline = "tools/code_rules_baseline.json"
 "morphobricks_preprocessing.design" = "io"
 "morphobricks_preprocessing.design_values" = "pure"
 "morphobricks_preprocessing.description_identity" = "pure"
+"morphobricks_preprocessing.physical_check" = "io"
 "morphobricks_preprocessing.description" = "pure"
 "morphobricks_preprocessing.description_write" = "pure"
 "morphobricks_preprocessing.description_transition" = "pure"