Version 0.3.2: data-flow audit fixes (PRs #40–#47)

AGENTS.md

@@ -767,7 +767,15 @@ jupyter lab notebooks/MorphoBricks_Preprocessing.ipynb
 - **v0.3.1** (to be tagged, question 36): `discovery.position_id`, the one function every
   MorphoBricks brick names positions with (D85), also removes `.png`, `.jpg`, `.jpeg`,
   `.bmp`, `.gif` and `.npy` (naming only) and refuses a name that is only an extension
-  (PR #33). Outputs unchanged.
+  (PR #33). Outputs unchanged. Released 29 October 2026.
+- **v0.3.2** (to be tagged, question 37): the fixes from the data-flow audit of
+  29 October 2026 (#35–#39): negative mask labels refused (PR #40); a malformed OME-Zarr
+  labels group is `unreadable_mask` (PR #41); differing channel names are an error,
+  compared exactly after trimming leading and trailing whitespace, recorded as
+  `channel_names_trimmed` (PRs #42, #45); masks get Z/T plane identity and a 2D mask for a
+  multi-plane image is refused (PR #43); strict manifest flags, per-file roles and uint64
+  labels (PR #44); a folder holding images and subfolders is an error (PR #46); the
+  normalization brick pinned to v0.3.2 (PR #47).
 - **Next (not started):** the notebook step for the masks (name each mask, confirm or
   correct the relationships) and a file saving those answers for the other bricks
   (question 32); 3D and time-lapse masks later.

docs/plan.md

@@ -896,3 +896,13 @@ Raised during review; to be decided before the milestones that need them:
     that is only an extension. Outputs and their schema versions are those of v0.3.0, with
     the normalization brick's v0.3.1. The version in `pyproject.toml` is 0.3.1 before
     tagging. Every brick pins this tag (D79), CellPatcher's core dependency included.*
+37. What does v0.3.2 hold?
+    *Decided (30 October 2026): v0.3.1 and the fixes of the data-flow audit of 29 October
+    2026 (issues #35–#39), PRs #40–#47: negative mask labels refused; malformed OME-Zarr
+    labels reported as `unreadable_mask`; differing channel names an error (exact after
+    trimming leading and trailing whitespace, recorded per file); mask Z/T plane identity,
+    with a 2D mask for a multi-plane image refused; strict manifest flags; a folder holding
+    images and subfolders an error; the normalization brick's v0.3.2, whose reader checks
+    each row's `plane_id`, `image_file` and `bit_depth`. Inputs that passed before may now be
+    refused. The version in `pyproject.toml` is 0.3.2 before
+    tagging. Every brick pins this tag (D79).*

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "morphobricks-preprocessing"
-version = "0.3.1"
+version = "0.3.2"
 description = "MorphoBricks preprocessing brick: per-plane intensity histograms and normalization methods for microscopy TIFFs."
 readme = "README.md"
 license = "MIT"