Version 0.3.4: declared axes and one design reader (PRs #58, #59)

AGENTS.md

@@ -796,11 +796,20 @@ jupyter lab notebooks/MorphoBricks_Preprocessing.ipynb
   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). Released 30 October 2026.
-- **v0.3.3** (to be tagged, question 39): the shared rules other bricks call instead of
+- **v0.3.3** (question 39): the shared rules other bricks call instead of
   copying them (MorphoBricks D86, question 38, contract §16), PRs #49–#55: length units,
   int32 labels, header axes, identity text and case, source checks against a run's
   manifest, masks named as images, pixel sizes within 0.1 %; and the
-  `unsupported_pixel_size_unit` warning (PR #56).
+  `unsupported_pixel_size_unit` warning (PR #56). Released 31 October 2026.
+- **v0.3.4** (to be tagged, question 41): core fixes for the other bricks. Declared axes
+  (PR #58): a plain stack's positional Y and X are left open, so a plain `QYX` stack
+  declared `YXC` is accepted; the named Y and X declared swapped are accepted and read
+  transposed (`declared_axes_transposed` reports it); any other disagreement is refused;
+  new `named_axes`, `series_axes_from_metadata`, `TiffMetadata.axes_from_metadata`. One
+  strict experiment-design reader for every brick (PR #59, question 40):
+  `read_confirmed_design`; edits to `experiment_design.csv` with an empty or NA-like
+  `repeat_group`, repeat groups differing only in case, or a `confirmed_on` that is not
+  `YYYY-MM-DD` are refused, naming the line and column.
 - **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

@@ -979,3 +979,15 @@ Raised during review; to be decided before the milestones that need them:
     `design_issues` reports such values in a design built in code
     (`invalid_experiment_design`), and the writer refuses them, so the brick only ever
     writes ISO dates.*
+41. What does v0.3.4 hold?
+    *Decided (31 October 2026): v0.3.3 and the core fixes of the owner's answers of 31
+    October 2026 (PRs #58, #59). Declared axes (question 38, amended): a plain stack's
+    positional Y and X are left open, so a plain stack declared `YXC` is accepted; a
+    declaration that differs from the named axes only by swapping Y and X is accepted and
+    the image read transposed (`declared_axes_transposed`); any other disagreement is
+    refused. One strict experiment-design reader for every brick, `read_confirmed_design`
+    (question 40). Inputs that passed before may now be refused: design edits with an empty
+    or NA-like `repeat_group` (an empty group no longer means the folder name), repeat
+    groups differing only in case, or a `confirmed_on` that is not `YYYY-MM-DD`. The
+    normalization brick stays at v0.3.2. The version in `pyproject.toml` is 0.3.4 before
+    tagging. Every brick pins this tag (D79).*

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "morphobricks-preprocessing"
-version = "0.3.3"
+version = "0.3.4"
 description = "MorphoBricks preprocessing brick: per-plane intensity histograms and normalization methods for microscopy TIFFs."
 readme = "README.md"
 license = "MIT"