Release v0.5.4: RGB header override and mask-only RGB requests

AGENTS.md

@@ -1099,10 +1099,11 @@ jupyter lab notebooks/MorphoBricks_Preprocessing.ipynb
 
 ---
 
-## 11. Status (current state, v0.5.3)
+## 11. Status (current state, v0.5.4)
 
-- **Released:** v0.5.3 (13 November 2026), with the normalization brick pinned at v0.6.0 (v0.5.2,
-  12 November 2026, pinned it at v0.5.0). The
+- **Released:** v0.5.4 (14 November 2026): the RGB header override (Spec RH1) and mask-only
+  requests on RGB units; the normalization brick stays pinned at v0.6.0 (since v0.5.3,
+  13 November 2026; v0.5.2, 12 November 2026, pinned it at v0.5.0). The
   per-release history is in [CHANGELOG.md](CHANGELOG.md); the milestones PP-0 to PP-13 are in
   [docs/archive/plan-milestones-v0.1-v0.4.md](docs/archive/plan-milestones-v0.1-v0.4.md); the older
   status log of this file is in

CHANGELOG.md

@@ -6,7 +6,13 @@ The design is `docs/restart/preprocessing-design-v0.4.md` in MorphoFeature, on b
 are in [docs/plan.md](docs/plan.md) §12. (The v0.3 to v0.4 migration guide was removed in
 v0.5.1: no run before v0.5.1 is read.)
 
-## Unreleased
+## v0.5.4 (14 November 2026)
+
+RGB scanner input: the RGB header override of Spec amendment RH1, and mask-only requests on RGB
+units (Fixed, below). The normalization pin stays at v0.6.0. Run manifest version 5,
+`plane_histograms.csv` schema version 5, resolver contract version 2 and conversion record
+version 4 are those of v0.5.3; the manifest's new unit keys are additive (only units declared
+`rgb` carry them), and a v0.5.3 run is read as it is. The Spec pin moves to `b635b7d` (Changed).
 
 ### Added
 
@@ -45,6 +51,15 @@ v0.5.1: no run before v0.5.1 is read.)
 - **Spec re-pinned to `b635b7d`** (Spec PR #37, RH1 merged; `v40`, `i140`, `i141`, `t14`,
   `t15` now vendored): notebook drafts saved under `69a58b3` are not carried over.
 
+### Fixed
+
+- **A mask-only request on an RGB unit was refused** (`A_RGB_NOT_SUPPORTED`) unless the consumer
+  declared `rgb_support`, so a brick's mask-only features (MorphoObjects shapes, MorphoRelate
+  relations and skeletons) could not run on an RGB slide (#298). Spec `experiment-v1.md` section 8
+  refuses only a request that includes the channels of an RGB unit; the resolver now counts only
+  the RGB images whose channels the request names. Naming one of `R`, `G`, `B` without
+  `rgb_support` is still refused. Owner decision of 14 November 2026: no new capability value.
+
 ## v0.5.3 (13 November 2026)
 
 A pin release: normalization is pinned at v0.6.0, so that every core package (and CellPatcher,

README.md

@@ -19,7 +19,7 @@ from there.
 
 ## Status
 
-Pre-alpha; the current release is v0.5.3 (what is planned next is in
+Pre-alpha; the current release is v0.5.4 (what is planned next is in
 [docs/roadmap.md](docs/roadmap.md)). Implemented and tested:
 
 - Folder discovery and validation, TIFF and OME-Zarr header inspection without reading pixels
@@ -61,7 +61,7 @@ converted. See the [CHANGELOG](CHANGELOG.md).
 ## Installation
 
 ```bash
-pip install "git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.3"
+pip install "git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.4"
 ```
 
 For development, from a clone:
@@ -71,7 +71,7 @@ pip install -e ".[dev]"
 ```
 
 The optional `notebook` extra installs the widget dependencies for the notebook
-(`pip install "morphobricks-preprocessing[notebook] @ git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.3"`).
+(`pip install "morphobricks-preprocessing[notebook] @ git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.4"`).
 The notebook's first code cell (**1. Install**) can set this up automatically: it uses a compatible nearby
 checkout or installed package, and installs missing requirements into the active kernel. A standalone
 download installs from GitHub if needed (internet access and Git required).
@@ -228,7 +228,7 @@ ruff format .
 pytest
 ```
 
-Coding conventions are described in [docs/development.md](docs/development.md). Planned work after v0.5.3 is in [docs/roadmap.md](docs/roadmap.md).
+Coding conventions are described in [docs/development.md](docs/development.md). Planned work after v0.5.4 is in [docs/roadmap.md](docs/roadmap.md).
 
 ## License
 

docs/colab-release-check.md

@@ -19,7 +19,7 @@ Write the date, the commit and any failure (as an issue number) next to each ite
 - **Time-lapse:** a small experiment of time-lapse images (optional; the tests cover it).
 
 **Before opening it.** `RELEASE_REF` in cell 1 is the release preparation commit, and cell 3's
-`PreprocessingNotebook(...)` call is that commit's API (v0.5.3: `PreprocessingNotebook()`). The
+`PreprocessingNotebook(...)` call is that commit's API (v0.5.4: `PreprocessingNotebook()`). The
 release PR moves `RELEASE_REF` and records the pair in `RELEASE_CALLS` of
 `tests/test_notebook_file.py`, which fails for a `RELEASE_REF` without one.
 
@@ -30,7 +30,7 @@ release PR moves `RELEASE_REF` and records the pair in `RELEASE_CALLS` of
    - [ ] One line: "… run cell 1 (Install MorphoBricks preprocessing) first …", no traceback;
      nothing is installed.
 3. Run **cell 1**.
-   - [ ] It prints **Ready** with the preprocessing (0.5.3), normalization (0.6.0) and
+   - [ ] It prints **Ready** with the preprocessing (0.5.4), normalization (0.6.0) and
      ipywidgets versions and the pinned source, then names cells 2 and 3. No restart or
      ipywidgets upgrade is asked for; Drive is not mounted.
    - [ ] Run it again: nothing is installed again, the same versions.

docs/conformance.md

@@ -6,6 +6,29 @@ real run; a skip is never counted as a pass. Owner rulings of 8 November 2026 (i
 "no skips" applies to the Spec conformance modules (`tests/test_spec_*.py`); a skip elsewhere
 in the suite is listed as **not run**, with its reason.
 
+## Release record: v0.5.4 (14 November 2026)
+
+A G1-style record of the v0.5.4 release candidate (as for v0.5.3 below): the RGB header override
+(Spec amendment RH1, #295) and mask-only requests on RGB units (#298). Normalization stays at
+v0.6.0. It does not decide a gate; deciding a gate is the owner's.
+
+| | |
+|---|---|
+| Release candidate | Measured on the tree of the v0.5.4 preparation commit (commit A of branch `claude/release-0.5.4`, from `main` at `052668e`: v0.5.3, #295 and #298) before this record was added; the record changes only this file. A keeps `RELEASE_REF` at v0.5.3's `14f6b1a`. Commit B then points the notebook's `RELEASE_REF` at A and records the pair in `RELEASE_CALLS` (the notebook and two test files only), so `git diff A B -- src pyproject.toml` is empty: the installed package is the one `RELEASE_REF` names |
+| Spec pin | `tests/spec_fixtures/PIN.toml`: MorphoBricks-Spec `b635b7d5bc950529bce9dcc5681cec34b75139b8` (RH1 merged; was `69a58b3` in v0.5.3), checked by `test_spec_pin` (16 passed) |
+| Environment | Linux, Python 3.13.18, the package from this tree (`PYTHONPATH=src` over an editable install of the same checkout) with `[dev,notebook,zarr]` (normalization 0.6.0 from its tag `v0.6.0` = `95e1d6d`, as pip's `direct_url.json` records; scikit-image not installed; numpy 2.5.4, tifffile 2026.11.12, ipywidgets 8.1.9, zarr 3.4.2, pytest 9.2.0); run as root on a case-sensitive file system |
+| Commands | `python tools/check.py` (Ruff, Ruff format, pytest over `tests/`, code rules); `python -m pytest -q -p no:cacheprovider -rsxX tests/test_spec_*.py` |
+| `tools/check.py` | Ruff clean, Ruff format 465 files already formatted, pytest **5600 passed, 4 skipped** (not run, below), 0 failed, code rules passed (exit status 0) |
+| Spec modules (`tests/test_spec_*.py`) | **1839 passed, 0 skipped, 0 xfailed, 0 failed**, from all 25 modules of `tests/spec_gate.py` `EXPECTED_MODULES` (40 more than v0.5.3: the RH1 cases `v40`, `i140`, `i141`, `t14`, `t15` of the re-pinned Spec) |
+
+**Not run (4 environment skips, outside the Spec modules):** the four of v0.5.3 below
+(`tests/test_cli_log.py:166`, `tests/test_folder_rules.py:199` and `:230`: the file system is
+case-sensitive; `tests/test_discovery.py:665`: run as root). These four behaviours are **not
+verified by this run**.
+
+**Still the owner's:** the Colab and JupyterLab browser check (`docs/colab-release-check.md`),
+before tagging.
+
 ## Release record: v0.5.3 (13 November 2026)
 
 A G1-style record of the v0.5.3 release candidate (as for v0.5.2 below), a pin release:

notebooks/MorphoBricks_Preprocessing.ipynb

@@ -80,12 +80,12 @@
     "from pathlib import Path\n",
     "\n",
     "# LabConstrictor version identifiers.\n",
-    "current_version = \"0.5.3\"\n",
+    "current_version = \"0.5.4\"\n",
     "notebook_name = \"MorphoBricks_Preprocessing\"\n",
     "\n",
     "# A downloaded/Colab notebook installs this immutable source revision.\n",
-    "RELEASE_TAG = \"v0.5.3\"\n",
-    "RELEASE_REF = \"14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a\"\n",
+    "RELEASE_TAG = \"v0.5.4\"\n",
+    "RELEASE_REF = \"05d763a1a0af2436957b860579a2c0636d3929de\"\n",
     "REPOSITORY = \"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/CellMigrationLab/morphobricks-preprocessing.git\"\n",
     "EXTRAS = \"notebook\"\n",
     "\n",

notebooks/notebook_latest_versions.yaml

@@ -1,3 +1,3 @@
 # Latest version of each notebook, read by LabConstrictor's version check by notebook_name.
 # Equal to the notebook's current_version and its RELEASE_TAG without the "v" (README, "Notebook").
-"MorphoBricks_Preprocessing": "0.5.3"
+"MorphoBricks_Preprocessing": "0.5.4"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "morphobricks-preprocessing"
-version = "0.5.3"
+version = "0.5.4"
 description = "MorphoBricks preprocessing brick: per-plane intensity histograms and normalization methods for microscopy TIFFs."
 readme = "README.md"
 license = "MIT"

tests/test_notebook_file.py

@@ -126,6 +126,8 @@ def test_notebook_uses_stable_page_api_not_a_new_app_method():
     "cadbed4bb049995b2385e3b8499c8d247d3754bd": "PreprocessingNotebook()",
     # v0.5.3: the same call.
     "14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a": "PreprocessingNotebook()",
+    # v0.5.4: the same call.
+    "05d763a1a0af2436957b860579a2c0636d3929de": "PreprocessingNotebook()",
 }
 CHECKOUT_CALL = "PreprocessingNotebook()"
 """The call of this checkout's code (every run described, no ``describe`` argument)."""

tests/test_notebook_setup.py

@@ -105,7 +105,7 @@ def setup_environment(tmp_path, monkeypatch):
         drive=tmp_path / "content/drive",
         namespace={},
         versions={
-            "morphobricks-preprocessing": "0.5.3",
+            "morphobricks-preprocessing": "0.5.4",
             "morphobricks-normalization": "0.6.0",
             "ipywidgets": "7.7.1",
         },
@@ -131,7 +131,7 @@ def install(command, *, check):
         assert check is True
         state.installs.append(command)
         state.available.update({*REQUIRED, ZARR})
-        state.versions["morphobricks-preprocessing"] = "0.5.3"
+        state.versions["morphobricks-preprocessing"] = "0.5.4"
 
     monkeypatch.setattr(subprocess, "run", install)
 
@@ -163,7 +163,7 @@ def checkout_at(path):
     package.mkdir(parents=True)
     (package / "__init__.py").write_text("", encoding="utf-8")
     (path / "pyproject.toml").write_text(
-        '[project]\nname = "morphobricks-preprocessing"\nversion = "0.5.3"\n',
+        '[project]\nname = "morphobricks-preprocessing"\nversion = "0.5.4"\n',
         encoding="utf-8",
     )
     return path
@@ -179,7 +179,7 @@ def test_setup_reuses_the_matching_installed_release(setup_environment, capsys):
         "morphobricks_preprocessing.notebook_ui",  # cell 3 shows it
     ]
     out = capsys.readouterr().out
-    assert "Ready: preprocessing 0.5.3" in out
+    assert "Ready: preprocessing 0.5.4" in out
     assert "ipywidgets 7.7.1" in out
 
 
@@ -193,8 +193,8 @@ def test_setup_installs_missing_package_from_the_exact_commit(setup_environment,
     target = command[5]
     assert target.startswith("morphobricks-preprocessing[notebook] @ git+")
     assert target.endswith("@" + namespace["RELEASE_REF"])
-    assert namespace["RELEASE_REF"] == "14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a"
-    assert "pinned v0.5.3 candidate" in capsys.readouterr().out
+    assert namespace["RELEASE_REF"] == "05d763a1a0af2436957b860579a2c0636d3929de"
+    assert "pinned v0.5.4 candidate" in capsys.readouterr().out
 
 
 def test_setup_replaces_a_mismatched_installed_release(setup_environment):
@@ -285,7 +285,7 @@ def test_an_explicit_development_override_uses_the_checkout_and_says_so(
     assert sys.path[0] == str(checkout / "src")
     assert f"commit {OTHER_COMMIT}, uncommitted changes" in out
     assert "DEVELOPMENT OVERRIDE is on" in out
-    assert "DEVELOPMENT OVERRIDE on" in out.split("Notebook 0.5.3")[1]
+    assert "DEVELOPMENT OVERRIDE on" in out.split("Notebook 0.5.4")[1]
     record = namespace["SETUP_RECORD"]
     assert record["checkout_commit"] == OTHER_COMMIT
     assert record["checkout_has_uncommitted_changes"] is True
@@ -428,7 +428,7 @@ def test_cell_1_installs_without_mounting_drive_or_showing_the_app(
     assert state.apps == []
     assert namespace["SETUP_RECORD"]["release_ref"] == RELEASE_REF
     out = capsys.readouterr().out
-    assert "Ready: preprocessing 0.5.3; normalization 0.6.0; ipywidgets 7.7.1." in out
+    assert "Ready: preprocessing 0.5.4; normalization 0.6.0; ipywidgets 7.7.1." in out
     assert "Next: run cell 2 (Mount Google Drive), then cell 3 (Run preprocessing)." in out
 
 
@@ -444,8 +444,8 @@ def test_running_cell_1_again_installs_nothing_more(setup_environment, capsys):
     assert len(state.installs) == 1
     assert "Installing notebook requirements" in first
     assert "Installing notebook requirements" not in again
-    assert "Ready: preprocessing 0.5.3" in again
-    assert state.namespace["SETUP_RECORD"]["preprocessing_version"] == "0.5.3"
+    assert "Ready: preprocessing 0.5.4" in again
+    assert state.namespace["SETUP_RECORD"]["preprocessing_version"] == "0.5.4"
     assert record["release_ref"] == state.namespace["SETUP_RECORD"]["release_ref"]