Release v0.5.3: normalization v0.6.0

AGENTS.md

@@ -33,7 +33,7 @@ brick**.
 - **Statistics code (from the normalization brick):** the per-plane histogram, the CSV
   reader and writer, pooling (`PooledHistogram`) and normalization parameters (`min_max`,
   `percentile_range`, `z_score`, `robust_z_score`) live in the required dependency
-  `morphobricks_normalization` (pinned to its release v0.5.0; first pinned at v0.2.0, plan §12 questions 27 and
+  `morphobricks_normalization` (pinned to its release v0.6.0; first pinned at v0.2.0, plan §12 questions 27 and
   28). This brick runs them over
   the experiment. Later bricks such as patch extraction use them to normalise any group of
   planes without rereading pixels. Import them from `morphobricks_normalization`; the
@@ -770,7 +770,7 @@ Technical details go to `logging` (shown in the notebook's "Technical details" p
 | Topic | Decision |
 |---|---|
 | Binning | Per-plane min–max, same bin count per experiment, pooled counts for groups (binning study) |
-| Core dependencies | `numpy`, `tifffile`, `scipy` (the mask step's piece counts, Q32) and `morphobricks-normalization` (git dependency pinned to its release tag v0.5.0, whose reader takes the schema version 5 table (channels by canonical ID, ADR 0003; since v0.5.0), and whose CSV reader checks each row's stored `plane_id`, `image_file` and `bit_depth` (since v0.3.2), refuses a blank `position_id` and tables of schema versions 1 to 3 (v0.4.0), and whose `PlaneRecord` requires a keyword-only `position_id` and which refuses corrupt or ambiguous statistics and parameters (v0.3.3); `[tool.hatch.metadata] allow-direct-references`). `ipywidgets` and `matplotlib` in the `notebook` extra; `zarr` in the `zarr` extra; `pytest` and `ruff` in `dev` |
+| Core dependencies | `numpy`, `tifffile`, `scipy` (the mask step's piece counts, Q32) and `morphobricks-normalization` (git dependency pinned to its release tag v0.6.0, which only adds the `stain` module and the optional `histology` extra (neither used here), whose reader takes the schema version 5 table (channels by canonical ID, ADR 0003; since v0.5.0), and whose CSV reader checks each row's stored `plane_id`, `image_file` and `bit_depth` (since v0.3.2), refuses a blank `position_id` and tables of schema versions 1 to 3 (v0.4.0), and whose `PlaneRecord` requires a keyword-only `position_id` and which refuses corrupt or ambiguous statistics and parameters (v0.3.3); `[tool.hatch.metadata] allow-direct-references`). `ipywidgets` and `matplotlib` in the `notebook` extra; `zarr` in the `zarr` extra; `pytest` and `ruff` in `dev` |
 | OME-Zarr (Q12) | Input may be TIFF and/or OME-Zarr (folders ending in `.zarr`), mixed. OME-Zarr axes come from their metadata and are matched by role; level 0 of a single image only, several images per store is `multiple_series`. *Removed in v0.4.0 (plan Q46): TIFF images are always read directly; the following describes v0.3.* TIFF choice once per experiment (`convert_tiffs`): read directly (default) or convert to `<output>/ome_zarr` (OME-NGFF 0.4) and compute rows from the copies; switching recomputes TIFF rows and removes unused copies. Reads OME-NGFF 0.4 and 0.5 (0.5 needs zarr 3). In the notebook: its own step-3 card "(Optional) Image conversion" after Settings (Q13): radio buttons (read directly = recommended), a disk-space warning (amber, red when the estimate exceeds free space, never blocking), and conversion settings (chunk size, compression + level, pyramid levels) shown only when converting. CLI `--convert-tiff` with `--chunk-size`, `--compression`, `--compression-level`, `--pyramid-levels`. No overlap setting: chunks never overlap |
 | System files (Q5) | Ignored silently; `single` check and sibling uniqueness are case-insensitive |
 | Too-deep folders (Q7) | Error |
@@ -1094,15 +1094,15 @@ jupyter lab notebooks/MorphoBricks_Preprocessing.ipynb
 
 ---
 
-## 11. Status (current state, v0.5.2)
+## 11. Status (current state, v0.5.3)
 
-- **Released:** v0.5.2 (12 November 2026), with the normalization brick pinned at v0.5.0. The
+- **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
   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
   [docs/archive/agents-status-history-v0.1-v0.3.md](docs/archive/agents-status-history-v0.1-v0.3.md).
-- **Unreleased:** the faster *Looks right: confirm the design* click (see the changelog's
-  "Unreleased" section).
+- **Unreleased:** none yet; later changes go in a new "Unreleased" section of the changelog.
 - **Scope:** 2-D per plane (a Z-stack is refused as `z_stack_not_supported`; since v0.5.2 the
   notebook saves Z-stacks as recorded projections); acquisitions may have different channel
   lists (v0.5.2, Stage 3 S3.3: manifest version 5, histogram table schema version 5; units of

CHANGELOG.md

@@ -6,7 +6,23 @@ 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
+## v0.5.3 (13 November 2026)
+
+A pin release: normalization is pinned at v0.6.0, so that every core package (and CellPatcher,
+fiberfeatures and MorphoFeature downstream) pins the same normalization URL. Nothing in
+preprocessing changes because of it, and no format changes: run manifest version 5,
+`plane_histograms.csv` schema version 5, resolver contract version 2 and conversion record
+version 4 are those of v0.5.2, and a v0.5.2 run is read as it is. The release also carries the
+faster *Looks right: confirm the design* click of #293, merged after v0.5.2 (Fixed, below).
+
+### Changed
+
+- **Normalization pinned at v0.6.0** (`@v0.6.0`, tag on `95e1d6d`; was `@v0.5.0`, `1291b09`).
+  Normalization v0.6.0 only adds: a new module `morphobricks_normalization.stain` (RGB-to-scalar
+  presets: `to_scalar`, `rgb_to_scalar`, `PRESETS`) and an optional extra `histology`
+  (scikit-image), which preprocessing neither uses nor installs. Its legacy API,
+  `NormalizationParameters`, `rgb.py`, the `plane_histograms.csv` schema version 5 and every
+  output of v0.5.0 are unchanged, and it still imports with NumPy only.
 
 ### Fixed
 

README.md

@@ -19,7 +19,7 @@ from there.
 
 ## Status
 
-Pre-alpha; the current release is v0.5.2 (what is planned next is in
+Pre-alpha; the current release is v0.5.3 (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
@@ -41,7 +41,7 @@ Pre-alpha; the current release is v0.5.2 (what is planned next is in
 Every feature, message code and output file is described in the [user guide](docs/user_guide.md).
 
 From the normalization brick (`morphobricks_normalization`, a required dependency, pinned
-to its release v0.5.0): per-plane histograms with the robust range and the range check
+to its release v0.6.0): per-plane histograms with the robust range and the range check
 (`histogram`, `ranges`), the histogram table (`csv_io`, schema version 5: channels by canonical
 ID, so acquisitions may have different channels), pooled group statistics
 (`pooling`) and normalization parameters (`normalization`); import them from
@@ -61,7 +61,7 @@ converted. See the [CHANGELOG](CHANGELOG.md).
 ## Installation
 
 ```bash
-pip install "git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.2"
+pip install "git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.3"
 ```
 
 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@v0.5.2"`).
+(`pip install "morphobricks-preprocessing[notebook] @ git+https://github.com/CellMigrationLab/morphobricks-preprocessing.git@v0.5.3"`).
 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 v0.5.2 is in [docs/roadmap.md](docs/roadmap.md).
+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).
 
 ## 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 (v0.5.2: `PreprocessingNotebook()`). The
+`PreprocessingNotebook(...)` call is that commit's API (v0.5.3: `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 (0.5.2), normalization (0.5.0) and
+   - [ ] It prints **Ready** with the preprocessing (0.5.3), 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: v0.5.3 (13 November 2026)
+
+A G1-style record of the v0.5.3 release candidate (as for v0.5.2 below), a pin release:
+normalization moves from v0.5.0 to v0.6.0, which only adds the `stain` module and the optional
+`histology` extra. It does not decide a gate; deciding a gate is the owner's.
+
+| | |
+|---|---|
+| Release candidate | Measured on the tree of the v0.5.3 preparation commit (commit A of branch `claude/release-0.5.3`, from `main` at `3c91e7c`: v0.5.2 and #293, the faster *Looks right: confirm the design* click) before this record was added; the record changes only this file. A keeps `RELEASE_REF` at v0.5.2's `cadbed4`. 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 `69a58b3e2f89b318364c4c1252c54caf676fb6bb` (unchanged), checked by `test_spec_pin` (16 passed) |
+| Environment | Linux, Python 3.13.18, `pip install -e '.[dev,notebook,zarr]'` in a fresh venv (normalization 0.6.0 from its tag `v0.6.0` = `95e1d6d`, as pip's `direct_url.json` records; scikit-image not installed, the `histology` extra is not requested; 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 --junitxml=… tests/test_spec_*.py` |
+| `tools/check.py` | Ruff clean, Ruff format 461 files already formatted, pytest **5493 passed, 4 skipped** (not run, below), 0 failed, code rules passed (exit status 0) |
+| Spec modules (`tests/test_spec_*.py`) | **1799 passed, 0 skipped, 0 xfailed, 0 failed**, from all 25 modules of `tests/spec_gate.py` `EXPECTED_MODULES` (JUnit: no `skipped`, `failure` or `error` element in any case); the cases per module are those of v0.5.2 below |
+
+**Not run (4 environment skips, outside the Spec modules):** the four of v0.5.2 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: v0.5.2 (12 November 2026)
 
 A G1-style record of the v0.5.2 release candidate (as for v0.5.1 below). It does not decide a

notebooks/MorphoBricks_Preprocessing.ipynb

@@ -80,12 +80,12 @@
     "from pathlib import Path\n",
     "\n",
     "# LabConstrictor version identifiers.\n",
-    "current_version = \"0.5.2\"\n",
+    "current_version = \"0.5.3\"\n",
     "notebook_name = \"MorphoBricks_Preprocessing\"\n",
     "\n",
     "# A downloaded/Colab notebook installs this immutable source revision.\n",
-    "RELEASE_TAG = \"v0.5.2\"\n",
-    "RELEASE_REF = \"cadbed4bb049995b2385e3b8499c8d247d3754bd\"\n",
+    "RELEASE_TAG = \"v0.5.3\"\n",
+    "RELEASE_REF = \"14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a\"\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": "0.5.2"
+"MorphoBricks_Preprocessing": "0.5.3"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "morphobricks-preprocessing"
-version = "0.5.2"
+version = "0.5.3"
 description = "MorphoBricks preprocessing brick: per-plane intensity histograms and normalization methods for microscopy TIFFs."
 readme = "README.md"
 license = "MIT"
@@ -26,7 +26,7 @@ dependencies = [
     "scipy>=1.10",
     # Per-plane histograms, the CSV table, pooling and normalization, pinned to a release tag;
     # what each pin brought is in CHANGELOG.md.
-    "morphobricks-normalization @ git+https://github.com/CellMigrationLab/morphobricks-normalization.git@v0.5.0",
+    "morphobricks-normalization @ git+https://github.com/CellMigrationLab/morphobricks-normalization.git@v0.6.0",
 ]
 
 [project.optional-dependencies]

tests/test_notebook_file.py

@@ -124,6 +124,8 @@ def test_notebook_uses_stable_page_api_not_a_new_app_method():
     "d023ff91289a2d2204e1ae56f7dee114d1a665e4": "PreprocessingNotebook()",
     # v0.5.2: the same call.
     "cadbed4bb049995b2385e3b8499c8d247d3754bd": "PreprocessingNotebook()",
+    # v0.5.3: the same call.
+    "14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a": "PreprocessingNotebook()",
 }
 CHECKOUT_CALL = "PreprocessingNotebook()"
 """The call of this checkout's code (every run described, no ``describe`` argument)."""

tests/test_notebook_setup.py

@@ -105,8 +105,8 @@ def setup_environment(tmp_path, monkeypatch):
         drive=tmp_path / "content/drive",
         namespace={},
         versions={
-            "morphobricks-preprocessing": "0.5.2",
-            "morphobricks-normalization": "0.5.0",
+            "morphobricks-preprocessing": "0.5.3",
+            "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"] = "0.5.2"
+        state.versions["morphobricks-preprocessing"] = "0.5.3"
 
     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 = "0.5.2"\n',
+        '[project]\nname = "morphobricks-preprocessing"\nversion = "0.5.3"\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 0.5.2" in out
+    assert "Ready: preprocessing 0.5.3" 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"] == "cadbed4bb049995b2385e3b8499c8d247d3754bd"
-    assert "pinned v0.5.2 candidate" in capsys.readouterr().out
+    assert namespace["RELEASE_REF"] == "14f6b1a0e37474d38f3dd54138bbfdcce69d6e9a"
+    assert "pinned v0.5.3 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 0.5.2")[1]
+    assert "DEVELOPMENT OVERRIDE on" in out.split("Notebook 0.5.3")[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 0.5.2; normalization 0.5.0; ipywidgets 7.7.1." in out
+    assert "Ready: preprocessing 0.5.3; 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 0.5.2" in again
-    assert state.namespace["SETUP_RECORD"]["preprocessing_version"] == "0.5.2"
+    assert "Ready: preprocessing 0.5.3" in again
+    assert state.namespace["SETUP_RECORD"]["preprocessing_version"] == "0.5.3"
     assert record["release_ref"] == state.namespace["SETUP_RECORD"]["release_ref"]