Read and write channel_names_trimmed as a strict manifest flag

docs/contract.md

@@ -166,7 +166,7 @@ file's schema or statistical interpretation.
 | `channels_from_rgb_samples` | `true` when the C role is the RGB samples axis of images stored as RGB colour (§13), `false` otherwise; absent in manifests written before it. Optional key. |
 | `intensity_checks` | The limits of the intensity checks run on the table (§14): `IntensityCheckSettings.to_dict()` of the normalization brick (`library_version`, `outlier_limit`, `saturation_limit`, `min_images`); absent in manifests written before it. Optional key. Changing the limits recomputes nothing. |
 | `narrow_histogram_ranges` | The channel planes whose range check found the central range too narrow (§4), sorted by plane and channel: `relative_path`, `plane_id`, `channel` and the fields of the normalization brick's `RangeCheck` (`histogram_range`, `central_percentiles`, `central_bins`, `robust_quantiles`, `robust_limits`, `outside_robust_count`, `robust_central_bins`, `min_central_bins`). Empty when there are none; absent in manifests written before follow-up P6. Optional key: the manifest stays version 1. |
-| Flags | `missing_as_singleton`, `convert_tiffs`, `read_in_blocks` and `channels_from_rgb_samples` are JSON booleans (`true`/`false`); any other value (`"false"`, `0`) makes the manifest malformed, never read as true or false, and `write_manifest` refuses to write one (`ValueError`), so a written manifest always reads back. |
+| Flags | `missing_as_singleton`, `convert_tiffs`, `read_in_blocks`, `channel_names_trimmed` and `channels_from_rgb_samples` are JSON booleans (`true`/`false`); any other value (`"false"`, `0`) makes the manifest malformed, never read as true or false, and `write_manifest` refuses to write one (`ValueError`), so a written manifest always reads back. |
 | `versions` | Versions of `morphobricks-preprocessing`, `morphobricks-normalization` (which computes the histograms and writes the CSV; absent in manifests written before it), `numpy`, `tifffile` and Python. Information only: a different version never causes a rebuild. |
 
 Channel names and significant bits come from OME metadata. Significant bits are for

src/morphobricks_preprocessing/manifest.py

@@ -544,7 +544,7 @@ def _file_dict(entry: FileEntry) -> dict:
         "ome_zarr_path": entry.ome_zarr_path,
         "read_in_blocks": _flag(entry.read_in_blocks, "read_in_blocks"),
         "position_id": entry.position_id,
-        "channel_names_trimmed": entry.channel_names_trimmed,
+        "channel_names_trimmed": _flag(entry.channel_names_trimmed, "channel_names_trimmed"),
         "roles": None if entry.roles is None else list(entry.roles),
     }
 
@@ -568,7 +568,7 @@ def _file_entry(data: dict) -> FileEntry:
         ome_zarr_path=None if data.get("ome_zarr_path") is None else str(data["ome_zarr_path"]),
         read_in_blocks=_flag(data.get("read_in_blocks", False)),
         position_id=None if data.get("position_id") is None else str(data["position_id"]),
-        channel_names_trimmed=bool(data.get("channel_names_trimmed", False)),
+        channel_names_trimmed=_flag(data.get("channel_names_trimmed", False)),
         roles=_roles(data.get("roles"), str(data["axes"])),
     )
 

tests/test_manifest.py

@@ -258,6 +258,7 @@ def test_bad_role_in_manifest_is_refused():
         ("settings", "missing_as_singleton"),
         ("settings", "convert_tiffs"),
         ("file", "read_in_blocks"),
+        ("file", "channel_names_trimmed"),
         ("top", "channels_from_rgb_samples"),
     ],
 )
@@ -271,15 +272,22 @@ def test_flags_must_be_json_booleans(where, key, value):
 
 
 def _with_flag(key, value):
-    if key == "read_in_blocks":
-        return manifest(files=(entry(read_in_blocks=value),))
+    if key in ("read_in_blocks", "channel_names_trimmed"):
+        return manifest(files=(entry(**{key: value}),))
     if key == "channels_from_rgb_samples":
         return manifest(channels_from_rgb_samples=value)
     return manifest(settings=replace(RunSettings(65_536, 2**30, False, ()), **{key: value}))
 
 
 @pytest.mark.parametrize(
-    "key", ["missing_as_singleton", "convert_tiffs", "read_in_blocks", "channels_from_rgb_samples"]
+    "key",
+    [
+        "missing_as_singleton",
+        "convert_tiffs",
+        "read_in_blocks",
+        "channel_names_trimmed",
+        "channels_from_rgb_samples",
+    ],
 )
 @pytest.mark.parametrize("value", ["false", 0, 1, np.bool_(True)])
 def test_the_writer_refuses_flags_that_are_not_booleans(tmp_path, key, value):