refactor(napari): ♻️ use the glasbey package for label LUTs (#39)

Drop the custom colorcet/CyclicLabelColormap helper; instead build the
palette with glasbey.create_palette (the approach from napari's gallery)
and hand the list straight to add_labels(colormap=...). Lightness biased
up so colours read on the dark canvas. Toggle via the `glasbey` arg.
Swap the napari extra dep colorcet -> glasbey.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

Author: lguerard

pyproject.toml

@@ -63,13 +63,13 @@ imaris = ["imaris-ims-file-reader"]
 # - ipykernel < 7: napari-console requires ipykernel < 7.
 # - lxml-html-clean: napari's notebook_display imports lxml.html.clean, split
 #   into a separate package in lxml >= 5.2 (else ImportError on Viewer()).
-# - colorcet: glasbey label LUTs for view_in_napari.
+# - glasbey: distinct high-contrast label LUTs for view_in_napari.
 napari = [
     "napari[all]>=0.5.5",
     "numpy<2.5",
     "ipykernel<7",
     "lxml-html-clean",
-    "colorcet",
+    "glasbey",
 ]
 # workflow runs the Snakemake pipeline (per-tile SLURM jobs across GPUs).
 workflow = ["snakemake>=8", "snakemake-executor-plugin-slurm"]

src/patchworks/plugins/napari.py

@@ -191,48 +191,6 @@ def _resolve_labels(
     return arr.astype("int32")
 
 
-def _label_colormap(name: str | None):
-    """Build a cyclic napari label colormap from a colorcet glasbey palette.
-
-    Parameters
-    ----------
-    name : str or None
-        A ``colorcet`` palette attribute, e.g. ``"glasbey_dark"`` (glasbey on a
-        dark background). ``None`` falls back to napari's default label colours.
-
-    Returns
-    -------
-    napari.utils.colormaps.CyclicLabelColormap or None
-        The colormap to pass to ``add_labels``, or ``None`` for the default.
-    """
-    if not name:
-        return None
-    try:
-        import colorcet
-    except ImportError:
-        logger.warning(
-            "colorcet not installed; using napari's default label colours "
-            "(pip install colorcet, or it ships with patchworks[napari])."
-        )
-        return None
-
-    palette = getattr(colorcet, name, None)
-    if palette is None:
-        logger.warning("colorcet has no palette %r; using default colours.", name)
-        return None
-
-    import numpy as np
-    from napari.utils.colormaps import CyclicLabelColormap
-
-    def _hex_to_rgba(h: str):
-        h = h.lstrip("#")
-        return (int(h[0:2], 16) / 255, int(h[2:4], 16) / 255,
-                int(h[4:6], 16) / 255, 1.0)
-
-    colors = np.array([_hex_to_rgba(c) for c in palette], dtype=float)
-    return CyclicLabelColormap(colors=colors)
-
-
 def view_in_napari(
     image: Union[da.Array, str, Path],
     labels: Union[da.Array, str, Path, None] = None,
@@ -241,7 +199,7 @@ def view_in_napari(
     labels_component: str = "labels",
     image_name: str = "image",
     labels_name: str = "labels",
-    label_colormap: str | None = "glasbey_dark",
+    glasbey: bool = True,
     show: bool = True,
     **add_image_kwargs: Any,
 ):
@@ -266,11 +224,10 @@ def view_in_napari(
         matching ``tile_process``'s ``output_component``).
     image_name, labels_name : str, optional
         Layer names shown in napari.
-    label_colormap : str or None, optional
-        ``colorcet`` palette for the label LUT; default ``"glasbey_dark"``
-        (glasbey on a dark background — many distinct, high-contrast colours).
-        Any colorcet name works (e.g. ``"glasbey_light"``); ``None`` uses
-        napari's default label colours. Needs ``colorcet`` (ships with
+    glasbey : bool, optional
+        Colour the labels with a glasbey palette (many distinct, high-contrast
+        colours, tuned to read on the dark canvas) instead of napari's default.
+        Default ``True``. Needs the ``glasbey`` package (ships with
         ``patchworks[napari]``).
     show : bool, optional
         Start the napari event loop (blocking). Set ``False`` in scripts/tests
@@ -299,8 +256,20 @@ def view_in_napari(
         **add_image_kwargs,
     )
 
-    cmap = _label_colormap(label_colormap)
-    label_kwargs = {"colormap": cmap} if cmap is not None else {}
+    label_kwargs: dict[str, Any] = {}
+    if glasbey:
+        try:
+            import glasbey as _glasbey
+
+            # bias lighter so colours read on napari's dark canvas
+            label_kwargs["colormap"] = _glasbey.create_palette(
+                256, lightness_bounds=(40, 100)
+            )
+        except ImportError:
+            logger.warning(
+                "glasbey not installed; using napari's default label colours "
+                "(pip install glasbey, or it ships with patchworks[napari])."
+            )
 
     if labels is not None:
         lab = _resolve_labels(labels, labels_component)