patchworks 0.11.8__tar.gz → 0.11.10__tar.gz

{patchworks-0.11.8 → patchworks-0.11.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.11.8
+Version: 0.11.10
 Summary: Tiled processing of arbitrarily large images with globally consistent labels
 Project-URL: Homepage, https://github.com/imcf/patchworks
 Project-URL: Issues, https://github.com/imcf/patchworks/issues
@@ -29,9 +29,12 @@ Requires-Dist: bioio-lif; extra == 'all'
 Requires-Dist: bioio-nd2; extra == 'all'
 Requires-Dist: bioio-ome-tiff; extra == 'all'
 Requires-Dist: bioio-tifffile; extra == 'all'
+Requires-Dist: glasbey; extra == 'all'
 Requires-Dist: imaris-ims-file-reader; extra == 'all'
+Requires-Dist: ipykernel<7; extra == 'all'
 Requires-Dist: lxml-html-clean; extra == 'all'
 Requires-Dist: napari[all]>=0.5.5; extra == 'all'
+Requires-Dist: numpy<2.5; extra == 'all'
 Requires-Dist: nvidia-ml-py; extra == 'all'
 Requires-Dist: psutil; extra == 'all'
 Requires-Dist: scikit-image; extra == 'all'
@@ -63,13 +66,20 @@ Provides-Extra: io
 Requires-Dist: psutil; extra == 'io'
 Requires-Dist: tqdm; extra == 'io'
 Provides-Extra: napari
+Requires-Dist: glasbey; extra == 'napari'
+Requires-Dist: ipykernel<7; extra == 'napari'
 Requires-Dist: lxml-html-clean; extra == 'napari'
 Requires-Dist: napari[all]>=0.5.5; extra == 'napari'
+Requires-Dist: numpy<2.5; extra == 'napari'
 Provides-Extra: workflow
 Requires-Dist: snakemake-executor-plugin-slurm; extra == 'workflow'
 Requires-Dist: snakemake>=8; extra == 'workflow'
 Description-Content-Type: text/markdown
 
+<p align="center">
+  <img src="docs/assets/logo.png" alt="patchworks logo" width="220">
+</p>
+
 # patchworks
 
 [![PyPI](https://img.shields.io/pypi/v/patchworks.svg)](https://pypi.org/project/patchworks/)

{patchworks-0.11.8 → patchworks-0.11.10}/README.md

@@ -1,3 +1,7 @@
+<p align="center">
+  <img src="docs/assets/logo.png" alt="patchworks logo" width="220">
+</p>
+
 # patchworks
 
 [![PyPI](https://img.shields.io/pypi/v/patchworks.svg)](https://pypi.org/project/patchworks/)

{patchworks-0.11.8 → patchworks-0.11.10}/docs/index.md

@@ -1,5 +1,9 @@
 # patchworks
 
+<p align="center">
+  <img src="assets/logo.png" alt="patchworks logo" width="200">
+</p>
+
 **Tiled processing of arbitrarily large images — any image, any function.**
 
 ```text

{patchworks-0.11.8 → patchworks-0.11.10}/mkdocs.yml

@@ -5,6 +5,8 @@ copyright: Copyright © 2025 IMCF Basel
 
 theme:
   name: material
+  logo: assets/logo.png
+  favicon: assets/logo.png
   palette:
   - scheme: default
     primary: deep orange

{patchworks-0.11.8 → patchworks-0.11.10}/pyproject.toml

@@ -59,9 +59,18 @@ imaris = ["imaris-ims-file-reader"]
 # napari enables the interactive viewer plugin.
 # - napari >= 0.5: NumPy 2.0 compatible (older 0.4.x uses np.array(copy=False),
 #   which raises under NumPy 2 -> ValidationError on Viewer()).
+# - numpy < 2.5: napari/numba don't support numpy 2.5 yet.
+# - 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()).
-napari = ["napari[all]>=0.5.5", "lxml-html-clean"]
+# - glasbey: distinct high-contrast label LUTs for view_in_napari.
+napari = [
+    "napari[all]>=0.5.5",
+    "numpy<2.5",
+    "ipykernel<7",
+    "lxml-html-clean",
+    "glasbey",
+]
 # workflow runs the Snakemake pipeline (per-tile SLURM jobs across GPUs).
 workflow = ["snakemake>=8", "snakemake-executor-plugin-slurm"]
 dev = ["pytest", "pytest-cov", "scikit-image", "psutil", "tqdm"]

{patchworks-0.11.8 → patchworks-0.11.10}/src/patchworks/plugins/napari.py

@@ -199,6 +199,7 @@ def view_in_napari(
     labels_component: str = "labels",
     image_name: str = "image",
     labels_name: str = "labels",
+    glasbey: bool = True,
     show: bool = True,
     **add_image_kwargs: Any,
 ):
@@ -223,6 +224,11 @@ def view_in_napari(
         matching ``tile_process``'s ``output_component``).
     image_name, labels_name : str, optional
         Layer names shown in napari.
+    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
         that manage the loop themselves.
@@ -250,9 +256,24 @@ def view_in_napari(
         **add_image_kwargs,
     )
 
+    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)
-        viewer.add_labels(lab, name=labels_name)
+        viewer.add_labels(lab, name=labels_name, **label_kwargs)
     elif _is_zarr(image):
         # No labels given → auto-overlay every label image stored inside the
         # OME-ZARR under labels/<name>/ (the default place tile_process writes
@@ -260,7 +281,9 @@ def view_in_napari(
         for name in _inner_label_names(image):
             levels = _multiscale_levels(f"{image}/labels/{name}", None)
             lab = [lvl.astype("int32") for lvl in levels]
-            viewer.add_labels(lab if len(lab) > 1 else lab[0], name=name)
+            viewer.add_labels(
+                lab if len(lab) > 1 else lab[0], name=name, **label_kwargs
+            )
             logger.info("auto-loaded labels/%s from %s", name, image)
 
     if show: