mcDETECT 2.0.10__tar.gz → 2.0.11__tar.gz

{mcdetect-2.0.10 → mcdetect-2.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.10
+Version: 2.0.11
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

mcdetect-2.0.11/mcDETECT/__init__.py

@@ -0,0 +1,6 @@
+__version__ = "2.0.11"
+
+from . import model
+from . import utils
+
+__all__ = ["model", "utils"]

{mcdetect-2.0.10 → mcdetect-2.0.11}/mcDETECT/model.py

@@ -122,10 +122,21 @@ class mcDETECT:
                     continue
                 temp_in_nucleus = np.sum(target["overlaps_nucleus"].values[mask])
                 temp_size = coords.shape[0]
-                # coords_unique = np.unique(coords, axis=0)
+                
                 temp = pd.DataFrame(coords, columns=["global_x", "global_y", "global_z"])
                 temp = temp.drop_duplicates()
-                center, r2 = miniball.get_bounding_ball(np.array(temp), epsilon=1e-8)
+                coords_unique = temp.to_numpy()
+                if coords_unique.shape[0] < self.low_bound:
+                    print(f"Skipping small cluster for gene {j}, cluster {k} (n = {coords_unique.shape[0]})")
+                    continue
+                try:
+                    center, r2 = miniball.get_bounding_ball(coords_unique, epsilon=1e-8)
+                except np.linalg.LinAlgError:
+                    print(f"Warning: singular matrix for gene {j}, cluster {k} —- using fallback sphere.")
+                    center = coords_unique.mean(axis=0)
+                    dists = np.linalg.norm(coords_unique - center, axis=1)
+                    r2 = (dists.max() ** 2)
+                
                 if self.type != "Xenium":
                     closest_z = closest(z_grid, center[2])
                 else:

{mcdetect-2.0.10 → mcdetect-2.0.11}/mcDETECT.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.10
+Version: 2.0.11
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

{mcdetect-2.0.10 → mcdetect-2.0.11}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name = "mcDETECT",
-    version = "2.0.10",
+    version = "2.0.11",
     packages = find_packages(),
     install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scikit-learn", "scipy", "shapely"],
     author = "Chenyang Yuan",

mcdetect-2.0.10/mcDETECT/__init__.py

@@ -1,6 +0,0 @@
-__version__ = "2.0.10"
-
-from . import model
-from . import utils
-
-__all__ = ["model", "utils"]