cellfinder 1.3.1__tar.gz → 1.3.3__tar.gz

{cellfinder-1.3.1 → cellfinder-1.3.3}/.github/workflows/test_and_deploy.yml

@@ -9,6 +9,9 @@ on:
       - "v**"
   # Run on all pull-requests
   pull_request:
+  schedule:
+  # Runs at 6:10am UTC on Monday
+    - cron: '10 6 * * 1'
   # Allow workflow dispatch from GitHub
   workflow_dispatch:
 
@@ -45,10 +48,8 @@ jobs:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
         python-version: ["3.10", "3.11", "3.12"]
-        # Include one windows and two macOS (intel based and arm based) runs
+        # Include one windows and one macOS (arm based) run
         include:
-          - os: macos-13
-            python-version: "3.12"
           - os: macos-latest
             python-version: "3.12"
           - os: windows-latest

{cellfinder-1.3.1 → cellfinder-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.1
+Version: 1.3.3
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -32,7 +32,7 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras>=3.0.0
+Requires-Dist: keras==3.5.0
 Requires-Dist: torch>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm

{cellfinder-1.3.1 → cellfinder-1.3.3}/cellfinder/core/classify/classify.py

@@ -68,6 +68,14 @@ def main(
         workers=workers,
     )
 
+    if trained_model and trained_model.suffix == ".h5":
+        print(
+            "Weights provided in place of the model, "
+            "loading weights into default model."
+        )
+        model_weights = trained_model
+        trained_model = None
+
     model = get_model(
         existing_model=trained_model,
         model_weights=model_weights,

{cellfinder-1.3.1 → cellfinder-1.3.3}/cellfinder/napari/curation.py

@@ -113,7 +113,7 @@ class CurationWidget(QWidget):
         layer_names = [
             layer.name
             for layer in self.viewer.layers
-            if type(layer) == layer_type
+            if isinstance(layer, layer_type)
         ]
 
         if layer_names:
@@ -329,7 +329,7 @@ class CurationWidget(QWidget):
 
         if len(self.viewer.layers.selection) == 1:
             layer = list(self.viewer.layers.selection)[0]
-            if type(layer) == napari.layers.Points:
+            if isinstance(layer, napari.layers.Points):
                 if len(layer.data) > 0:
                     if point_type == "cell":
                         destination_layer = self.training_data_cell_layer

{cellfinder-1.3.1 → cellfinder-1.3.3}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.1
+Version: 1.3.3
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -32,7 +32,7 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras>=3.0.0
+Requires-Dist: keras==3.5.0
 Requires-Dist: torch>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm

{cellfinder-1.3.1 → cellfinder-1.3.3}/cellfinder.egg-info/requires.txt

@@ -7,7 +7,7 @@ numba
 numpy
 scikit-image
 scikit-learn
-keras>=3.0.0
+keras==3.5.0
 torch>=2.1.0
 tifffile
 tqdm

{cellfinder-1.3.1 → cellfinder-1.3.3}/pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "numpy",
     "scikit-image",
     "scikit-learn",
-    "keras>=3.0.0",
+    "keras==3.5.0",
     "torch>=2.1.0",
     "tifffile",
     "tqdm",