cellfinder 1.3.0rc0__tar.gz → 1.3.0rc1__tar.gz

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/.github/workflows/test_and_deploy.yml

@@ -48,11 +48,11 @@ jobs:
         # Include one windows and two macOS (intel based and arm based) runs
         include:
           - os: macos-13
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - name: Cache brainglobe directory
@@ -98,7 +98,7 @@ jobs:
       # Run test suite with numba disabled
       - uses: neuroinformatics-unit/actions/test@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
@@ -125,10 +125,10 @@ jobs:
         with:
           repository: 'brainglobe/brainglobe-workflows'
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install test dependencies
         run: |

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc0
+Version: 1.3.0rc1
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -18,6 +18,7 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/cellfinder/__init__.py

@@ -27,7 +27,6 @@ except PackageNotFoundError as e:
 # Set the Keras backend to torch
 os.environ["KERAS_BACKEND"] = "torch"
 
-__author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
 __license__ = "BSD-3-Clause"
 
 DEFAULT_CELLFINDER_DIRECTORY = Path.home() / ".brainglobe" / "cellfinder"

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/cellfinder/core/tools/system.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import keras
 from brainglobe_utils.general.exceptions import CommandLineInputError
 
 
@@ -80,3 +81,12 @@ def memory_in_bytes(memory_amount, unit):
         )
     else:
         return memory_amount * 10 ** supported_units[unit]
+
+
+def force_cpu():
+    """
+    Forces the CPU to be used, even if a GPU is available
+    """
+    keras.src.backend.common.global_state.set_global_attribute(
+        "torch_device", "cpu"
+    )

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc0
+Version: 1.3.0rc1
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -18,6 +18,7 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown

cellfinder-1.3.0rc1/cellfinder.egg-info/SOURCES.txt

@@ -0,0 +1,68 @@
+.gitignore
+CITATION.cff
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+.github/workflows/test_and_deploy.yml
+.github/workflows/test_include_guard.yaml
+.napari/config.yml
+cellfinder/__init__.py
+cellfinder/cli_migration_warning.py
+cellfinder.egg-info/PKG-INFO
+cellfinder.egg-info/SOURCES.txt
+cellfinder.egg-info/dependency_links.txt
+cellfinder.egg-info/entry_points.txt
+cellfinder.egg-info/requires.txt
+cellfinder.egg-info/top_level.txt
+cellfinder/core/__init__.py
+cellfinder/core/main.py
+cellfinder/core/types.py
+cellfinder/core/classify/__init__.py
+cellfinder/core/classify/augment.py
+cellfinder/core/classify/classify.py
+cellfinder/core/classify/cube_generator.py
+cellfinder/core/classify/resnet.py
+cellfinder/core/classify/tools.py
+cellfinder/core/config/__init__.py
+cellfinder/core/config/cellfinder.conf
+cellfinder/core/detect/__init__.py
+cellfinder/core/detect/detect.py
+cellfinder/core/detect/filters/__init__.py
+cellfinder/core/detect/filters/setup_filters.py
+cellfinder/core/detect/filters/plane/__init__.py
+cellfinder/core/detect/filters/plane/classical_filter.py
+cellfinder/core/detect/filters/plane/plane_filter.py
+cellfinder/core/detect/filters/plane/tile_walker.py
+cellfinder/core/detect/filters/volume/__init__.py
+cellfinder/core/detect/filters/volume/ball_filter.py
+cellfinder/core/detect/filters/volume/structure_detection.py
+cellfinder/core/detect/filters/volume/structure_splitting.py
+cellfinder/core/detect/filters/volume/volume_filter.py
+cellfinder/core/download/__init__.py
+cellfinder/core/download/cli.py
+cellfinder/core/download/download.py
+cellfinder/core/tools/__init__.py
+cellfinder/core/tools/array_operations.py
+cellfinder/core/tools/geometry.py
+cellfinder/core/tools/image_processing.py
+cellfinder/core/tools/prep.py
+cellfinder/core/tools/source_files.py
+cellfinder/core/tools/system.py
+cellfinder/core/tools/tiff.py
+cellfinder/core/tools/tools.py
+cellfinder/core/train/__init__.py
+cellfinder/core/train/train_yml.py
+cellfinder/napari/__init__.py
+cellfinder/napari/curation.py
+cellfinder/napari/input_container.py
+cellfinder/napari/napari.yaml
+cellfinder/napari/sample_data.py
+cellfinder/napari/utils.py
+cellfinder/napari/detect/__init__.py
+cellfinder/napari/detect/detect.py
+cellfinder/napari/detect/detect_containers.py
+cellfinder/napari/detect/thread_worker.py
+cellfinder/napari/train/__init__.py
+cellfinder/napari/train/train.py
+cellfinder/napari/train/train_containers.py

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc1}/pyproject.toml

@@ -16,6 +16,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
 requires-python = ">=3.9"

cellfinder-1.3.0rc0/cellfinder/core/config/cellfinder.conf.custom

@@ -1,3 +0,0 @@
-[model]
-    model_path = '/home/adam/.cellfinder/model_weights/resnet50_tv.h5'
-    model_type = '50-layer'