cellfinder 1.3.2__tar.gz → 1.3.3__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of cellfinder might be problematic. Click here for more details.

Files changed (70) hide show
  1. {cellfinder-1.3.2 → cellfinder-1.3.3}/.github/workflows/test_and_deploy.yml +4 -3
  2. {cellfinder-1.3.2 → cellfinder-1.3.3}/PKG-INFO +3 -3
  3. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/classify.py +8 -0
  4. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/PKG-INFO +3 -3
  5. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/requires.txt +2 -2
  6. {cellfinder-1.3.2 → cellfinder-1.3.3}/pyproject.toml +2 -2
  7. {cellfinder-1.3.2 → cellfinder-1.3.3}/.github/workflows/test_include_guard.yaml +0 -0
  8. {cellfinder-1.3.2 → cellfinder-1.3.3}/.gitignore +0 -0
  9. {cellfinder-1.3.2 → cellfinder-1.3.3}/.napari/config.yml +0 -0
  10. {cellfinder-1.3.2 → cellfinder-1.3.3}/CITATION.cff +0 -0
  11. {cellfinder-1.3.2 → cellfinder-1.3.3}/LICENSE +0 -0
  12. {cellfinder-1.3.2 → cellfinder-1.3.3}/MANIFEST.in +0 -0
  13. {cellfinder-1.3.2 → cellfinder-1.3.3}/README.md +0 -0
  14. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/__init__.py +0 -0
  15. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/cli_migration_warning.py +0 -0
  16. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/__init__.py +0 -0
  17. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/__init__.py +0 -0
  18. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/augment.py +0 -0
  19. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/cube_generator.py +0 -0
  20. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/resnet.py +0 -0
  21. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/tools.py +0 -0
  22. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/config/__init__.py +0 -0
  23. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/config/cellfinder.conf +0 -0
  24. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/__init__.py +0 -0
  25. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/detect.py +0 -0
  26. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/__init__.py +0 -0
  27. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/plane/__init__.py +0 -0
  28. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/plane/classical_filter.py +0 -0
  29. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/plane/plane_filter.py +0 -0
  30. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/plane/tile_walker.py +0 -0
  31. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/setup_filters.py +0 -0
  32. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/volume/__init__.py +0 -0
  33. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/volume/ball_filter.py +0 -0
  34. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/volume/structure_detection.py +0 -0
  35. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/volume/structure_splitting.py +0 -0
  36. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/detect/filters/volume/volume_filter.py +0 -0
  37. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/download/__init__.py +0 -0
  38. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/download/cli.py +0 -0
  39. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/download/download.py +0 -0
  40. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/main.py +0 -0
  41. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/__init__.py +0 -0
  42. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/array_operations.py +0 -0
  43. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/geometry.py +0 -0
  44. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/image_processing.py +0 -0
  45. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/prep.py +0 -0
  46. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/source_files.py +0 -0
  47. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/system.py +0 -0
  48. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/tiff.py +0 -0
  49. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/tools/tools.py +0 -0
  50. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/train/__init__.py +0 -0
  51. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/train/train_yml.py +0 -0
  52. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/types.py +0 -0
  53. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/__init__.py +0 -0
  54. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/curation.py +0 -0
  55. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/detect/__init__.py +0 -0
  56. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/detect/detect.py +0 -0
  57. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/detect/detect_containers.py +0 -0
  58. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/detect/thread_worker.py +0 -0
  59. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/input_container.py +0 -0
  60. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/napari.yaml +0 -0
  61. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/sample_data.py +0 -0
  62. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/train/__init__.py +0 -0
  63. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/train/train.py +0 -0
  64. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/train/train_containers.py +0 -0
  65. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/napari/utils.py +0 -0
  66. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/SOURCES.txt +0 -0
  67. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/dependency_links.txt +0 -0
  68. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/entry_points.txt +0 -0
  69. {cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/top_level.txt +0 -0
  70. {cellfinder-1.3.2 → cellfinder-1.3.3}/setup.cfg +0 -0
{cellfinder-1.3.2 → cellfinder-1.3.3}/.github/workflows/test_and_deploy.yml RENAMED
@@ -9,6 +9,9 @@ on:
9
9
  - "v**"
10
10
  # Run on all pull-requests
11
11
  pull_request:
12
+ schedule:
13
+ # Runs at 6:10am UTC on Monday
14
+ - cron: '10 6 * * 1'
12
15
  # Allow workflow dispatch from GitHub
13
16
  workflow_dispatch:
14
17
 
@@ -45,10 +48,8 @@ jobs:
45
48
  # Run all supported Python versions on linux
46
49
  os: [ubuntu-latest]
47
50
  python-version: ["3.10", "3.11", "3.12"]
48
- # Include one windows and two macOS (intel based and arm based) runs
51
+ # Include one windows and one macOS (arm based) run
49
52
  include:
50
- - os: macos-13
51
- python-version: "3.12"
52
53
  - os: macos-latest
53
54
  python-version: "3.12"
54
55
  - os: windows-latest
{cellfinder-1.3.2 → cellfinder-1.3.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: cellfinder
3
- Version: 1.3.2
3
+ Version: 1.3.3
4
4
  Summary: Automated 3D cell detection in large microscopy images
5
5
  Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
6
6
  License: BSD-3-Clause
@@ -29,10 +29,10 @@ Requires-Dist: dask[array]
29
29
  Requires-Dist: fancylog>=0.0.7
30
30
  Requires-Dist: natsort
31
31
  Requires-Dist: numba
32
- Requires-Dist: numpy<2
32
+ Requires-Dist: numpy
33
33
  Requires-Dist: scikit-image
34
34
  Requires-Dist: scikit-learn
35
- Requires-Dist: keras>=3.0.0
35
+ Requires-Dist: keras==3.5.0
36
36
  Requires-Dist: torch>=2.1.0
37
37
  Requires-Dist: tifffile
38
38
  Requires-Dist: tqdm
{cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder/core/classify/classify.py RENAMED
@@ -68,6 +68,14 @@ def main(
68
68
  workers=workers,
69
69
  )
70
70
 
71
+ if trained_model and trained_model.suffix == ".h5":
72
+ print(
73
+ "Weights provided in place of the model, "
74
+ "loading weights into default model."
75
+ )
76
+ model_weights = trained_model
77
+ trained_model = None
78
+
71
79
  model = get_model(
72
80
  existing_model=trained_model,
73
81
  model_weights=model_weights,
{cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: cellfinder
3
- Version: 1.3.2
3
+ Version: 1.3.3
4
4
  Summary: Automated 3D cell detection in large microscopy images
5
5
  Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
6
6
  License: BSD-3-Clause
@@ -29,10 +29,10 @@ Requires-Dist: dask[array]
29
29
  Requires-Dist: fancylog>=0.0.7
30
30
  Requires-Dist: natsort
31
31
  Requires-Dist: numba
32
- Requires-Dist: numpy<2
32
+ Requires-Dist: numpy
33
33
  Requires-Dist: scikit-image
34
34
  Requires-Dist: scikit-learn
35
- Requires-Dist: keras>=3.0.0
35
+ Requires-Dist: keras==3.5.0
36
36
  Requires-Dist: torch>=2.1.0
37
37
  Requires-Dist: tifffile
38
38
  Requires-Dist: tqdm
{cellfinder-1.3.2 → cellfinder-1.3.3}/cellfinder.egg-info/requires.txt RENAMED
@@ -4,10 +4,10 @@ dask[array]
4
4
  fancylog>=0.0.7
5
5
  natsort
6
6
  numba
7
- numpy<2
7
+ numpy
8
8
  scikit-image
9
9
  scikit-learn
10
- keras>=3.0.0
10
+ keras==3.5.0
11
11
  torch>=2.1.0
12
12
  tifffile
13
13
  tqdm
{cellfinder-1.3.2 → cellfinder-1.3.3}/pyproject.toml RENAMED
@@ -27,10 +27,10 @@ dependencies = [
27
27
  "fancylog>=0.0.7",
28
28
  "natsort",
29
29
  "numba",
30
- "numpy<2",
30
+ "numpy",
31
31
  "scikit-image",
32
32
  "scikit-learn",
33
- "keras>=3.0.0",
33
+ "keras==3.5.0",
34
34
  "torch>=2.1.0",
35
35
  "tifffile",
36
36
  "tqdm",
{cellfinder-1.3.2 → cellfinder-1.3.3}/.gitignore RENAMED
File without changes
{cellfinder-1.3.2 → cellfinder-1.3.3}/CITATION.cff RENAMED
File without changes
{cellfinder-1.3.2 → cellfinder-1.3.3}/LICENSE RENAMED
File without changes
{cellfinder-1.3.2 → cellfinder-1.3.3}/MANIFEST.in RENAMED
File without changes
{cellfinder-1.3.2 → cellfinder-1.3.3}/README.md RENAMED
File without changes
{cellfinder-1.3.2 → cellfinder-1.3.3}/setup.cfg RENAMED
File without changes