cellfinder 1.5.0__py3-none-any.whl → 1.6.0__py3-none-any.whl

cellfinder/core/classify/classify.py

@@ -11,7 +11,7 @@ from brainglobe_utils.general.system import get_num_processes
 from cellfinder.core import logger, types
 from cellfinder.core.classify.cube_generator import CubeGeneratorFromFile
 from cellfinder.core.classify.tools import get_model
-from cellfinder.core.train.train_yml import depth_type, models
+from cellfinder.core.train.train_yaml import depth_type, models
 
 
 def main(

cellfinder/core/main.py

@@ -6,7 +6,7 @@ from brainglobe_utils.cells.cells import Cell
 
 from cellfinder.core import logger
 from cellfinder.core.download.download import model_type
-from cellfinder.core.train.train_yml import depth_type
+from cellfinder.core.train.train_yaml import depth_type
 
 
 def main(

cellfinder/napari/curation.py

@@ -406,7 +406,7 @@ class CurationWidget(QWidget):
             self.update_status_label("Ready")
 
     def __prep_directories_for_save(self):
-        self.yaml_filename = self.output_directory / "training.yml"
+        self.yaml_filename = self.output_directory / "training.yaml"
         self.cell_cube_dir = self.output_directory / "cells"
         self.no_cell_cube_dir = self.output_directory / "non_cells"
 

cellfinder/napari/train/train.py

@@ -7,7 +7,7 @@ from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_info
 from qtpy.QtWidgets import QScrollArea
 
-from cellfinder.core.train.train_yml import run as train_yml
+from cellfinder.core.train.train_yaml import run as train_yaml
 from cellfinder.napari.utils import cellfinder_header, html_label_widget
 
 from .train_containers import (
@@ -26,7 +26,7 @@ def run_training(
     misc_training_inputs: MiscTrainingInputs,
 ):
     print("Running training")
-    train_yml(
+    train_yaml(
         **training_data_inputs.as_core_arguments(),
         **optional_network_inputs.as_core_arguments(),
         **optional_training_inputs.as_core_arguments(),

cellfinder/napari/train/train_containers.py

@@ -5,7 +5,7 @@ from typing import Optional
 from magicgui.types import FileDialogMode
 
 from cellfinder.core.download.download import model_filenames
-from cellfinder.core.train.train_yml import models
+from cellfinder.core.train.train_yaml import models
 from cellfinder.napari.input_container import InputContainer
 from cellfinder.napari.utils import html_label_widget
 
@@ -31,7 +31,7 @@ class TrainingDataInputs(InputContainer):
                 "yaml_files",
                 custom_label="YAML files",
                 mode=FileDialogMode.EXISTING_FILES,
-                filter="*.yml",
+                filter="*.yaml",
             ),
             output_directory=cls._custom_widget(
                 "output_directory", mode=FileDialogMode.EXISTING_DIRECTORY

{cellfinder-1.5.0.dist-info → cellfinder-1.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: cellfinder
-Version: 1.5.0
+Version: 1.6.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,11 +16,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
@@ -36,6 +36,7 @@ Requires-Dist: keras>=3.7.0
 Requires-Dist: torch!=2.4,>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
+Requires-Dist: qt-niu
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
@@ -47,7 +48,6 @@ Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pooch>=1; extra == "dev"
-Requires-Dist: qt-niu; extra == "dev"
 Provides-Extra: napari
 Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"

{cellfinder-1.5.0.dist-info → cellfinder-1.6.0.dist-info}/RECORD

@@ -1,11 +1,11 @@
 cellfinder/__init__.py,sha256=S5oQ3EORuyQTMYC4uUuzGKZ23J3Ya6q-1DOBib1KfiA,1166
 cellfinder/cli_migration_warning.py,sha256=gPtNrtnXvWpl5q0k_EGAQZg0DwcpCmuBTgpg56n5NfA,1578
 cellfinder/core/__init__.py,sha256=pRFuQsl78HEK0S6gvhJw70QLbjjSBzP-GFO0AtVaGtk,62
-cellfinder/core/main.py,sha256=QiLo8qtK6hRT_cu-xSP9k93EE-dZjmb2xxocsY-hTwU,3836
+cellfinder/core/main.py,sha256=6PdZxqrAYHauT_K6R4H_u8Eyc3kbrNormySDiWSgTRo,3837
 cellfinder/core/types.py,sha256=lTqWE4v0SMM0qLAZJdyAzqV1nLgDtobEpglNJcXt160,106
 cellfinder/core/classify/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/classify/augment.py,sha256=8dMbM7KhimM6NMgdMC53oHoCfYj1CIB-h3Yk8CZAxPw,6321
-cellfinder/core/classify/classify.py,sha256=p3TvpnTVCVa9xCSgHm7QsgHeYeNZaoSbvf9fgZ3uF0c,3560
+cellfinder/core/classify/classify.py,sha256=UkZJa8DUnyaACx8hazHMi-JSSYosuzBWXkbVhgNo78g,3561
 cellfinder/core/classify/cube_generator.py,sha256=jC5aogTVy213PHouViSR9CgKkuOks3yk6csQC5kRoOE,17125
 cellfinder/core/classify/resnet.py,sha256=vGa85y_NcQnOXwAt5EtatLx5mrO8IoShCcNKtJ5-EFg,10034
 cellfinder/core/classify/tools.py,sha256=s5PEKAsZVbVuoferZ_nqMUM0f2bV_8WEKsdKe3SXEuE,2560
@@ -39,9 +39,9 @@ cellfinder/core/tools/threading.py,sha256=EmDLF22ZvXJnsWg7g6sv4cZgNweC0YrVw2o7QX
 cellfinder/core/tools/tiff.py,sha256=NzIz6wq2GzxmcIhawFMwZADe-uQO2rIG46H7xkpGKLs,2899
 cellfinder/core/tools/tools.py,sha256=opMGC5GBBsId0dmL8V0KQrI4U70w_D_KtGQYpZNeHYQ,9390
 cellfinder/core/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/train/train_yml.py,sha256=9QXv2wk24G8hYskMnBij7OngEELUWySK2fH4NFbYWw4,13260
+cellfinder/core/train/train_yaml.py,sha256=9QXv2wk24G8hYskMnBij7OngEELUWySK2fH4NFbYWw4,13260
 cellfinder/napari/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/napari/curation.py,sha256=Egp56_ke1x1s1ZO9FK8oWgxG-xerBYWG76_V56JJ3eQ,21425
+cellfinder/napari/curation.py,sha256=-m9w0SwjmCminZ6FPj_CKHzTeaxyFdI8DL_-s2KfA9c,21426
 cellfinder/napari/input_container.py,sha256=tkm0dkPt7kSL8Xkvs1fh8M6vKWw57QLIt_wv74HFkGk,2150
 cellfinder/napari/napari.yaml,sha256=WMR1CIAmYIVyQngbdbomTRZLvlDbb6LxsXsvTRClQnE,921
 cellfinder/napari/sample_data.py,sha256=oUST23q09MM8dxHbUCmO0AjtXG6OlR_32LLqP0EU2UA,732
@@ -51,11 +51,11 @@ cellfinder/napari/detect/detect.py,sha256=EC71KN0AEr49hMjvS8yzvGvfRctqKqn_lNERyx
 cellfinder/napari/detect/detect_containers.py,sha256=j9NTsIyyDNrhlI2dc7hvc7QlxvI1NRHlCe137v7fsPg,5467
 cellfinder/napari/detect/thread_worker.py,sha256=PWM3OE-FpK-dpdhaE_Gi-2lD3u8sL-SJ13mp0pMhTyI,3078
 cellfinder/napari/train/__init__.py,sha256=xo4CK-DvSecInGEc2ohcTgQYlH3iylFnGvKTCoq2WkI,35
-cellfinder/napari/train/train.py,sha256=zJY7zKcLqDTDtD76thmbwViEU4tTFCmXZze-zHsTpoo,5941
-cellfinder/napari/train/train_containers.py,sha256=1wZ_GPe7B5XsLYs5XIx4m8GMw5KeVhg6SchhPtXu4V8,4386
-cellfinder-1.5.0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
-cellfinder-1.5.0.dist-info/METADATA,sha256=3P9j6iSAWD_CVf4ho8C-RRX5Jf_r7A4mSaBfdeeNmTE,7158
-cellfinder-1.5.0.dist-info/WHEEL,sha256=nn6H5-ilmfVryoAQl3ZQ2l8SH5imPWFpm1A5FgEuFV4,91
-cellfinder-1.5.0.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
-cellfinder-1.5.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-1.5.0.dist-info/RECORD,,
+cellfinder/napari/train/train.py,sha256=5TwGiPkgAStjVuxv3LLzV3-gh_d2Ms7DjdShs0XC7aE,5944
+cellfinder/napari/train/train_containers.py,sha256=ryx7g_wSdktB6UbdveM7-YfK5py4pFAcO4Ls8Kre1FA,4388
+cellfinder-1.6.0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
+cellfinder-1.6.0.dist-info/METADATA,sha256=TvB9qXprasFvS2tcWk6iPtECmqnFsC-0XhflNBLaFaI,7142
+cellfinder-1.6.0.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+cellfinder-1.6.0.dist-info/entry_points.txt,sha256=n2n3muDgifENJtTRz1JqYStxvuprROCwmKLt-VxvEHk,248
+cellfinder-1.6.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-1.6.0.dist-info/RECORD,,

{cellfinder-1.5.0.dist-info → cellfinder-1.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.1)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{cellfinder-1.5.0.dist-info → cellfinder-1.6.0.dist-info}/entry_points.txt

@@ -1,7 +1,7 @@
 [console_scripts]
 cellfinder = cellfinder.cli_migration_warning:cli_catch
 cellfinder_download = cellfinder.core.download.cli:main
-cellfinder_train = cellfinder.core.train.train_yml:cli
+cellfinder_train = cellfinder.core.train.train_yaml:cli
 
 [napari.manifest]
 cellfinder = cellfinder.napari:napari.yaml