cellfinder 1.5.0__tar.gz → 1.6.0__tar.gz

{cellfinder-1.5.0 → cellfinder-1.6.0}/.github/workflows/test_and_deploy.yml

@@ -50,13 +50,13 @@ jobs:
       matrix:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # Include one windows and one macOS (arm based) run
         include:
           - os: macos-latest
-            python-version: "3.12"
+            python-version: "3.13"
           - os: windows-latest
-            python-version: "3.12"
+            python-version: "3.13"
 
     steps:
       - uses: actions/checkout@v4

{cellfinder-1.5.0 → cellfinder-1.6.0}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.5.0 → cellfinder-1.6.0}/PKG-INFO

@@ -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 → cellfinder-1.6.0}/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-1.5.0 → cellfinder-1.6.0}/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-1.5.0 → cellfinder-1.6.0}/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-1.5.0 → cellfinder-1.6.0}/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-1.5.0 → cellfinder-1.6.0}/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 → cellfinder-1.6.0}/cellfinder.egg-info/PKG-INFO

@@ -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 → cellfinder-1.6.0}/cellfinder.egg-info/SOURCES.txt

@@ -54,7 +54,7 @@ cellfinder/core/tools/threading.py
 cellfinder/core/tools/tiff.py
 cellfinder/core/tools/tools.py
 cellfinder/core/train/__init__.py
-cellfinder/core/train/train_yml.py
+cellfinder/core/train/train_yaml.py
 cellfinder/napari/__init__.py
 cellfinder/napari/curation.py
 cellfinder/napari/input_container.py

{cellfinder-1.5.0 → cellfinder-1.6.0}/cellfinder.egg-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

{cellfinder-1.5.0 → cellfinder-1.6.0}/pyproject.toml

@@ -14,12 +14,12 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "brainglobe-utils>=0.5.0",
     "brainglobe-napari-io>=0.3.4",
@@ -34,6 +34,7 @@ dependencies = [
     "torch>=2.1.0,!=2.4",
     "tifffile",
     "tqdm",
+    "qt-niu"
 ]
 dynamic = ["version"]
 
@@ -52,7 +53,6 @@ dev = [
     "pytest",
     "tox",
     "pooch >= 1",
-    "qt-niu"
 ]
 napari = [
     "brainglobe-napari-io",
@@ -66,7 +66,7 @@ napari = [
 
 [project.scripts]
 cellfinder_download = "cellfinder.core.download.cli:main"
-cellfinder_train = "cellfinder.core.train.train_yml:cli"
+cellfinder_train = "cellfinder.core.train.train_yaml:cli"
 cellfinder = "cellfinder.cli_migration_warning:cli_catch"
 
 [project.urls]
@@ -81,7 +81,7 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = 'setuptools.build_meta'
 
 [tool.black]
-target-version = ['py310','py311', 'py312']
+target-version = ['py311','py312', 'py313']
 skip-string-normalization = false
 line-length = 79
 
@@ -113,14 +113,14 @@ markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 legacy_tox_ini = """
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{310,311,312}
+envlist = py{311,312,313}
 isolated_build = true
 
 [gh-actions]
 python =
-    3.10: py310
     3.11: py311
     3.12: py312
+    3.13: py313
 
 [testenv]
 commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml

{cellfinder-1.5.0 → cellfinder-1.6.0}/cellfinder.egg-info/requires.txt

@@ -11,6 +11,7 @@ keras>=3.7.0
 torch!=2.4,>=2.1.0
 tifffile
 tqdm
+qt-niu
 
 [dev]
 black
@@ -23,7 +24,6 @@ pytest-timeout
 pytest
 tox
 pooch>=1
-qt-niu
 
 [napari]
 brainglobe-napari-io