Merge branch 'cellfinder-merge' of github.com:brainglobe/cellfinder-c…

…ore into cellfinder-merge

.github/workflows/test_and_deploy.yml

@@ -3,7 +3,7 @@ name: tests
 on:
   # Only run on pushes to main, or when version tags are pushed
   push:
-    branches: 
+    branches:
       - "main"
     tags:
       - "v**"

.pre-commit-config.yaml

@@ -30,9 +30,6 @@ repos:
             args: [--config-file, pyproject.toml]
             exclude: 
               - benchmarks/benchmarks/tools/IO.py
-              - examples/*
-              - resources/*
-              - cellfinder/napari*
             additional_dependencies:
               - types-setuptools
               - types-requests

MANIFEST.in

@@ -14,4 +14,4 @@ graft cellfinder
 prune benchmarks
 prune examples
 prune resources
-prune tests
+prune tests

cellfinder/napari/detect/detect.py

@@ -3,12 +3,12 @@
 from typing import Optional
 
 import napari
-from cellfinder.core.classify.cube_generator import get_cube_depth_min_max
 from magicgui import magicgui
 from magicgui.widgets import FunctionGui, ProgressBar
 from napari.utils.notifications import show_info
 from qtpy.QtWidgets import QScrollArea
 
+from cellfinder.core.classify.cube_generator import get_cube_depth_min_max
 from cellfinder.napari.utils import (
     add_layers,
     header_label_widget,

cellfinder/napari/detect/thread_worker.py

@@ -1,7 +1,8 @@
-from cellfinder.core.main import main as cellfinder_run
 from napari.qt.threading import WorkerBase, WorkerBaseSignals
 from qtpy.QtCore import Signal
 
+from cellfinder.core.main import main as cellfinder_run
+
 from .detect_containers import (
     ClassificationInputs,
     DataInputs,

cellfinder/napari/train/train.py

@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Optional
 
-from cellfinder.core.train.train_yml import run as train_yml
 from magicgui import magicgui
 from magicgui.widgets import FunctionGui, PushButton
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_info
 
+from cellfinder.core.train.train_yml import run as train_yml
 from cellfinder.napari.utils import (
     header_label_widget,
     html_label_widget,

cellfinder/napari/train/train_containers.py

@@ -2,10 +2,10 @@
 from pathlib import Path
 from typing import Optional
 
-from cellfinder.core.download.models import model_weight_urls
-from cellfinder.core.train.train_yml import models
 from magicgui.types import FileDialogMode
 
+from cellfinder.core.download.models import model_weight_urls
+from cellfinder.core.train.train_yml import models
 from cellfinder.napari.input_container import InputContainer
 from cellfinder.napari.utils import html_label_widget
 

tests/napari/test_train_containers.py

@@ -1,8 +1,8 @@
 from inspect import signature
 
 import pytest
-from cellfinder.core.train.train_yml import run
 
+from cellfinder.core.train.train_yml import run
 from cellfinder.napari.train.train_containers import (
     MiscTrainingInputs,
     OptionalNetworkInputs,