Various small changes (#157)

* fix typo

* remove unused code

* reduce duplication

* remove unecessary comment

* remove unecessary comments

* Update pyproject

* update badge

* Remove warning supression

README.md

@@ -3,7 +3,7 @@
 [![Wheel](https://img.shields.io/pypi/wheel/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation)
 [![Development Status](https://img.shields.io/pypi/status/brainglobe-segmentation.svg)](https://github.com/brainglobe/brainglobe-segmentation)
 [![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)](https://github.com/brainglobe/brainglobe-segmentation/actions)
-[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)
+[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 

brainglobe_segmentation/image/utils.py

@@ -4,7 +4,7 @@
 
 def create_KDTree_from_image(image, value=0):
     """
-    Create a KDTree of points equalling a given value
+    Create a KDTree of points equaling a given value
     :param image: Image to be converted to points
     :param value: Value of image to be used
     :return: scipy.spatial.cKDTree object

brainglobe_segmentation/layout/gui_constants.py

@@ -32,9 +32,3 @@
 IMAGE_FILE_EXT = ".tiff"
 BOUNDARIES_STRING = "Boundaries"
 HEMISPHERES_STRING = "Hemispheres"
-
-# ORIENTATIONS = [
-#     "asl",
-#     "lsa",
-#     "sla",
-# ]  # When rolling through orientations of the brain, adhere to this order

brainglobe_segmentation/regions/IO.py

@@ -3,6 +3,7 @@
 import imio
 import numpy as np
 from brainglobe_utils.general.pathlib import append_to_pathlib_stem
+from brainglobe_utils.IO.surfaces import marching_cubes_to_obj
 from skimage import measure
 
 
@@ -26,27 +27,6 @@ def extract_and_save_object(
     )
 
 
-def marching_cubes_to_obj(marching_cubes_out, output_file):
-    """
-    Saves the output of skimage.measure.marching_cubes as an .obj file
-    :param marching_cubes_out: tuple
-    :param output_file: str
-    """
-
-    verts, faces, normals, _ = marching_cubes_out
-    with open(output_file, "w") as f:
-        for item in verts:
-            f.write(f"v {item[0]} {item[1]} {item[2]}\n")
-        for item in normals:
-            f.write(f"vn {item[0]} {item[1]} {item[2]}\n")
-        for item in faces:
-            f.write(
-                f"f {item[0]}//{item[0]} {item[1]}//{item[1]} "
-                f"{item[2]}//{item[2]}\n"
-            )
-        f.close()
-
-
 def volume_to_vector_array_to_obj_file(
     image,
     output_path,

brainglobe_segmentation/segmentation_panels/regions.py

@@ -1,4 +1,3 @@
-# RegionSeg
 from qtpy.QtWidgets import QGridLayout, QGroupBox
 
 from brainglobe_segmentation.layout.gui_constants import (
@@ -122,9 +121,6 @@ def add_region_panel(self, row):
         self.region_panel.setVisible(False)
 
     def toggle_region_panel(self):
-        # TODO: Change color scheme directly when theme is switched
-        # TODO: "text-align" property should follow constant
-        # SEGM_METHODS_PANEL_ALIGN
         if self.region_panel.isVisible():
             self.region_panel.setVisible(False)
             if self.parent.viewer.theme == "dark":

pyproject.toml

@@ -10,12 +10,11 @@ classifiers = [
     "Framework :: napari",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "Operating System :: Microsoft :: Windows :: Windows 10",
-    "Operating System :: POSIX :: Linux",
+    "Operating System :: OS Independent",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 requires-python = ">=3.9"
 dependencies = [
@@ -74,28 +73,8 @@ include = ["brainglobe_segmentation*"]
 
 [tool.setuptools_scm]
 
-[tool.pytest.ini_options]
-filterwarnings = [
-    "error",
-    # Emitted by scikit-image on import, see https://github.com/scikit-image/scikit-image/issues/6663
-    # This filter should be removed when scikit-image 0.20 is released
-    "ignore:`np.bool8` is a deprecated alias for `np.bool_`",
-    # Emitted by nptyping, see https://github.com/ramonhagenaars/nptyping/issues/102
-    # for upstream issue
-    "ignore:`np.object0` is a deprecated alias for ``np.object0`",
-    "ignore:`np.int0` is a deprecated alias for `np.intp`",
-    "ignore:`np.uint0` is a deprecated alias for `np.uintp`",
-    "ignore:`np.void0` is a deprecated alias for `np.void`",
-    "ignore:`np.bytes0` is a deprecated alias for `np.bytes_`",
-    "ignore:`np.str0` is a deprecated alias for `np.str_`",
-    # Warning comes from vispy - fixed in vispy 0.12.0. napari 0.5.0 will bump
-    # vispy to 0.5.0, so this filter should be removed when napari 0.5.0
-    # is released
-    "ignore:distutils Version classes are deprecated:DeprecationWarning",
-]
-
 [tool.black]
-target-version = ['py38', 'py39', 'py310']
+target-version = ['py39', 'py310', 'py311']
 skip-string-normalization = false
 line-length = 79