Upgrade python support to 3.10-3.12, fix deprecation errors

napari_cellseg3d/_tests/test_weight_download.py

@@ -1,10 +1,16 @@
+import os
+import pytest
+
 from napari_cellseg3d.code_models.workers_utils import (
     PRETRAINED_WEIGHTS_DIR,
     WeightsDownloader,
 )
 
 
-# DISABLED, causes GitHub actions to freeze
+@pytest.mark.skipif(
+    os.getenv("GITHUB_ACTIONS") == "true",
+    reason="This test causes GitHub Actions to freeze",
+)
 def test_weight_download():
     downloader = WeightsDownloader()
     downloader.download_weights("test", "test.pth")

napari_cellseg3d/code_models/worker_inference.py

@@ -1,4 +1,5 @@
 """Contains the :py:class:`~InferenceWorker` class, which is a custom worker to run inference jobs in."""
+
 import platform
 import sys
 from pathlib import Path
@@ -268,7 +269,6 @@ def load_layer(self):
                 f" please check for extra channel/batch dimensions"
             )
         volume = utils.correct_rotation(volume)
-        # volume = np.reshape(volume, newshape=(1, 1, *volume.shape))
 
         dims_check = volume.shape
 
@@ -280,7 +280,7 @@ def load_layer(self):
             if self.config.model_info.name != "WNet3D"
             else lambda x: x
         )
-        volume = np.reshape(volume, newshape=(1, *volume.shape))
+        volume = volume.reshape((1, *volume.shape))
         if self.config.sliding_window_config.is_enabled():
             load_transforms = Compose(
                 [

napari_cellseg3d/dev_scripts/correct_labels.py

@@ -211,7 +211,8 @@ def relabel(
             np.isin(artefact, i_labels_to_add), 0, artefact
         )
         if viewer is None:
-            viewer = napari.view_image(image)
+            viewer = napari.Viewer()
+            images = viewer.add_image(image, name="image")
         else:
             viewer = viewer
             viewer.add_image(image, name="image")

pyproject.toml

@@ -14,9 +14,9 @@ classifiers = [
     "Topic :: Software Development :: Testing",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Operating System :: OS Independent",
     "License :: OSI Approved :: MIT License",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
@@ -43,17 +43,19 @@ dependencies = [
 #    "nibabel",
 #    "pillow",
     "pyclesperanto",
-    "tqdm",
     "matplotlib",
     "pydensecrf2",
 ]
-dynamic = ["version", "entry-points"]
+dynamic = ["version"]
 
 [project.urls]
 Homepage  = "https://github.com/AdaptiveMotorControlLab/CellSeg3D"
 Documentation = "https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html"
 Issues = "https://github.com/AdaptiveMotorControlLab/CellSeg3D/issues"
 
+[project.entry-points."napari.manifest"]
+"napari_cellseg3d" = "napari_cellseg3d:napari.yaml"
+
 [build-system]
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
@@ -65,7 +67,7 @@ include-package-data = true
 where = ["."]
 
 [tool.setuptools.package-data]
-"*" = ["res/*.png", "code_models/models/pretrained/*.json", "*.yaml"]
+"*" = ["res/*.png", "code_models/models/pretrained/*.json", "*.yaml", "napari.yaml"]
 
 [tool.ruff]
 select = [
@@ -79,7 +81,7 @@ select = [
     "PTH",
     "RET",
     "SIM",
-    "TCH",
+    "TC",
     "NPY",
 ]
 # Never enforce `E501` (line length violations) and 'E741' (ambiguous variable names)
@@ -116,23 +118,13 @@ exclude = [
 [tool.ruff.pydocstyle]
 convention = "google"
 
-[tool.black]
-line-length = 79
-
-[tool.isort]
-profile = "black"
-line_length = 79
-
 [project.optional-dependencies]
-pyqt5 = [
-    "pyqt5",
-]
-pyside2 = [
-    "pyside2",
-]
 pyside6 = [
     "pyside6",
 ]
+pyqt6 = [
+    "PyQt6",
+]
 onnx-cpu = [
     "onnx",
     "onnxruntime"
@@ -145,11 +137,8 @@ wandb = [
     "wandb"
 ]
 dev = [
-    "isort",
-    "black",
     "ruff",
     "pre-commit",
-    "tuna",
     "twine",
 ]
 docs = [
@@ -165,3 +154,6 @@ test = [
     "onnx",
     "onnxruntime",
 ]
+crf = [
+    "pydensecrf2",
+]

tox.ini

@@ -1,26 +1,25 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{38,39,310}-{linux}
-; envlist = py{38,39,310}-{linux,macos,windows}
+envlist = py{310,311,312}-{linux}
 isolated_build=true
 
 [gh-actions]
 python =
-    3.8: py38
-    3.9: py39
     3.10: py310
+    3.11: py311
+    3.12: py312
 
 [gh-actions:env]
 PLATFORM =
     ubuntu-latest: linux
-    ; windows-latest: windows
-    ; macos-latest: macos
+    windows-latest: windows
+    macos-latest: macos
 
 [testenv]
 platform =
     linux: linux
-    ; windows: win32
-    ; macos: darwin
+    windows: win32
+    macos: darwin
 passenv =
     CI
     PYTHONPATH
@@ -29,20 +28,6 @@ passenv =
     XAUTHORITY
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
-deps =
-    pytest  # https://docs.pytest.org/en/latest/contents.html
-    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
-    napari
-    PyQt5
-    magicgui
-    pytest-qt
-    qtpy
-    git+https://github.com/lucasb-eyer/pydensecrf.git@master#egg=pydensecrf
-    onnx
-    onnxruntime
-    monai[tifffile]
-;    pyopencl[pocl]
-;    opencv-python
-extras = crf
+extras = test,crf,pyqt6
 usedevelop = true
 commands = pytest -v --color=yes --cov=napari_cellseg3d --cov-report=xml