Merge branch 'main' into pytorch

.github/workflows/test_and_deploy.yml

@@ -48,10 +48,8 @@ jobs:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
         python-version: ["3.10", "3.11", "3.12"]
-        # Include one windows and two macOS (intel based and arm based) runs
+        # Include one windows and one macOS (arm based) run
         include:
-          - os: macos-13
-            python-version: "3.12"
           - os: macos-latest
             python-version: "3.12"
           - os: windows-latest

.pre-commit-config.yaml

@@ -16,10 +16,10 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.4.7
+      rev: v0.5.6
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 24.8.0
       hooks:
           - id: black

README.md

@@ -44,11 +44,8 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
-
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
-
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
 ## Citation
 If you find this package useful, and use it in your research, please cite the following paper:

cellfinder/napari/curation.py

@@ -113,7 +113,7 @@ def _get_layer_names(
         layer_names = [
             layer.name
             for layer in self.viewer.layers
-            if type(layer) == layer_type
+            if isinstance(layer, layer_type)
         ]
 
         if layer_names:
@@ -329,7 +329,7 @@ def mark_point_as_type(self, point_type: str):
 
         if len(self.viewer.layers.selection) == 1:
             layer = list(self.viewer.layers.selection)[0]
-            if type(layer) == napari.layers.Points:
+            if isinstance(layer, napari.layers.Points):
                 if len(layer.data) > 0:
                     if point_type == "cell":
                         destination_layer = self.training_data_cell_layer

pyproject.toml

@@ -27,11 +27,12 @@ dependencies = [
     "fancylog>=0.0.7",
     "natsort",
     "numba",
+    "numpy<2.0.0; sys_platform=='win32'",
     "numpy",
     "scikit-image",
     "scikit-learn",
-    "keras>=3.0.0",
-    "torch>=2.1.0,!=2.4",
+    "keras>=3.5.0",
+    "torch>=2.1.0,!=2.4.0",
     "tifffile",
     "tqdm",
 ]

tests/napari/test_curation.py

@@ -24,6 +24,7 @@ def curation_widget(make_napari_viewer):
     return widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_add_new_training_layers(curation_widget):
     viewer = curation_widget.viewer
     layers = viewer.layers
@@ -38,6 +39,7 @@ def test_add_new_training_layers(curation_widget):
     assert layers[1].name == "Training data (non cells)"
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_cell_marking(curation_widget, tmp_path):
     """
     Check that marking cells and non-cells works as expected.
@@ -130,13 +132,15 @@ def valid_curation_widget(make_napari_viewer) -> CurationWidget:
     return curation_widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_for_extraction(valid_curation_widget):
     """
     Check valid curation widget has extractable data.
     """
     assert valid_curation_widget.check_image_data_for_extraction()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_wrong_shape(valid_curation_widget):
     """
     Check curation widget shows expected user message if images don't have
@@ -156,6 +160,7 @@ def test_check_image_data_wrong_shape(valid_curation_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_missing_signal(valid_curation_widget):
     """
     Check curation widget shows expected user message if signal image is
@@ -170,12 +175,14 @@ def test_check_image_data_missing_signal(valid_curation_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_is_data_extractable(curation_widget, valid_curation_widget):
     """Check is_data_extractable works as expected."""
     assert not curation_widget.is_data_extractable()
     assert valid_curation_widget.is_data_extractable()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_get_output_directory(valid_curation_widget):
     """Check get_output_directory returns expected value."""
     with patch(

tests/napari/test_detection.py

@@ -43,6 +43,7 @@ def test_detect_worker():
     worker.work()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 @pytest.mark.parametrize(
     argnames="analyse_local",
     argvalues=[True, False],  # increase test coverage by covering both cases
@@ -67,6 +68,7 @@ def test_run_detect_without_inputs():
         assert show_info.called
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_reset_defaults(get_detect_widget):
     """Smoke test that restore defaults doesn't error."""
     get_detect_widget.reset_button.clicked()

tests/napari/test_training.py

@@ -23,6 +23,7 @@ def get_training_widget(make_napari_viewer):
     return widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_reset_to_defaults(get_training_widget):
     """
     A simple test for the reset button.
@@ -45,6 +46,7 @@ def test_reset_to_defaults(get_training_widget):
     assert get_training_widget.test_fraction.value == 0.10
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_run_with_no_yaml_files(get_training_widget):
     """
     Checks whether expected info message will be shown to user if they don't
@@ -57,6 +59,7 @@ def test_run_with_no_yaml_files(get_training_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_run_with_virtual_yaml_files(get_training_widget):
     """
     Checks that training is run with expected set of parameters.

tests/napari/test_utils.py

@@ -1,4 +1,5 @@
 import numpy as np
+import pytest
 from brainglobe_utils.cells.cells import Cell
 
 from cellfinder.napari.utils import (
@@ -10,6 +11,7 @@
 )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_add_classified_layers(make_napari_viewer):
     """Smoke test for add_classified_layers utility"""
     cell_pos = [1, 2, 3]