Merge pull request #635 from AllenCell/bugfix/fix_layers_changed_deprecation

Bugfix/fix layers changed deprecation

Author: yrkim98

.github/workflows/test_lint.yml

@@ -48,7 +48,7 @@ jobs:
       - name: Force opencv-python-headless
         run: |
           pip uninstall -y opencv-python
-          pip install opencv-python-headless
+          pip install "numpy<2.0" opencv-python-headless
       - name: Test with pytest
         run: |
           pytest -v --color=yes --cov=allencell_ml_segmenter --cov-report=xml

.github/workflows/test_lint_pr.yaml

@@ -16,4 +16,4 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, windows-latest]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10"]

.github/workflows/test_lint_push.yml

@@ -14,4 +14,4 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10"]

docs/user_docs/conf.py

@@ -10,7 +10,7 @@
 project = "Segmenter ML Plugin for napari"
 copyright = "2024, Allen Institute for Cell Science"
 author = "Segmenter ML plugin team"
-release = "1.0.0"
+release = "1.0.1rc1"
 
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -8,10 +8,10 @@ build-backend = "setuptools.build_meta"
 # https://peps.python.org/pep-0621/
 [project]
 name = "allencell-segmenter-ml"
-version = "1.0.0"
+version = "1.0.1rc1"
 description = "A plugin to leverage ML segmentation in napari"
 readme = "README.md"
-requires-python = ">=3.9,<3.11"
+requires-python = ">=3.10,<3.11"
 license = { file = "LICENSE" }
 
 classifiers = [
@@ -24,14 +24,13 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
 
 dependencies = [
     "npe2>=0.6.2",
-    "numpy",
+    "numpy<2.0",
     "hydra-core==1.3.2",
     "bioio==1.1.0",
     "bioio-base==1.0.4",
@@ -51,7 +50,7 @@ Documentation = "https://github.com/AllenCell/allencell-ml-segmenter#README.md"
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
 napari = [
-    "napari>=0.4.18",
+    "napari>=0.6.2",
     "pyqt5",
 ]
 
@@ -67,7 +66,7 @@ test_lint = [
     "mypy",
     "toml",
     "bumpver",
-    "napari>=0.4.18",
+    "napari>=0.6.2",
     "magicgui"
 ]
 
@@ -118,7 +117,7 @@ where = ["src"]
 
 # https://pypi.org/project/bumpver
 [tool.bumpver]
-current_version = "1.0.0"
+current_version = "1.0.1rc1"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message  = "Bump version {old_version} -> {new_version}"
 commit          = true

src/allencell_ml_segmenter/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1rc1"
 
 from allencell_ml_segmenter.napari.napari_reader import napari_get_reader
 from allencell_ml_segmenter.napari.sample_data import make_sample_data

src/allencell_ml_segmenter/_tests/main/test_main_widget.py

@@ -13,6 +13,8 @@
 from allencell_ml_segmenter.main.main_widget import MainWidget
 from unittest.mock import Mock, patch
 import napari
+from napari.utils.events import EmitterGroup
+
 
 # IMPORTANT NOTE: MainWidget is different from the other widgets since we do not directly
 # instantiate it in our code. So, it will always receive a napari.Viewer object in
@@ -21,6 +23,20 @@
 # but for now I'm just mocking it here.
 
 
+class FakeLayers:
+    def __init__(self):
+        self.events = EmitterGroup(
+            source=self,
+            inserting=None,
+            inserted=None,
+            removing=None,
+            removed=None,
+            moving=None,
+            moved=None,
+            changed=None,
+        )  # all napari layer events
+
+
 @pytest.fixture
 def main_widget(qtbot: QtBot) -> MainWidget:
     """
@@ -155,10 +171,14 @@ def test_experiments_home_initialized(qtbot: QtBot) -> None:
     settings.set_user_experiments_path(
         None
     )  # Simulates state where users has not yet chosen an experiments home.
+    viewer = Mock(
+        spec="napari.Viewer"
+    )  # set up fake viewer with layers that can emit events
+    viewer.layers = FakeLayers()
 
     # ACT
     MainWidget(
-        Mock(spec=napari.Viewer), settings
+        viewer, settings
     )  # If the users settings does not find an experiments home path, it will prompt the user for one and persist it.
 
     # ASSERT

src/allencell_ml_segmenter/main/viewer.py

@@ -121,7 +121,12 @@ def get_layers_nonthreshold(self) -> list[Layer]:
     def subscribe_layers_change_event(
         self, function: Callable[[NapariEvent], None]
     ) -> None:
-        self.viewer.events.layers_change.connect(function)
+        # keeps layer list synced with the layer checkboxes in our plugin when
+        # items are added, removed, moved, or changed
+        self.viewer.layers.events.changed.connect(function)
+        self.viewer.layers.events.inserted.connect(function)
+        self.viewer.layers.events.removed.connect(function)
+        self.viewer.layers.events.moved.connect(function)
 
     def _get_layer_by_name(self, name: str) -> Optional[Layer]:
         layers: list[Layer] = self.get_layers()