Merge branch 'main' into contrast_test

Author: samcunliffe

.github/workflows/docs.yml

@@ -17,9 +17,9 @@ jobs:
     name: Build & Upload Artifact
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
@@ -38,7 +38,7 @@ jobs:
           working-directory: ./docs
 
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: docs
           path: docs/_build
@@ -49,8 +49,8 @@ jobs:
     needs: build-docs
     if: contains(github.ref, 'tags')
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/download-artifact@v3
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4.1.7
       with:
         name: docs
 

.github/workflows/test_and_deploy.yml

@@ -27,10 +27,10 @@ jobs:
         python-version: ['3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -54,7 +54,7 @@ jobs:
         run: python -m tox
 
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.platform }} py${{ matrix.python-version }}
           path: reports/
@@ -83,9 +83,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install build

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 25.1.0
     hooks:
       - id: black
 
@@ -17,14 +17,14 @@ repos:
       - id: napari-plugin-checks
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.15.0
     hooks:
      - id: mypy
        additional_dependencies: [numpy, matplotlib]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.5.1'
+    rev: 'v0.9.9'
     hooks:
       - id: ruff
 

README.md

@@ -15,7 +15,7 @@ A plugin to create Matplotlib plots from napari layers
 ## Introduction
 `napari-matplotlib` is a bridge between `napari` and `matplotlib`, making it easy to create publication quality `Matplotlib` plots based on the data loaded in `napari` layers.
 
-Documentaiton can be found at https://napari-matplotlib.github.io/
+Documentation can be found at https://napari-matplotlib.github.io/
 
 ## Contributing
 

pyproject.toml

@@ -13,10 +13,18 @@ filterwarnings = [
     "ignore:distutils Version classes are deprecated:DeprecationWarning",
     "ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning",
     # Coming from pydantic via napari
-    "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning"
+    "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning",
+    # Until we stop supporting older numpy versions (<2.1)
+    "ignore:(?s).*`newshape` keyword argument is deprecated.*$:DeprecationWarning",
 ]
 qt_api = "pyqt6"
-addopts = ["--mpl", "--mpl-baseline-relative", "--strict-config", "--strict-markers", "-ra"]
+addopts = [
+    "--mpl",
+    "--mpl-baseline-relative",
+    "--strict-config",
+    "--strict-markers",
+    "-ra",
+]
 minversion = "7"
 testpaths = ["src/napari_matplotlib/tests"]
 log_cli_level = "INFO"
@@ -54,17 +62,15 @@ ignore = [
 convention = "numpy"
 
 [tool.mypy]
-python_version = "3.10"
+python_version = "3.12"
 # Block below are checks that form part of mypy 'strict' mode
 strict = true
 disallow_subclassing_any = false # TODO: fix
-warn_return_any = false # TODO: fix
+warn_return_any = false          # TODO: fix
 ignore_missing_imports = true
 
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 
 [[tool.mypy.overrides]]
-module = [
-    "napari_matplotlib/tests/*",
-]
+module = ["napari_matplotlib/tests/*"]
 disallow_untyped_defs = false

setup.cfg

@@ -28,7 +28,7 @@ project_urls =
 packages = find:
 install_requires =
     matplotlib
-    napari<0.5
+    napari>=0.5
     numpy>=1.23
     tinycss2
 python_requires = >=3.10

src/napari_matplotlib/base.py

@@ -42,7 +42,7 @@ def __init__(
         super().__init__(parent=parent)
         self.viewer = napari_viewer
         self.napari_theme_style_sheet = style_sheet_from_theme(
-            get_theme(napari_viewer.theme, as_dict=False)
+            get_theme(napari_viewer.theme)
         )
 
         # Sets figure.* style
@@ -84,7 +84,7 @@ def _on_napari_theme_changed(self, event: Event) -> None:
             Event that triggered the callback.
         """
         self.napari_theme_style_sheet = style_sheet_from_theme(
-            get_theme(event.value, as_dict=False)
+            get_theme(event.value)
         )
         self._replace_toolbar_icons()
 
@@ -97,7 +97,7 @@ def _napari_theme_has_light_bg(self) -> bool:
         bool
             True if theme's background colour has hsl lighter than 50%, False if darker.
         """
-        theme = napari.utils.theme.get_theme(self.viewer.theme, as_dict=False)
+        theme = napari.utils.theme.get_theme(self.viewer.theme)
         _, _, bg_lightness = theme.background.as_hsl_tuple()
         return bg_lightness > 0.5
 

src/napari_matplotlib/histogram.py

@@ -28,7 +28,7 @@
 def _get_bins(
     data: npt.NDArray[Any],
     num_bins: int = 100,
-) -> npt.NDArray[Any]:
+) -> npt.NDArray[np.floating]:
     """Create evenly spaced bins with a given interval.
 
     Parameters
@@ -161,13 +161,13 @@ def draw(self) -> None:
             for i, c in enumerate("rgb"):
                 self.axes.hist(
                     data[..., i].ravel(),
-                    bins=bins.tolist(),
+                    bins=bins.tolist(),  # type: ignore[arg-type]
                     label=c,
                     histtype="step",
                     color=_COLORS[c],
                 )
         else:
-            self.axes.hist(data.ravel(), bins=bins.tolist(), label=layer.name)
+            self.axes.hist(data.ravel(), bins=bins.tolist(), label=layer.name)  # type: ignore[arg-type]
 
         self._contrast_lines = [
             self.axes.axvline(lim, color="white")
@@ -297,7 +297,7 @@ def draw(self) -> None:
 
         bins = _get_bins(data)
 
-        _, bins, patches = self.axes.hist(data, bins=bins.tolist())
+        _, bins, patches = self.axes.hist(data, bins=bins.tolist())  # type: ignore[arg-type]
         patches = cast(BarContainer, patches)
 
         # recolor the histogram plot

src/napari_matplotlib/tests/scatter/baseline/test_scatter_2D.png

@@ -15,7 +15,9 @@ def test_scatter_2D(make_napari_viewer, astronaut_data):
     viewer.add_image(astronaut_data[0], **astronaut_data[1], name="astronaut")
 
     viewer.add_image(
-        astronaut_data[0] * -1, **astronaut_data[1], name="astronaut_reversed"
+        astronaut_data[0] * -1.0,
+        **astronaut_data[1],
+        name="astronaut_reversed",
     )
     # De-select existing selection
     viewer.layers.selection.clear()
@@ -36,7 +38,7 @@ def test_scatter_3D(make_napari_viewer, brain_data):
     viewer.add_image(brain_data[0], **brain_data[1], name="brain")
 
     viewer.add_image(
-        brain_data[0] * -1, **brain_data[1], name="brain_reversed"
+        brain_data[0] * -1.0, **brain_data[1], name="brain_reversed"
     )
     # De-select existing selection
     viewer.layers.selection.clear()

src/napari_matplotlib/tests/scatter/test_scatter.py

@@ -29,7 +29,7 @@ def _mock_up_theme() -> None:
     Based on:
     https://napari.org/stable/gallery/new_theme.html
     """
-    blue_theme = napari.utils.theme.get_theme("dark", False)
+    blue_theme = napari.utils.theme.get_theme("dark")
     blue_theme.label = "blue"
     blue_theme.background = "#4169e1"  # my favourite shade of blue
     napari.utils.theme.register_theme(