Merge branch 'main' into color-histogram-bars

Author: dstansby

.github/workflows/test_and_deploy.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
@@ -17,14 +17,14 @@ repos:
       - id: napari-plugin-checks
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.0
     hooks:
      - id: mypy
-       additional_dependencies: [numpy, matplotlib<3.8]
+       additional_dependencies: [numpy, matplotlib]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.288'
+    rev: 'v0.0.292'
     hooks:
       - id: ruff
 

pyproject.toml

@@ -23,7 +23,7 @@ profile = "black"
 line_length = 79
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py39"
 select = ["I", "UP", "F", "E", "W", "D"]
 ignore = [
     "D100", # Missing docstring in public module
@@ -45,7 +45,7 @@ fix = true
 convention = "numpy"
 
 [tool.mypy]
-python_version = "3.8"
+python_version = "3.9"
 # Block below are checks that form part of mypy 'strict' mode
 warn_unused_configs = true
 warn_redundant_casts = true

setup.cfg

@@ -27,11 +27,11 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    matplotlib<3.8
+    matplotlib
     napari
     numpy
     tinycss2
-python_requires = >=3.8
+python_requires = >=3.9
 include_package_data = True
 package_dir =
     =src
@@ -49,6 +49,7 @@ napari.manifest =
 docs =
     napari[all]==0.4.17
     numpydoc
+    pydantic<2
     pydata-sphinx-theme
     qtgallery
     sphinx

src/napari_matplotlib/base.py

@@ -1,12 +1,12 @@
 import os
 from pathlib import Path
-from typing import List, Optional, Tuple
+from typing import Optional
 
 import matplotlib
 import matplotlib.style as mplstyle
 import napari
-from matplotlib.backends.backend_qtagg import (
-    FigureCanvas,
+from matplotlib.backends.backend_qtagg import (  # type: ignore[attr-defined]
+    FigureCanvasQTAgg,
     NavigationToolbar2QT,
 )
 from matplotlib.figure import Figure
@@ -49,12 +49,10 @@ def __init__(
 
         # Sets figure.* style
         with mplstyle.context(self.mpl_style_sheet_path):
-            self.canvas = FigureCanvas()
+            self.canvas = FigureCanvasQTAgg()  # type: ignore[no-untyped-call]
 
         self.canvas.figure.set_layout_engine("constrained")
-        self.toolbar = NapariNavigationToolbar(
-            self.canvas, parent=self
-        )  # type: ignore[no-untyped-call]
+        self.toolbar = NapariNavigationToolbar(self.canvas, parent=self)
         self._replace_toolbar_icons()
         # callback to update when napari theme changed
         # TODO: this isn't working completely (see issue #140)
@@ -97,7 +95,7 @@ def add_single_axes(self) -> None:
         # Sets axes.* style.
         # Does not set any text styling set by axes.* keys
         with mplstyle.context(self.mpl_style_sheet_path):
-            self.axes = self.figure.subplots()
+            self.axes = self.figure.add_subplot()
 
     def _on_napari_theme_changed(self) -> None:
         """
@@ -184,7 +182,7 @@ class NapariMPLWidget(BaseNapariMPLWidget):
     #: Number of layers taken as input
     n_layers_input = Interval(None, None)
     #: Type of layer taken as input
-    input_layer_types: Tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
+    input_layer_types: tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
 
     def __init__(
         self,
@@ -193,7 +191,7 @@ def __init__(
     ):
         super().__init__(napari_viewer=napari_viewer, parent=parent)
         self._setup_callbacks()
-        self.layers: List[napari.layers.Layer] = []
+        self.layers: list[napari.layers.Layer] = []
 
         helper_text = self.n_layers_input._helper_text
         if helper_text is not None:
@@ -260,7 +258,7 @@ def _draw(self) -> None:
             isinstance(layer, self.input_layer_types) for layer in self.layers
         ):
             self.draw()
-        self.canvas.draw()
+        self.canvas.draw()  # type: ignore[no-untyped-call]
 
     def clear(self) -> None:
         """
@@ -309,8 +307,8 @@ def clear(self) -> None:
 class NapariNavigationToolbar(NavigationToolbar2QT):
     """Custom Toolbar style for Napari."""
 
-    def __init__(self, *args, **kwargs):  # type: ignore[no-untyped-def]
-        super().__init__(*args, **kwargs)
+    def __init__(self, *args, **kwargs) -> None:  # type: ignore[no-untyped-def]
+        super().__init__(*args, **kwargs)  # type: ignore[no-untyped-call]
         self.setIconSize(
             from_napari_css_get_size_of(
                 "QtViewerPushButton", fallback=(28, 28)
@@ -319,7 +317,7 @@ def __init__(self, *args, **kwargs):  # type: ignore[no-untyped-def]
 
     def _update_buttons_checked(self) -> None:
         """Update toggle tool icons when selected/unselected."""
-        super()._update_buttons_checked()
+        super()._update_buttons_checked()  # type: ignore[no-untyped-call]
         icon_dir = self.parentWidget()._get_path_to_icon()
 
         # changes pan/zoom icons depending on state (checked or not)

src/napari_matplotlib/histogram.py

@@ -1,4 +1,4 @@
-from typing import Any, List, Optional, Tuple
+from typing import Any, Optional
 
 import napari
 import numpy as np
@@ -107,7 +107,7 @@ def _set_axis_keys(self, x_axis_key: str) -> None:
         self._x_axis_key = x_axis_key
         self._draw()
 
-    def _get_valid_axis_keys(self) -> List[str]:
+    def _get_valid_axis_keys(self) -> list[str]:
         """
         Get the valid axis keys from the layer FeatureTable.
 
@@ -122,7 +122,7 @@ def _get_valid_axis_keys(self) -> List[str]:
         else:
             return self.layers[0].features.keys()
 
-    def _get_data(self) -> Tuple[Optional[npt.NDArray[Any]], str]:
+    def _get_data(self) -> tuple[Optional[npt.NDArray[Any]], str]:
         """Get the plot data.
 
         Returns

src/napari_matplotlib/scatter.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 import napari
 import numpy.typing as npt
@@ -40,7 +40,7 @@ def draw(self) -> None:
         self.axes.set_xlabel(x_axis_name)
         self.axes.set_ylabel(y_axis_name)
 
-    def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+    def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
         """
         Get the plot data.
 
@@ -67,7 +67,7 @@ class ScatterWidget(ScatterBaseWidget):
     n_layers_input = Interval(2, 2)
     input_layer_types = (napari.layers.Image,)
 
-    def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+    def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
         """
         Get the plot data.
 
@@ -106,7 +106,7 @@ def __init__(
 
         self.layout().addLayout(QVBoxLayout())
 
-        self._selectors: Dict[str, QComboBox] = {}
+        self._selectors: dict[str, QComboBox] = {}
         for dim in ["x", "y"]:
             self._selectors[dim] = QComboBox()
             # Re-draw when combo boxes are updated
@@ -147,7 +147,7 @@ def y_axis_key(self, key: str) -> None:
         self._selectors["y"].setCurrentText(key)
         self._draw()
 
-    def _get_valid_axis_keys(self) -> List[str]:
+    def _get_valid_axis_keys(self) -> list[str]:
         """
         Get the valid axis keys from the layer FeatureTable.
 
@@ -186,7 +186,7 @@ def draw(self) -> None:
         if self._ready_to_scatter():
             super().draw()
 
-    def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+    def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
         """
         Get the plot data from the ``features`` attribute of the first
         selected layer.

src/napari_matplotlib/slice.py

@@ -1,4 +1,4 @@
-from typing import Any, List, Optional, Tuple
+from typing import Any, Optional
 
 import matplotlib.ticker as mticker
 import napari
@@ -99,7 +99,7 @@ def current_dim_index(self) -> int:
         return self._dim_names.index(self.current_dim_name)
 
     @property
-    def _dim_names(self) -> List[str]:
+    def _dim_names(self) -> list[str]:
         """
         List of dimension names. This is a property as it varies depending on the
         dimensionality of the currently selected data.
@@ -111,7 +111,7 @@ def _dim_names(self) -> List[str]:
         else:
             raise RuntimeError("Don't know how to handle ndim != 2 or 3")
 
-    def _get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
+    def _get_xy(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any]]:
         """
         Get data for plotting.
         """

src/napari_matplotlib/tests/baseline/test_custom_theme.png

@@ -1,5 +1,5 @@
 from copy import deepcopy
-from typing import Any, Dict, Tuple
+from typing import Any
 
 import numpy as np
 import numpy.typing as npt
@@ -34,7 +34,7 @@ def test_features_scatter_widget_2D(
 
 
 def make_labels_layer_with_features() -> (
-    Tuple[npt.NDArray[np.uint16], Dict[str, Any]]
+    tuple[npt.NDArray[np.uint16], dict[str, Any]]
 ):
     label_image: npt.NDArray[np.uint16] = np.zeros((100, 100), dtype=np.uint16)
     for label_value, start_index in enumerate([10, 30, 50], start=1):

src/napari_matplotlib/tests/baseline/test_histogram_2D.png

@@ -1,5 +1,5 @@
 from copy import deepcopy
-from typing import Any, Dict, Tuple, Type
+from typing import Any
 
 import numpy as np
 import numpy.typing as npt
@@ -61,8 +61,8 @@ def test_change_features_layer(
 
 def assert_features_plot_changes(
     viewer: Viewer,
-    widget_cls: Type[NapariMPLWidget],
-    data: Tuple[npt.NDArray[np.generic], Dict[str, Any]],
+    widget_cls: type[NapariMPLWidget],
+    data: tuple[npt.NDArray[np.generic], dict[str, Any]],
 ) -> None:
     """
     When the selected layer is changed, make sure the plot generated

src/napari_matplotlib/tests/baseline/test_histogram_3D.png

@@ -187,6 +187,6 @@ def test_custom_stylesheet(make_napari_viewer, image_data):
         assert widget.figure.patch.get_facecolor() == to_rgba("#fdf6e3")
         for gridline in ax.get_xgridlines() + ax.get_ygridlines():
             assert gridline.get_visible() is True
-            assert gridline.get_color() == "#fdf6e3"
+            assert gridline.get_color() == "#b0b0b0"
     finally:
         os.remove(style_sheet_path)

src/napari_matplotlib/tests/baseline/test_slice_2D.png

@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Union
 from warnings import warn
 
 import napari.qt
@@ -76,7 +76,7 @@ def _helper_text(self) -> Optional[str]:
         return helper_text
 
 
-def _has_id(nodes: List[tinycss2.ast.Node], id_name: str) -> bool:
+def _has_id(nodes: list[tinycss2.ast.Node], id_name: str) -> bool:
     """
     Is `id_name` in IdentTokens in the list of CSS `nodes`?
     """
@@ -86,7 +86,7 @@ def _has_id(nodes: List[tinycss2.ast.Node], id_name: str) -> bool:
 
 
 def _get_dimension(
-    nodes: List[tinycss2.ast.Node], id_name: str
+    nodes: list[tinycss2.ast.Node], id_name: str
 ) -> Union[int, None]:
     """
     Get the value of the DimensionToken for the IdentToken `id_name`.
@@ -108,7 +108,7 @@ def _get_dimension(
 
 
 def from_napari_css_get_size_of(
-    qt_element_name: str, fallback: Tuple[int, int]
+    qt_element_name: str, fallback: tuple[int, int]
 ) -> QSize:
     """
     Get the size of `qt_element_name` from napari's current stylesheet.

src/napari_matplotlib/tests/baseline/test_slice_3D.png

@@ -1,19 +1,14 @@
 [tox]
-envlist = py{38,39,310,311}
+envlist = py{39,310,311}
 isolated_build = true
 
 [gh-actions]
 python =
-    3.8: py38
     3.9: py39
     3.10: py310
+    3.11: py311
 
 [testenv]
 extras = testing
-allowlist_externals =
-    cp
-    ls
 commands =
-    cp -R {toxinidir}/src/napari_matplotlib/tests/baseline {envdir}/baseline
-    ls {toxinidir}/src/napari_matplotlib/tests/baseline
     python -m pytest --mpl --mpl-generate-summary=html --mpl-results-path={toxinidir}/reports -v --color=yes --cov=napari_matplotlib --cov-report=xml