Merge pull request #262 from dstansby/nep29

Adhere to SPEC0

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: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v3
@@ -64,7 +64,7 @@ jobs:
         if: github.event_name != 'merge_group'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
 
 

docs/changelog.rst

@@ -1,5 +1,14 @@
 Changelog
 =========
+2.0.2
+-----
+Dependencies
+~~~~~~~~~~~~
+napari-matplotlib now adheres to `SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_, and has:
+- Dropped support for Python 3.9
+- Added support for Python 3.12
+- Added a minimum required numpy verison of 1.23
+
 2.0.1
 -----
 Bug fixes

pyproject.toml

@@ -12,6 +12,8 @@ filterwarnings = [
     # Coming from vispy
     "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"
 ]
 qt_api = "pyqt6"
 addopts = "--mpl --mpl-baseline-relative"
@@ -24,7 +26,7 @@ profile = "black"
 line_length = 79
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 select = ["I", "UP", "F", "E", "W", "D"]
 ignore = [
     "D100", # Missing docstring in public module
@@ -46,7 +48,7 @@ fix = true
 convention = "numpy"
 
 [tool.mypy]
-python_version = "3.9"
+python_version = "3.10"
 # Block below are checks that form part of mypy 'strict' mode
 strict = true
 disallow_subclassing_any = false # TODO: fix

setup.cfg

@@ -29,9 +29,9 @@ packages = find:
 install_requires =
     matplotlib
     napari
-    numpy
+    numpy>=1.23
     tinycss2
-python_requires = >=3.9
+python_requires = >=3.10
 include_package_data = True
 package_dir =
     =src

src/napari_matplotlib/base.py

@@ -1,6 +1,5 @@
 import os
 from pathlib import Path
-from typing import Optional
 
 import matplotlib.style as mplstyle
 import napari
@@ -38,7 +37,7 @@ class BaseNapariMPLWidget(QWidget):
     def __init__(
         self,
         napari_viewer: napari.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(parent=parent)
         self.viewer = napari_viewer
@@ -173,7 +172,7 @@ class NapariMPLWidget(BaseNapariMPLWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(napari_viewer=napari_viewer, parent=parent)
         self._setup_callbacks()
@@ -282,7 +281,7 @@ class SingleAxesWidget(NapariMPLWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(napari_viewer=napari_viewer, parent=parent)
         self.add_single_axes()

src/napari_matplotlib/histogram.py

@@ -1,4 +1,4 @@
-from typing import Any, Optional, cast
+from typing import Any, cast
 
 import napari
 import numpy as np
@@ -44,7 +44,7 @@ class HistogramWidget(SingleAxesWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(napari_viewer, parent=parent)
         self._update_layers(None)
@@ -121,7 +121,7 @@ class FeaturesHistogramWidget(SingleAxesWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(napari_viewer, parent=parent)
 
@@ -137,12 +137,12 @@ def __init__(
         self._update_layers(None)
 
     @property
-    def x_axis_key(self) -> Optional[str]:
+    def x_axis_key(self) -> str | None:
         """Key to access x axis data from the FeaturesTable"""
         return self._x_axis_key
 
     @x_axis_key.setter
-    def x_axis_key(self, key: Optional[str]) -> None:
+    def x_axis_key(self, key: str | None) -> None:
         self._x_axis_key = key
         self._draw()
 
@@ -166,7 +166,7 @@ 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[npt.NDArray[Any] | None, str]:
         """Get the plot data.
 
         Returns

src/napari_matplotlib/scatter.py

@@ -1,4 +1,4 @@
-from typing import Any, Optional, Union
+from typing import Any
 
 import napari
 import numpy.typing as npt
@@ -100,7 +100,7 @@ class FeaturesScatterWidget(ScatterBaseWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         super().__init__(napari_viewer, parent=parent)
 
@@ -118,7 +118,7 @@ def __init__(
         self._update_layers(None)
 
     @property
-    def x_axis_key(self) -> Union[str, None]:
+    def x_axis_key(self) -> str | None:
         """
         Key for the x-axis data.
         """
@@ -133,7 +133,7 @@ def x_axis_key(self, key: str) -> None:
         self._draw()
 
     @property
-    def y_axis_key(self) -> Union[str, None]:
+    def y_axis_key(self) -> str | None:
         """
         Key for the y-axis data.
         """

src/napari_matplotlib/slice.py

@@ -1,4 +1,4 @@
-from typing import Any, Optional
+from typing import Any
 
 import matplotlib.ticker as mticker
 import napari
@@ -30,7 +30,7 @@ class SliceWidget(SingleAxesWidget):
     def __init__(
         self,
         napari_viewer: napari.viewer.Viewer,
-        parent: Optional[QWidget] = None,
+        parent: QWidget | None = None,
     ):
         # Setup figure/axes
         super().__init__(napari_viewer, parent=parent)

src/napari_matplotlib/util.py

@@ -1,4 +1,3 @@
-from typing import Optional, Union
 from warnings import warn
 
 import napari.qt
@@ -12,7 +11,7 @@ class Interval:
     An integer interval.
     """
 
-    def __init__(self, lower_bound: Optional[int], upper_bound: Optional[int]):
+    def __init__(self, lower_bound: int | None, upper_bound: int | None):
         """
         Parameters
         ----------
@@ -48,7 +47,7 @@ def __contains__(self, val: int) -> bool:
         return True
 
     @property
-    def _helper_text(self) -> Optional[str]:
+    def _helper_text(self) -> str | None:
         """
         Helper text for widgets.
         """
@@ -86,9 +85,7 @@ def _has_id(nodes: list[tinycss2.ast.Node], id_name: str) -> bool:
     )
 
 
-def _get_dimension(
-    nodes: list[tinycss2.ast.Node], id_name: str
-) -> Union[int, None]:
+def _get_dimension(nodes: list[tinycss2.ast.Node], id_name: str) -> int | None:
     """
     Get the value of the DimensionToken for the IdentToken `id_name`.
 

tox.ini

@@ -1,12 +1,12 @@
 [tox]
-envlist = py{39,310,311}
+envlist = py{310,311,312}
 isolated_build = true
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [testenv]
 extras = testing