Merge branch 'main' into bugfix/337-ds-point-transformation

.github/workflows/test.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.9", "3.10"]
+        python: ["3.10", "3.12"]
         os: [ubuntu-latest]
 
     env:
@@ -49,7 +49,7 @@ jobs:
           pip install pytest-cov
       - name: Install dependencies
         run: |
-          pip install --pre -e ".[dev,test]"
+          pip install --pre -e ".[dev,test,pre]"
       - name: Test
         env:
           MPLBACKEND: agg

.mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
@@ -25,4 +25,4 @@ no_warn_no_return = True
 
 show_error_codes = True
 show_column_numbers = True
-error_summary = True
+error_summary = True

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 ci:
   skip: []

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 urls.Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/index.html"
 urls.Source = "https://github.com/scverse/spatialdata-plot.git"
 urls.Home-page = "https://github.com/scverse/spatialdata-plot.git"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dynamic= [
   "version" # allow version to be set by git tags
 ]
@@ -75,7 +75,7 @@ filterwarnings = [
 
 [tool.black]
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 (
@@ -158,7 +158,7 @@ lint.select = [
     "PGH", # pygrep-hooks
 ]
 lint.unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
-target-version = "py39"
+target-version = "py310"
 [tool.ruff.lint.per-file-ignores]
     "tests/*" = ["D", "PT", "B024"]
     "*/__init__.py" = ["F401", "D104", "D107", "E402"]

src/spatialdata_plot/pl/basic.py

@@ -5,7 +5,7 @@
 from collections import OrderedDict
 from copy import deepcopy
 from pathlib import Path
-from typing import Any, Union
+from typing import Any
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -14,14 +14,13 @@
 import spatialdata as sd
 from anndata import AnnData
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from matplotlib.axes import Axes
 from matplotlib.colors import Colormap, Normalize
 from matplotlib.figure import Figure
 from spatialdata import get_extent
 from spatialdata._utils import _deprecation_alias
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata_plot._accessor import register_spatial_data_accessor
 from spatialdata_plot.pl.render import (
@@ -62,7 +61,7 @@
 # replace with
 # from spatialdata._types import ColorLike
 # once https://github.com/scverse/spatialdata/pull/689/ is in a release
-ColorLike = Union[tuple[float, ...], str]
+ColorLike = tuple[float, ...] | str
 
 
 @register_spatial_data_accessor("pl")
@@ -952,7 +951,7 @@ def show(
                     if wanted_labels_on_this_cs:
                         if (table := params_copy.table_name) is not None:
                             colors = sc.get.obs_df(sdata[table], params_copy.color)
-                            if isinstance(colors.dtype, pd.CategoricalDtype):
+                            if isinstance(colors[params_copy.color].dtype, pd.CategoricalDtype):
                                 _maybe_set_colors(
                                     source=sdata[table],
                                     target=sdata[table],

src/spatialdata_plot/pl/render.py

@@ -3,7 +3,6 @@
 import warnings
 from collections import abc
 from copy import copy
-from typing import Union
 
 import dask
 import datashader as ds
@@ -15,7 +14,6 @@
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
-from datatree import DataTree
 from matplotlib.cm import ScalarMappable
 from matplotlib.colors import ListedColormap, Normalize
 from scanpy._settings import settings as sc_settings
@@ -24,6 +22,8 @@
 from spatialdata.transformations import get_transformation, set_transformation
 from spatialdata.transformations.transformations import Identity, Sequence
 
+from xarray import DataTree
+
 from spatialdata_plot._logging import logger
 from spatialdata_plot.pl.render_params import (
     FigParams,
@@ -55,7 +55,7 @@
     to_hex,
 )
 
-_Normalize = Union[Normalize, abc.Sequence[Normalize]]
+_Normalize = Normalize | abc.Sequence[Normalize]
 
 
 def _render_shapes(
@@ -466,7 +466,7 @@ def _render_points(
     if col_for_color is not None:
         cols = sc.get.obs_df(adata, col_for_color)
         # maybe set color based on type
-        if isinstance(cols.dtype, pd.CategoricalDtype):
+        if isinstance(cols[col_for_color].dtype, pd.CategoricalDtype):
             _maybe_set_colors(
                 source=adata,
                 target=adata,

src/spatialdata_plot/pl/render_params.py

@@ -2,7 +2,7 @@
 
 from collections.abc import Callable, Sequence
 from dataclasses import dataclass
-from typing import Literal, Union
+from typing import Literal
 
 from matplotlib.axes import Axes
 from matplotlib.colors import Colormap, ListedColormap, Normalize
@@ -14,7 +14,7 @@
 # replace with
 # from spatialdata._types import ColorLike
 # once https://github.com/scverse/spatialdata/pull/689/ is in a release
-ColorLike = Union[tuple[float, ...], str]
+ColorLike = tuple[float, ...] | str
 
 
 @dataclass