Support MultiPolygons in render_shapes()

[timtreis]

import spatialdata as sd
import spatialdata_plot
from spatialdata.models import ShapesModel, TableModel
from shapely.geometry import Polygon, MultiPolygon, Point
import pandas as pd
import geopandas as gpd
import anndata

import numpy as np
def _make_multi():
    hole = MultiPolygon([(
        ((0.0, 0.0), (0.0, 1.0), (1.0, 1.0), (1.0, 0.0)),
         [((0.2,0.2), (0.2,0.8), (0.8,0.8), (0.8,0.2))]
    )])
    overlap = MultiPolygon([
        Polygon([(2.0, 0.0), (2.0, 0.8), (2.8, 0.8), (2.8, 0.0)]),
        Polygon([(2.2, 0.2), (2.2, 1.0), (3.0, 1.0), (3.0, 0.2)])
    ])
    poly = Polygon([(4.0, 0.0), (4.0, 1.0), (5.0, 1.0), (5.0, 0.0)])
    circ = Point(6.0, 0.5)
    polygon_series = gpd.GeoSeries([hole, overlap, poly, circ])
    cell_polygon_table = gpd.GeoDataFrame(geometry=polygon_series)
    sd_polygons = ShapesModel.parse(cell_polygon_table)
    sd_polygons.loc[:, "radius"] = [None, None, None, 0.3]
    
    return sd_polygons

multi = _make_multi()
sdata = sd.SpatialData(shapes={"p": _make_multi()})
adata = anndata.AnnData(pd.DataFrame({"p": ["hole", "overlap", "square", "circle"]}))
adata.obs.loc[:, "region"] = "p"
adata.obs.loc[:, "val"] = [1,2,3,4]
table = TableModel.parse(adata, region="p", region_key="region", instance_key="val")
sdata.table = table
print(sdata)
sdata.pl.render_shapes(color="val", outline=True, fill_alpha=0.3).pl.show()

Todo:

• verify that other plotting elements work with this solution, f.e. coloring by columns -> most likely fails because multipolygons result in a patch list that is longer than the color list

[codecov-commenter]

Codecov Report

❌ Patch coverage is 86.48649% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.19%. Comparing base (a77e2f6) to head (08d2137).
⚠️ Report is 462 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_plot/pl/utils.py	74.35%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #93      +/-   ##
==========================================
+ Coverage   76.53%   78.19%   +1.65%     
==========================================
  Files          10       10              
  Lines        1219     1284      +65     
==========================================
+ Hits          933     1004      +71     
+ Misses        286      280       -6     

Files with missing lines	Coverage Δ
src/spatialdata_plot/pl/render.py	94.07% <100.00%> (+2.30%)	⬆️
src/spatialdata_plot/pl/utils.py	63.29% <74.35%> (+2.50%)	⬆️

... and 1 file with indirect coverage changes

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[giovp]

this is quite nice, how's the coloring gonna work out? plot same color/annotation for all polygons in a multipolygon entry?

[timtreis]

Yeah, that was the idea. Didn't get to implementing that yet though

[LucaMarconato]

Yeah, that was the idea. Didn't get to implementing that yet though

Is it ready for review? (if not please mark the PR as draft).

[LucaMarconato]

Reviewed at a high-level, looks good to me, great work! I let @Sonja-Stockhaus do a more in-depth review of the code.

[Sonja-Stockhaus]

Looks nice!
Didn't notice anything odd and everything worked as it should when I ran it on my machine