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pl.show() still not working (?) in interactive mode #68
Description
I am using the latest code from main. If I run this code as a script, the plot is shown. If I set a breakpoint (I am using PyCharm) in the line with pl.render_points()..., and then run that line in the Python interactive console, then no plot is shown and I need to call plt.show() explicitly. I think the bug was once fixed, maybe it slipped in again.
from spatialdata import SpatialData
from spatialdata.models import PointsModel, ShapesModel
from shapely import polygons, linearrings
from geopandas import GeoDataFrame
import pandas as pd
import geopandas as gpd
import numpy as np
def _make_points():
"""Helper function to make a Points element."""
coordinates = np.array([[10, 10], [20, 20], [20, 30]], dtype=float)
return PointsModel.parse(
coordinates, annotation=pd.DataFrame({"genes": np.repeat("a", len(coordinates))}), feature_key="genes"
)
def _make_squares() -> polygons:
centroid_coordinates = np.array([[10, 10], [10, 80], [80, 20], [70, 60]])
half_width = 6
linear_rings = []
for centroid in centroid_coordinates:
min_coords = centroid - half_width
max_coords = centroid + half_width
linear_rings.append(
linearrings(
[
[min_coords[0], min_coords[1]],
[min_coords[0], max_coords[1]],
[max_coords[0], max_coords[1]],
[max_coords[0], min_coords[1]],
]
)
)
s = polygons(linear_rings)
polygon_series = gpd.GeoSeries(s)
cell_polygon_table = gpd.GeoDataFrame(geometry=polygon_series)
sd_polygons = ShapesModel.parse(cell_polygon_table)
return sd_polygons
def _make_circles() -> GeoDataFrame:
centroid_coordinates = np.array([[10, 10], [10, 80], [80, 20], [70, 60]])
radius = 10
circles = ShapesModel.parse(centroid_coordinates, geometry=0, radius=radius)
return circles
points = _make_points()
squares = _make_squares()
circles = _make_circles()
import spatialdata_plot
sdata = SpatialData(points={'p': points}, shapes={'s': squares, 'c': circles})
sdata.pl.render_points().pl.render_shapes().pl.show()
# import matplotlib.pyplot as plt
# plt.show()
Activity
[-]`pl.show()` still not working (?) in interactive mode?[/-][+]`pl.show()` still not working (?) in interactive mode[/+]LucaMarconato commentedon Nov 5, 2023
It seems like the bug resurfaced. By running the code of this comment here (please delete the
Interactive()calls) scverse/napari-spatialdata#175 (comment), in a Python console, the plots are shown only ifplt.show()is called explicitly.LucaMarconato commentedon Nov 5, 2023
It seems like that the check:
doesn't cover the case in which we are in Python console.
II think that the solution proposed in #71, would solve both bugs: I suggest to add a parameter
show: bool = None. Ifaxis notNone,showis set toFalse, otherwise it is set toTrue.Then I would replace the line
if not hasattr(sys, "ps1"):withif show:. Anyway I kindly ask you to double check please.grst commentedon Feb 15, 2024
You could also look into
plt.ion()/plt.ioff().If interactive mode is activated, figures will be shown and redrawn automatically on each update. In jupyter notebooks, this is active by default.
I lean towards reducing the number of options like
show =Falseand instead educate the users about such matplotlib options in the tutorials.Improve interactive mode detection for plt.show() auto-behavior
Tomaz-Vieira commentedon Jun 24, 2026
I might be having the same problem today. Running spatial-data master (471ae71dcc84754fe5c2cd48d9fe46a153ee2dee) and spatialdata-plot also at master (227434d):
python myscript.py, thenpl.show()will show the plot.pytho -i, the plot is shown but further attempts to show the plot don't work;manually calling
matplotlib.interactive(True)makes the plotting work again for the remainder of the sessiontimtreis commentedon Jun 24, 2026
Hey @Tomaz-Vieira, could you try #745?