IndexError when conducting spatial join with empty polygons

Hey, not sure if this addressed elsewhere, but a search of past results suggests it’s not.

import geopandas, numpy, shapely.geometry as geom

center = geom.Point((0,0))
circle = center.buffer(1)
empty = center.buffer(0)

empty_df = geopandas.GeoDataFrame(geometry=[circle, empty])

points = [geom.Point(x) for x in numpy.random.random(size=(10,2))]
points_df = geopandas.GeoDataFrame(geometry=points)

geopandas.sjoin(points_df, empty_df, op='intersects') # raises an IndexError but completes

I get a result from this join, but I also get an IndexError:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
_ctypes/callbacks.c in 'calling callback function'()

~/anaconda3/envs/ana/lib/python3.7/site-packages/rtree/index.py in py_next_item(p_id, p_mins, p_maxs, p_dimension, p_data, p_length)
    708             # xmin, xmax, ymin, ymax, zmin, zmax
    709             for i in range(dimension):
--> 710                 mins[i] = coordinates[i*2]
    711                 maxs[i] = coordinates[(i*2)+1]
    712 

IndexError: list index out of range

Not sure how this IndexError relates to the result, but I didn’t see another issue mentioning this, so I thought I’d raise it.

rtree 0.8.3 geopandas 0.4.1 shapely 1.6.4.post1

[jorisvandenbossche]

so I hope we will be able to merge it before 0.6 release

That sounds good!

[julietsitron]

@martinfleis @jorisvandenbossche thank you!