I have a feature class of points, a few thousands I have now, but I expect to deal with hundreds of thousands of points. I would like find pair of points that is within a specific distance. The points I have is typically spread apart spatially so I don't expect to find many pairs. How I can find those pairs.

Right now the points are originally from ESRI shapefile, and read into geopandas geodataframe. I tried to tbl = df['geometry'].distance(df['geometry']) see if I can get distance of all pairs.

But I got the error "python: GeometryComponentFilter.cpp:34: virtual void geos::geom::GeometryComponentFilter::filter_ro(const geos::geom::Geometry*): Assertion `0' failed.". Beside

But, I don't want to get full set of distance as I am only interested in points that are close to each other.

I have a version of code which uses ArcGIS, and GenerateNearTable_analysis is what I used for the purpose.

I want to run code with open source code now.

My solution has to be python and should run on Linux.

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