ImportError: Spatial indexes require either `rtree` or `pygeos` in geopanda but rtree is installed

Question

I am trying to clip spatial data in python but when I run my code...

europe = gpd.clip(worldmap, europe_bound_gdf)

... I get the error:

(ImportError: Spatial indexes require either rtreeorpygeos`.)

When I try to install rtree using:

pip3 install rtree

I'm told:

Requirement already satisfied: rtree in /Users/joshuajones/.pyenv/versions/3.9.4/lib/python3.9/site-packages (0.9.7`)

So why is my code not working?

Answer 1

I had the same issue and this solved it for me:

pip uninstall rtree
sudo apt install libspatialindex-dev
pip install rtree

Found the answer here.

Answer 2

In my case, the only thing that helped:

install and import condalab, run twice.

!pip install -q condacolab -q

import condacolab

condacolab.install()

install geopandas, this could take long

!conda install geopandas

import geopandas as gpd