Can't import geopandas to python when running in docker container

Question

I installed both shapely and geopandas in the docker image:

COPY ["requirement.txt", "/app/"]
RUN pip install -r requirement.txt

The base of the image:

FROM python:3.7-slim

In the requirement.txt, I have geopandas, shapely and pygeos installed:

geopandas==0.8.1
pygeos==0.9
Shapely==1.7.1

When I run the python script in the docker container, I am receiving this warning message:

/usr/local/lib/python3.7/site-packages/geopandas/_compat.py:88: UserWarning: The Shapely GEOS version (3.8.0-CAPI-1.13.1 ) is incompatible with the GEOS version PyGEOS was compiled with (3.9.0-CAPI-1.16.2). Conversions between both will be slow.
  shapely_geos_version, geos_capi_version_string

and following that I am receiving this error message:

  File "SIMILARITY_RANK.py", line 16, in <module>
    import geopandas as gpd
  File "/usr/local/lib/python3.7/site-packages/geopandas/__init__.py", line 3, in <module>
    from geopandas.geoseries import GeoSeries  # noqa
  File "/usr/local/lib/python3.7/site-packages/geopandas/geoseries.py", line 12, in <module>
    from geopandas.base import GeoPandasBase, _delegate_property
  File "/usr/local/lib/python3.7/site-packages/geopandas/base.py", line 13, in <module>
    from .array import GeometryArray, GeometryDtype
  File "/usr/local/lib/python3.7/site-packages/geopandas/array.py", line 25, in <module>
    from . import _vectorized as vectorized
  File "/usr/local/lib/python3.7/site-packages/geopandas/_vectorized.py", line 39, in <module>
    type_mapping = {p.value: _names[p.name] for p in pygeos.GeometryType}
  File "/usr/local/lib/python3.7/site-packages/geopandas/_vectorized.py", line 39, in <dictcomp>
    type_mapping = {p.value: _names[p.name] for p in pygeos.GeometryType}
KeyError: 'MISSING'

It seems something is wrong with the installation of pygeos.

I could run the code in the local virtual environment, and all the packages are the same in the requirement.txt.

Thank you in advance!

question from:https://stackoverflow.com/questions/65921476/cant-import-geopandas-to-python-when-running-in-docker-container

Answer 1

As mentioned in the comment by @Georgy:

See this issue: https://github.com/geopandas/geopandas/issues/1793. Looks like using 0.8.2 version of GeoPandas should solve the problem.

GeoPandas 0.8.1 is not compatible with new pygeos 0.9. You will need to use GeoPandas 0.8.2, which fixes the issue or downgrade pygeos to 0.8.