Not to long ago I posted about Cartopy and how it was easy to install it. Well, I must say it is not as easy as running pip install cartopy. While the installation could go without a warning message, the execution of some code could quickly lead to problems.

The issue

Here is an example of code that created the problem (let’s save it a file test_carto.py to be used later):

import cartopy.crs as ccrs
import matplotlib.pyplot as plt
ax = plt.axes(projection=ccrs.PlateCarree())
ax.coastlines()
plt.show()

which lead to the error message:

Geometry must be a Point or LineString
python: geos_ts_c.cpp:3991: int GEOSCoordSeq_getSize_r(GEOSContextHandle_t, const geos::geom::CoordinateSequence*, unsigned int*): Assertion `0 != cs' failed.
Aborted (core dumped)

Toward the solution

Your friend: StackOverFlow

The first thing I found on a research was from StackOverFlow:

The problem is a wrong version of shapely, with Cartopy the binary package shouldn’t be used, it should be built from source instead.

But is it really a wrong version? (by the way, what is a wrong version?)?
Let’s check with pip show shapely:

Name: Shapely
Version: 1.7.1
Summary: Geometric objects, predicates, and operations
Home-page: https://github.com/Toblerity/Shapely
Author: Sean Gillies
Author-email: sean.gillies@gmail.com
License: BSD
Location: /home/ctroupin/Software/PythonEnvs/OpenDriftCanary/lib/python3.8/site-packages
Requires:
Required-by: Cartopy

1.7.1 was released in August 2020, maybe I should try a more recent version: 1.8a1, released in March 2021. I tried

pip uninstall shapely
pip install shapely --no-binary shapely

then re-run the cartopy installation. Still failing.

Reading the doc

According to shapely documentation, one should run this:

GEOS_CONFIG=/path/to/geos-config pip install shapely

where GEOS_CONFIG environment variable has to be set according to the GEOS library you are using. I did a quick search with find:

find / -name 'geos-config' -type f

and it turned out I had 20 locations containing geos-config… Not sure which one to use.

/bin/geos-config
/usr/bin/geos-config
/usr/local/lib/bin/geos-config
/usr/local/bin/geos-config
...

So I tried with the latest version I had previously installed, 3.9.1, but again, that did not solve the initial problem. Then I tried with version 3.6.1:

GEOS_CONFIG=/home/ctroupin/Software/geos-3.6.1/tools/geos-config pip install shapely

Still failing when running the example.

Building cartopy from source

According to cartopy doc, we can do:

git clone https://github.com/SciTools/cartopy.git
cd cartopy
python setup.py install

which should work if all the prerequisites were installed. Here there is also a subtlety: if the installation of done using the master branch from the GitHub repository, the last line issued on the screen is:

Finished processing dependencies for Cartopy==0.0.0

i.e., the version doesn’t seem correct. Then in a Python session, the command

import cartopy

yields this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ctroupin/Software/PythonEnvs/ToDelete/lib/python3.8/site-packages/Cartopy-0.0.0-py3.8-linux-x86_64.egg/cartopy/__init__.py", line 7, in <module>
    from ._version import version as __version__  # noqa: F401
ImportError: cannot import name 'version' from 'cartopy._version' (/home/ctroupin/Software/PythonEnvs/ToDelete/lib/python3.8/site-packages/Cartopy-0.0.0-py3.8-linux-x86_64.egg/cartopy/_version.py)

which seems to be related to the version number.

Solution:

1. a dirty way to solve that is to comment the line 7 of __init__.py. That works…
2. Otherwise, switch to another branch and re-run the installation:

   git checkout v0.18.0
   python setup.py install
   

Missing GEOS library

Running again the example from the beginning leads to this error:

OSError: /home/username/PythonEnvironments/GPXproc/lib/libgeos_c.so: cannot open shared object file: No such file or directory

which I solved in a not very clever way: by creating a soft link to the existing library libgeos_c.so in the lib directory of my virtual environment.

cd /home/username/PythonEnvironments/GPXproc/lib/
ln -sfv /usr/local/lib/lib/libgeos_c.so .

Summary

Here is the list of commands that lead to a working environment. For sure they are things that can be improved, for example the step in which the libgeos_c file is linked in the lib directory of the virtual environment.

venvname="ToDelete"
mkvirtualenv --python=/usr/local/bin/python3.8 ${venvname}
pip install matplotlib
pip install scipy
pip install cython
pip uninstall shapely
pip install shapely --no-binary shapely
GEOS_CONFIG=/home/ctroupin/Software/geos-3.6.1/tools/geos-config pip install shapely
ln -sv /usr/local/lib/lib/libgeos_c.so ${WORKON_HOME}/${venvname}/lib/libgeos_c.so
git clone git@github.com:SciTools/cartopy.git
cd cartopy
git checkout v0.18.0
python setup.py install
cd ..
python test_carto.py

Edit [March 28]

One year later the installation story is not yet completed for me. I re-ran the procedure above, just trying to use a more recent release of Cartopy (0.20), but the command python setup.py install gave me an error:

GEOS version 3.3.3 is installed, but cartopy requires at least version 3.7.2.

even if I was using 3.6.1… so I don’t know. Sticking to 0.18 works so I won’t dig deeper right now.