A classical problem, I’m sure it is already well documented in different places, but I’ve had recently some issues with the installation, hence this short post, which may be useful only to me.

Creation of the virtual environment

Nothing fancy here, we use the virtualenvwrapper and specify the python version we’re using (3.8 as at the time of this post):

mkvirtualenv --python=/usr/local/bin/python3.8 Argo3.8
workon Argo3.8

Basemap

Yes, we now it is deprecated in favor of Cartopy, but for some reasons, let’s say we want to continue with Basemap for some more time.

Download the last release from https://github.com/matplotlib/basemap/releases/, here we save it in a directory ~/Software, for example.

Update: I have encountered issues with basemap-1.2.2rel, while the previous version, basemap-1.2.1rel was working fine.

Compile geos library

It is a necessary step before installing Basemap. We need to specify the directory where the libgeos.* files are located. In our case: /usr/local/lib. This is stored in the variable GEOS_DIR.

cd ~/Software/basemap-1.2.2rel
cd geos-3.3.3
export GEOS_DIR=/usr/local/lib
./configure --prefix=$GEOS_DIR
make
sudo make install

If you don’t have the permissions to write in /usr/local/lib and similar directories, for instance on a cluster, you can use another one, typically:

export GEOS_DIR=~/.local/

(ensuring the directory has already been created).

Install Basemap

Almost done, just run the following command to install the module:

cd ..
python setup.py install

which should end with the message:

Finished processing dependencies for basemap==1.2.1

Testing

Open a python terminal and run

from mpl_toolkits.basemap import Basemap

We get the error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'mpl_toolkits.basemap'

though we’re sure the module has been properly installed, since pip list returns:

Package                       Version
----------------------------- -----------
...
basemap                       1.2.1
...

What’s the problem then?

I check the directory storing the different virtual environments:
{VIRTUALENVDIR}/Argo3.8/lib/python3.8/site-packages
and found, among many directories:

• basemap-1.2.1-py3.8-linux-x86_64.egg/mpl_toolkits, which was installed a few minutes before
• mpl_toolkits, installed some days ago.

So my assumption (and I must apologise because I won’t take the time to verify it), is that mpl_toolkits has been installed at the same time as matplotlib. Seems plausible.

Then, when I run in Python from mpl_toolkits import ... it searches for Basemap in this older directory.

Solution

I created a link inside the old mpl_toolkits directory toward the newly installed basemap directory:

cd ${VIRTUALENVDIR}/Argo3.8/lib/python3.8/site-packages/mpl_toolkits
ln -sfv ../basemap-1.2.1-py3.8-linux-x86_64.egg/mpl_toolkits/basemap/ .

This way, when typing from mpl_toolkits.basemap import Basemap, Python find the expected directory.

With IPython

Side note: the command can work in a Python terminal but not with IPython. Why?

When you type ipython in a terminal, you need to be sure that it is the ipython relative to the virtual environment that is run.

A possibility for that is to call it with

python -m IPython

Now we’re done with Basemap.

Problem with ‘dedent’

In some installations I encountered this issue:

ImportError: cannot import name 'dedent' from 'matplotlib.cbook'

It is documented here, and the solution detailed below.

Solution

Find the path of the file proj.py with the command:

import pyproj
pyproj.__file__

In my case it ends with basemap-1.2.1-py3.8-linux-x86_64.egg/mpl_toolkits/basemap/proj.py.

In this file, replace
from matplotlib.cbook import dedent with
from inspect import cleandoc as dedent.

Okay, another dirty fix, but there is no time now to be much cleaner.

Cartopy

Let’s repeat: Basemap is deprecated and we should use Cartopy. Their documentation starts with Conda stuffs, we’re not using it too much as we prefer the classical pip approach.

pip

Let’s start with a pip install cartopy.

On other occasions, we got error messages, but this time it seems everything is in place to avoid us some troubles. Lucky me.