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Working with Matplotlib in Virtual environments

Introduction

When running matplotlib in a virtual environment you may discover a few issues. matplotlib itself has no issue with virtual environments. However, the GUI frameworks that matplotlib uses for interactive figures have some issues with virtual environments. Everything below assumes some familiarity with the Matplotlib backends as found in What is a backend?.

If you only use the IPython/Jupyter Notebook‘s inline and notebook backends and non interactive backends you should not have any issues and can ignore everything below.

GUI Frameworks

Interactive Matplotlib relies heavily on the interaction with external GUI frameworks.

Most GUI frameworks are not pip installable. This makes it tricky to install them within a virtual environment. This problem does not exist if you use Conda environments where you can install all Conda supported GUI frameworks directly into the environment. In regular virtualenv environment various workarounds exist. Some of these are given here:

  • The TKAgg backend doesn’t require any external dependencies and is normally always available.
  • The QT4 framework PySide is pip installable.
  • The upcoming WX Phoenix toolkit is pip installable.

Other frameworks are harder to install into a virtual environment. There are at least two possible ways to get access to these in a virtual environment.

One often suggested solution is to use the --system-site-packages option to virtualenv when creating an environment. This adds all system wide packages to the virtual environment. However, this breaks the isolation between the virtual environment and the system install. Among other issues it results in hard to debug problems with system packages shadowing the environment packages. If you use virtualenvwrapper this can be toggled with the toggleglobalsitepackages command.

Alternatively, you can manually symlink the GUI frameworks into the environment. I.e. to use PyQt5, you should symlink PyQt5 and sip from your system site packages directory into the environment taking care that the environment and the systemwide install use the same python version.

OSX

Short version

If you are on Python 3, use venv instead of virtualenv:

python -m venv my-virtualenv
source my-virtualenv/bin/activate

Otherwise you will need one of the workarounds below.

Long version

On OSX, two different types of Python Builds exist: a regular build and a framework build. In order to interact correctly with OSX through some GUI frameworks you need a framework build of Python. At the time of writing the macosx, WX and WXAgg backends require a framework build to function correctly. Unfortunately virtualenv creates a non framework build even if created from a framework build of Python. Conda environments are framework builds. From Matplotlib 1.5 onwards the macosx backend checks that a framework build is available and fails if a non framework build is found. WX has a similar check build in.

The issue has been reported on the virtualenv bug tracker here and here

Until this is fixed, one of the following workarounds must be used:

PYTHONHOME Script

The best known workaround, borrowed from the WX wiki, is to use the non virtualenv python along with the PYTHONHOME environment variable. This can be implemented in a script as below. To use this modify PYVER and PATHTOPYTHON and put the script in the virtualenv bin directory i.e. PATHTOVENV/bin/frameworkpython

#!/bin/bash

# what real Python executable to use
PYVER=2.7
PATHTOPYTHON=/usr/local/bin/
PYTHON=${PATHTOPYTHON}python${PYVER}

# find the root of the virtualenv, it should be the parent of the dir this script is in
ENV=`$PYTHON -c "import os; print(os.path.abspath(os.path.join(os.path.dirname(\"$0\"), '..')))"`

# now run Python with the virtualenv set as Python's HOME
export PYTHONHOME=$ENV
exec $PYTHON "[email protected]"

With this in place you can run frameworkpython to get an interactive framework build within the virtualenv. To run a script you can do frameworkpython test.py where test.py is a script that requires a framework build. To run an interactive IPython session with the framework build within the virtual environment you can do frameworkpython -m IPython

PYTHONHOME Function

Alternatively you can define a function in your .bashrc using

function frameworkpython {
    if [[ ! -z "$VIRTUAL_ENV" ]]; then
        PYTHONHOME=$VIRTUAL_ENV /usr/local/bin/python "[email protected]"
    else
        /usr/local/bin/python "[email protected]"
    fi
}

This function can then be used in all of your virtualenvs without having to fix every single one of them.

PythonW Compiler

In addition virtualenv-pythonw-osx provides an alternative workaround which may be used to solve the issue.