To install the PyEMMA Python package, you need a few Python package dependencies. If these dependencies are not available in their required versions, the installation will fail. We recommend one particular way for the installation that is relatively safe, but you are welcome to try another approaches if you know what you are doing.

Python Package Index (PyPI)

If you do not like Anaconda for some reason you should use the Python package manager pip to install. This is not recommended, because in the past, various problems have arisen with pip in compiling the packages that PyEMMA depends upon.

  1. If you do not have pip, please read the install guide: install guide.

  2. Make sure pip is enabled to install so called wheel packages:

    pip install wheel

    Now you are able to install binaries if you use MacOSX or Windows. At the moment of writing PyPI does not support Linux binaries at all, so Linux users have to compile by themselves.

  3. Install PyEMMA using

    pip install pyemma
  4. Check your installation

    >>> import pyemma
    >>> pyemma.__version__

    should print 1.2 or later

    >>> import IPython
    >>> IPython.__version__

    should print 3.1 or later. If ipython is not up to date, update it by pip install ipython

Building from Source

If you refuse to use Anaconda, you will build PyEMMA from the source. In this approach, all PyEMMA dependencies will be built from the source too. Building these from source is sometimes (if not usually) tricky, takes a long time and is error prone - though it is not recommended nor supported by us. If unsure, use the Anaconda installation.

  1. Ensure that you fulfill the following prerequisites:

    • C/C++ compiler

    • setuptools > 18

    • cython >= 0.22

    • numpy >= 1.6

    • scipy >= 0.11

    • matplotlib >= 1.4

    If you do not fulfill these requirements, try to upgrade all packages:

    pip install --upgrade setuptools
    pip install --upgrade cython
    pip install --upgrade numpy
    pip install --upgrade scipy
    pip install --upgrade matplotlib

    Note that if pip finds a newer version, it will trigger an update which will most likely involve compilation. Especially NumPy and SciPy are hard to build. You might want to take a look at this guide here:

2. The build and install process is in one step, as all dependencies are dragged in via the provided script. So you only need to get the source of Emma and run it to build Emma itself and all of its dependencies (if not already supplied) from source.

pip install pyemma

For Developers

If you are a developer, clone the code repository from GitHub and install it as follows

  1. Ensure the prerequisites (point 1) described for “Building from Source” above.

  2. Make a suitable directory, and inside clone the repository via

    git clone
  3. install pyemma via

    python develop [--user]

    The develop install has the advantage that if only python scripts are being changed e.g. via an pull or a local edit, you do not have to re-install anything, because the setup command simply created a link to your working copy. Repeating point 3 is only necessary if any of PyEMMA C-files change and need to be rebuilt.

Frequently Asked Questions (FAQ)

  • Q: Installation went fine with conda, but import pyemma leads to the following error:

    ImportError: No module named PySide

    A: install pyside manually with conda:

    conda install pyside
  • Q: My conda installation raises errors during import

    A: check if you have a file called ‘easy-install.pth’ in our home directory


    and validate it contains only packages you want (eg. Python packages you have installed with pip prior the usage of Anaconda/miniconda. If the list in this file contains important dependencies of PyEMMA like SciPy or NumPy this can cause trouble, since these packages are being used in favour of the conda installation and are not compatible. You should also make sure that this file does not contain a reference to the systems provided python installation like /usr/lib/python etc. because of the same reason.

  • Q: I’m using conda, but recently during installations/updates I get the following error message:

    $ conda install binstar
    Fetching package metadata: .....Error: Could not find URL:
    A: This occurs because has been removed to (10/2015).

    To resolve this you need to remove the channel definition by invoking:

    conda config --remove channels --force

    and add the new channel living on

    conda config --add channels omnia
  • Q: I’m using Windows, have a fresh Anaconda installation and I get strange errors during “import xyz”.

    A: Possible answer 1: you have probably mixed 32 and 64 bit. Using 32 bit Python

    on 64 bit Windows is fine, but not the other way around. Possible answer 2: Do you have Python2 and Python3 on the same computer? To figure that you, open a cmd prompt and type in:

    where python

    This should only display one line like. If it is displaying more than one .exe, you either know what you are doing or you should remove one installation (eg. decide, which branch of Python [2 or 3] to keep).