Installation¶

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.

Anaconda install (Recommended)¶

We strongly recommend to use the Anaconda scientific python distribution in order to install python-based software, including pyEMMA. Python-based software is not trivial to distribute and this approach saves you many headaches and problems that frequently arise in other installation methods. You are free to use a different approach (see below) if you know how to sort out problems, but play at your own risk.

If you already have a conda installation, directly go to step 3:

Download and install miniconda for Python 2.7, 32 or 64 bit depending on your system:

http://conda.pydata.org/miniconda.html

select yes to add conda to the PATH variable.
If you have installed from a Linux shell, either open a new shell to have an updated PATH, or update your PATH variable by source ~/.bashrc (or .tcsh, .csh - whichever shell you are using).
Add the omnia-md software channel, and install (or update) pyemma:
```
conda config --add channels http://conda.binstar.org/omnia
conda install binstar # to be able to get packages from binstar
conda install pyemma
```
if the command conda is unknown, the PATH variable is probably not set correctly (see 1. and 2.)
Check installation:
```
conda list
```
shows you the installed python packages. You should find a pyemma 1.2 (or later) and ipython, ipython-notebook 3.1 (or later). If ipython is not up to date, you can still use pyemma, but you won’t be able to load our example notebooks. In that case, update it by
```
conda install ipython-notebook
```

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.

If you do not have pip, please read the install guide: install guide.
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.
Install pyEMMA using
```
pip install pyemma
```
Check your installation
```
python
>>> 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.

Ensure that you fulfill the following prerequesites:
- C/C++ compiler
- setuptools > 3.6
- 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: http://www.scipy.org/scipylib/building/

2. The build and install process is in one step, as all dependencies are dragged in via the provided setup.py 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

Ensure the Prerequesites (point 1) described for “Building from Source” above.
Make a suitable directory, and inside clone the reposity via
```
git clone https://github.com/markovmodel/PyEMMA.git
```
install pyemma via
```
python setup.py 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 reinstall anything, because the setup command simply created a link to your working copy. Repeating point 3 is only necessary if any of pyEMMA’s 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
```