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 want to use Miniconda on Linux or OSX, you can run this script to download and install everything:
curl -s https://raw.githubusercontent.com/markovmodel/PyEMMA/devel/install_miniconda%2Bpyemma.sh | bash
After the script finishes, you have a miniconda installation and inside of this a ‘pyemma’ environment. You need to activate the new environment by invoking:
conda activate pyemma
in order to work with this new environment. An environment encapsulates all software used by PyEMMA and is independent of other things. Further reading here.
If you want to download and install manually, please perform the following steps:
If you already have a conda installation, directly go to step 3.
Download and install miniconda for Python3, 32 or 64 bit depending on your system.
For Windows users, who do not know what to choose for 32 or 64 bit, it is strongly recommended to read the second question of this FAQ first:
Run the installer and 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 conda-forge software channel, and install (or update) PyEMMA:
conda config --add channels conda-forge conda install pyemma
if the command conda is unknown, the PATH variable is probably not set correctly (see 1. and 2.)
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 prerequisites:
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: 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
If you are a developer, clone the code repository from GitHub and install it as follows
Ensure the prerequisites (point 1) described for “Building from Source” above.
Make a suitable directory, and inside clone the repository 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 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: http://conda.binstar.org/omnia/osx-64/
- A: This occurs because binstar.org has been removed to anaconda.org (10/2015).
To resolve this you need to remove the channel definition by invoking:
conda config --remove channels http://conda.binstar.org/omnia --force
and add the new channel living on anaconda.org:
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 "X:\\somepath\\miniconda2\\Scripts\\python.exe"
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).