To install the msmtools 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 msmtools. 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 or 3, 32 or 64 bit depending on your system: http://conda.pydata.org/miniconda.html
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: http://windows.microsoft.com/en-us/windows/32-bit-and-64-bit-windows
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 omnia-md software channel, and install (or update) msmtools:
conda config --add channels omnia conda install msmtools
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 msmtools 1.1 (or later) and ipython, ipython-notebook 3.1 (or later). If ipython is not up to date, you can still use msmtools, 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 msmtools 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 msmtools using
pip install msmtools
Check your installation
python >>> import msmtools >>> msmtools.__version__
should print 1.1 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 msmtools from the source. In this approach, all msmtools 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. You can install either with pip or conda, as long as you met the version requirements.
- C/C++ compiler
- setuptools > 18
- cython >= 0.22
- numpy >= 1.6
- scipy >= 0.11
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
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 msmtools
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/msmtools.git
install msmtools 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 msmtools C-files change and need to be rebuilt.