• Download Miniconda for Python 3.5 (http://conda.pydata.org/miniconda.html)
• conda config --add channels omnia
• conda install pyemma-dev to get the development version
• conda remove msmtools --force to avoid interference with locally-built msmtools
• Download msmtools from https://github.com/alexlafleur/msmtools and unzip
• execute python setup.py install in the msmtools root directory
• Download or clone LDStreamHMMLearn (see Running Scripts below for options)
• execute python setup.py install in the LDStreamHMMLearn root directory
• execute conda config --add channels conda-forge
• execute conda update msmtools

• Create a PyCharm project containing LDStreamHMMLearn (e.g. clone it within Pycharm)
• From Preferences > Project: LDStreamHMMLearn > Project Interpreter, select the miniconda python interpreter (3.5.2 at the time of writing)

examplary evaluation script execution:

python -c 'from evaluate_deciles import Decile_Evaluator as s; dec = s(); dec.test_evaluate_deciles_qmm_mu()'