conda install numpy scipy pandas joblib
pip install argh whatami lockfile

cd /opt/matlab/extern/engines/python  # if matlab is installed in /opt/matlab
python setup.py install  # unfortunately, pip would fail here

pip install oct2py

# You can install the last release from pypi
pip install pyopy

# Alternatively, you can install master directly from github
pip install https://github.com/strawlab/pyopy/tarball/master


# Finally, you could also install a development version
cd wherever
git clone https://github.com/strawlab/pyopy.git
pip install -e pyopy

# For HCTSA, using matlab is highly recommended.

 hctsa-cli install --engine matlab --force-download --generate-bindings

#
# This command will download or clone HCTSA from github into
#   ~/.pyopy/toolboxes/hctsa/
# Then it will patch it and mex extensions using either matlab or octave.
# This version of HCTSA will be dynamically added to the matlab/octave
# path each time "hctsa.prepare()" is called.
#

#
# The command will also regenerate the python bindings.
# This means regenerating the module:
#   "pyopy/hctsa/hctsa_bindings.py"
# Note that for the bindings to be regenerated succesfully,
# "hctsa-cli" needs write permissions on the directory where
# pyopy has been installed.
# This should not be a problem if you used "pip install -e" or
# if installed to a conda/virtualenv on your user dir.
#


# If you want to generate the mexes for the other engine, run:

 hctsa-cli install --engine octave

#
# Note not "--force-download" (otherwise the mex extensions for the
# first engine would be removed) nor ""--generate-bindings"
# (these need to be generated only once) should be specified.
# The same effect can be achieved running this command:
#   hctsa-cli install --engine all --force-download --generate-bindings
#

# As a final note, mexing can be redone when changing matlab/octave by:
 hctsa-cli mex --engine matlab

hctsa-cli summary

Number of operators (functions in mfiles):    164
Number of operations (function + parameters): 1057
Number of features (operation + outvalue):     7778
Functions without operation: ['CO_TSTL_amutual', 'DN_Cumulants', 'DN_nlogL_norm', 'IN_AutoMutualInfo', 'IN_Initialize_MI', 'IN_MutualInfo', 'MF_GP_LearnHyperp', 'MF_ResidualAnalysis', 'NL_CaosMethod', 'PP_PreProcess', 'SB_CoarseGrain', 'SD_MakeSurrogates', 'TSTL_predict']
Operations without functions: ['DK_TheilerQ', 'DK_crinkle_statistic', 'DK_timerev_1', 'DK_timerev_2', 'DK_timerev_3', 'DK_timerev_4']
    (these are probably calls into other toolboxes)
Features without operations: []
    (usually this should be empty)

ipython