IDTxl Packaging

First make IDTxl importable. For that to work, we use the common folder structure for Python packages:

IDTxl/
    setup.py   # your setuptools Python package metadata
    MANIFEST.in  # spefify non py-files that should be installed
    COPYING.txt  # license text
    README.txt  # description of the package and its installation
    README.md   # the same in markdown for GitHub
    idtxl/     # actual code
        __init__.py  # for now, this is empty
        multivariate_te.py
        ...
    test/      # unit and system tests
        test_multivariate_te.py
        ...

Make sure, every module uses explicit relative imports, otherwise Python will choke. Relative imports look like this:

from . import stats
from .network_analysis import Network_analysis

Include the JIDT jar-file in the MANIFEST.in. The MANIFEST.in lists all non-.py files that should still go into the installed package (see here for further info). Python calls such files Resources.

To access ressources from package modules one can use the pkg_resources API, which provides convenience functions to load and find ressources in Python packages (see also here and here)

For example, the JIDT jar-file is loaded by the estimators_cmi.py like this:

from pkg_resources import resource_filename
jarLocation = resource_filename(__name__, 'infodynamics.jar')
if not jp.isJVMStarted():
    jp.startJVM(jp.getDefaultJVMPath(), '-ea', ('-Djava.class.path=' +
                jarLocation))

Check that everything is correct by going into the top-folder IDTxl and run import idtxl in a Python session.

To be able to call import idtxl from everywhere on the system, install the package using pip3 (from the IDTxl folder):

$ pip3 install .

As long as IDTxl is still under construction you can use

$ pip3 install -e .   # install package using setup.py in editable mode

instead. This will install IDTxl in 'editable' or development mode, which means pip creates a soft link in Python's site-packages to the current IDTxl location (see here for details). This way you can keep making changes in the Package without the need to reinstall it after each change.

It is also possible to make an editable install of a repository:

$ pip install -e git+http://repo/my_project.git#egg=SomeProject

See here for further info.