INSTALL.md

Prerequisites

The following software is required for dyconnmap to work properly:

1. Python 3.6, or Python 3.8+

2. numpy

3. scipy

4. maplotlib

5. networkx

6. Brain Connectivity Toolbox for Python (bctpy)

7. pytest (optional)

   This is required for executing the tests.

8. Sphinx (optional)

   This is required for building the documentation from the source code.

Consult the accompanying requirement.txt file for specific versions.

Installation

Using pip

The easiest way to install dyconnmap is through pip. From a terminal just type:

$ pip search dyconnmap

dyconnmap (1.0.4) - A dynamic connectome mapping module.

and to install it:

$ pip install dyconnmap

You may want to check also the testing repository:

$ pip install --index-url https://test.pypi.org/simple dyconnmap

in an Anaconda distribution

Activate your installation and give:

$ pip install --extra-index-url https://pypi.anaconda.org/makism/simple dyconnmap

From source code

First clone the github repository, navigate into the directory and run:

$ python setup.py install

If you prefer to install dyconnmap locally, instead run:

$ python setupy.py install --prefix=$HOME/.local

If you opt for the later option, you will have to set the environmental variable $PYTHONPATH from the terminal as follows:

$ export PYTHONPATH="$HOME/.local/dyconnmap/lib/python3.6/site-packages/"

Documentation

Once you have installed dyconnmap, navigate into the source directory and run:

$ sphinx-apidoc -f -o docs/ dyconnmap/

$ cd docs

$ make html

Testing

Once you have installed dyconnmap, navigate into the tests directory and run:

$ pytest .