Installation

Talon runs only on Python 3. The installation has the following dependencies:

  • Numpy

  • Scipy

  • NiBabel

  • PyUnLocBox

  • PyOpenCL (only if you plan to exploit the GPU capabilities)

If you are an Anaconda user, you may want to create a dedicated talon-env environment and populate it with the right dependencies, then install talon.

conda env create -n talon-env -f environment.yml
pip install cobcom-talon

Alternatively, you can install the dependencies and talon all via pip.

pip install numpy
pip install scipy
pip install nibabel
pip install pyunlocbox
# pip install pyopencl  # uncomment for GPU capabilities

pip install cobcom-talon

To install talon directly from the source, clone this repository and run the standard local setup commands.

git clone https://gitlab.inria.fr/cobcom/talon.git
cd talon
pip install -U .

Check installation

To check that talon has been properly installed, try to import the talon and the talon.cli modules into a Python session as follows. If no error is raised, the installation has been successful.

>>> import talon
>>> import talon.cli

To further check that the GPU capabilities are active, try to import the talon.opencl. If no error is raised, the installation has been successful.

>>> import talon.opencl

For developers

If you are thinking about developing your own fork of talon, you may want to use the latest version in the devel branch of the repository and install it in editable mode.

git clone https://gitlab.inria.fr/cobcom/talon.git
cd talon
git checkout devel
pip install -e .

Tests

The package uses unittest as a testing suite. To run all the tests, execute the following command in the source’s root directory.

python -m unittest -v

Test coverage can be checked with coverage as follows.

coverage run -m unittest
coverage report -m

Documentation

The sources of the documentation are in the doc folder. The compilation requires the sphinx package and the theme to be installed.

pip install sphinx
pip install sphinx_rtd_theme

To compile the documentation, move to the doc folder and run make <format>, where the format can be html, latex or any other sphinx-compatible format. To get a local copy of the the html documentation, run the make html command.

cd doc
make clean  # deletes results of previous compilations
make html