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