Installation¶

Uncertainpy works with with Python 3. Uncertainpy can easily be installed using pip. The minimum install is:

pip install uncertainpy

To install all requirements you can write:

pip install uncertainpy[all]

Specific optional requirements can also be installed, see below for an explanation. Uncertainpy can also be installed by cloning the Github repository:

$ git clone https://github.com/simetenn/uncertainpy
$ cd /path/to/uncertainpy
$ python setup.py install

setup.py are able to install different set of dependencies. For all options run:

$ python setup.py --help

Alternatively, Uncertainpy can be easily installed (minimum install) with conda using conda-forge channel:

$ conda install -c conda-forge uncertainpy

The above installation, within a conda environment, is only compatible with Python 3.x.

Dependencies¶

Uncertainpy has the following dependencies:

chaospy
tqdm
h5py
multiprocess
numpy
scipy
seaborn
matplotlib
xvfbwrapper
six
SALib
exdir

These are installed with the minimum install.

xvfbwrapper requires xvfb, which can be installed with:

sudo apt-get install xvfb

Additionally Uncertainpy has a few optional dependencies for specific classes of models and for features of the models.

EfelFeatures¶

uncertainpy.EfelFeatures requires the Python package

efel

which can be installed with:

pip install uncertainpy[efel_features]

or:

pip install efel

or through:

python setup.py install --efel_features

NetworkFeatures¶

uncertainpy.NetworkFeatures requires the Python packages

elephant
neo
quantities

which can be installed with:

pip install uncertainpy[network_features]

or:

pip install elephant, neo, quantities

or through:

python setup.py install --network_features

NeuronModel¶

uncertainpy.NeuronModel requires the external simulator NEURON (with Python), a simulator for neurons. NEURON must be installed by the user.

NestModel¶

uncertainpy.NestModel requires the external simulator NEST (with Python), a simulator for network of neurons. NEST must be installed by the user.

Test suite¶

Uncertainpy comes with an extensive test suite that can be run with the test.py script. For how to use test.py run:

$ python test.py --help

test.py has all the above dependencies in addition to:

click

These dependencies can be installed with:

pip install uncertainpy[tests]

or:

pip install click

or through:

python setup.py install --tests

Documentation¶

The documentation is generated through sphinx, and has the following dependencies:

sphinx
sphinx_rtd_theme

These dependencies can be installed with:

pip install uncertainpy[docs]

or:

pip install sphinx, sphinx_rtd_theme

or through:

python setup.py install --docs

The documentation is build by:

cd docs
make html