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
$ cd /path/to/uncertainpy
$ python install are able to install different set of dependencies. For all options run:

$ python --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.


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.


uncertainpy.EfelFeatures requires the Python package

  • efel

which can be installed with:

pip install uncertainpy[efel_features]


pip install efel

or through:

python install --efel_features


uncertainpy.NetworkFeatures requires the Python packages

  • elephant
  • neo
  • quantities

which can be installed with:

pip install uncertainpy[network_features]


pip install elephant, neo, quantities

or through:

python install --network_features


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


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 script. For how to use run:

$ python --help has all the above dependencies in addition to:

  • click

These dependencies can be installed with:

pip install uncertainpy[tests]


pip install click

or through:

python install --tests


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]


pip install sphinx, sphinx_rtd_theme

or through:

python install --docs

The documentation is build by:

cd docs
make html