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
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