PUQ: Python package for parallel uncertainty quantification

Dependencies

PUQ has been tested on Unix/Linux and MacOS systems.

PUQ's base has the following dependencies:

• Python 3.6+
• NumPy -- for data structures and performant numerical linear algebra
• SciPy -- for scientific calculations needed for specific modules
• libEnsemble -- for parallel implementation

Installation

From the command line, use the following command to install PUQ:

pip install PUQ==0.1.0

Alternatively, the source code can be downloaded to the local folder, and the package can be installed from the .tar file.

Testing

The test suite requires the pytest and pytest-cov packages to be installed and can be run from the tests/ directory of the source distribution by running:

./run-tests.sh

If you have the source distribution, you can run the tests in the top-level directory containing the setup script with :

python setup.py test

Further options are available for testing. To see a complete list of options, run:

./run-tests.sh -h

Coverage reports are produced under the relevant directory only if all tests are used.

Documentation

The documentation is stored in docs/ and is compiled with the Sphinx Python documentation generator. It is written in the reStructuredText format. These files are hosted at Read the Docs.

To compile the documentation, first ensure that Sphinx is installed. Then, to generate documentation, run command make html from terminal within this directory as follows :

cd docs
make html

The HTML files are then stored in docs/_build/html

Citation:

• Please use the following to cite PUQ in a publication:

@techreport{PUQ2022,
  author      = {Özge Sürer, Matthew Plumlee, Stefan M. Wild},
  title       = {PUQ Users Manual},
  institution = {},
  number      = {Version 0.1.0},
  year        = {2022},
  url         = {https://github.com/parallelUQ/PUQ}
}

Examples

We provide examples in the examples/ directory to illustrate the basic usage of PUQ.