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INSTALLATION

PUQ works on Linux systems. It has also been run successfully on MacOSX and Windows using anaconda. It has been tested with Python 2.7 and 3.5.

To install, you should first install the dependencies listed below. Then change to the puq directory and

python setup.py install

Dependencies

Before installation, the following must be installed. You may want to install the other dependencies using the normal package installation process on your system.

  • Python : Version 2.7 or later.
  • NumPy : The fundamental package for scientific computing with Python.
  • HDF5 (1.8.0 or newer): A data model, library, and file format for storing and managing data.

The installer will attempt to install the following, if not present. Due to installer bugs present with some versions, I recommend you install them before the installation process.

  • SymPy : SymPy is a Python library for symbolic mathematics. Note: If you get an error when the setup script installs sympy, you may have to run "pip install sympy" by hand.
  • matplotlib : 2D plotting library which produces publication quality figures in a variety of image formats and interactive environments.

In addition, the following packages will be installed, if necessary, during the installation process.

  • h5py : A Pythonic interface to the HDF5 binary data format. Requires the HDF5 library.
  • SciPy : Library of algorithms for mathematics, science and engineering.
  • `pytest`_ : A Python unit testing tool.
  • poster : poster provides a set of classes and functions to faciliate making HTTP POST (or PUT) requests using the standard multipart/form-data encoding.
  • jsonpickle : jsonpickle is a Python library for serialization and deserialization of complex Python objects to and from JSON.
  • PyMC : PyMC is a python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo.

Testing

Run tests with "python setup.py test"

Documentation

The documentation is built with Sphinx and requires the napoleon extension.

To build the documentation, cd to the doc directory and type:

  • make html - to build HTML docs
  • make latexpdf - to build a PDF