pyunicorn 0.8.0

Unified complex network and recurrence analysis toolbox

About

pyunicorn (Unified Complex Network and RecurreNce analysis toolbox) is an object-oriented Python package for the advanced analysis and modeling of complex networks. Beyond the standard measures of complex network theory (such as degree, betweenness and clustering coefficients), it provides some uncommon but interesting statistics like Newman’s random walk betweenness. pyunicorn also provides novel node-weighted (node splitting invariant) network statistics, measures for analyzing networks of interacting/interdependent networks, and special tools to model spatially embedded complex networks.

Moreover, pyunicorn allows one to easily construct networks from uni- and multivariate time series and event data (functional/climate networks and recurrence networks). This involves linear and nonlinear measures of time series analysis for constructing functional networks from multivariate data (e.g., Pearson correlation, mutual information, event synchronization and event coincidence analysis). pyunicorn also features modern techniques of nonlinear analysis of time series (or pairs thereof), such as recurrence quantification analysis (RQA), recurrence network analysis and visibility graphs.

pyunicorn is fast, because all costly computations are performed in compiled C code. It can handle large networks through the use of sparse data structures. The package can be used interactively, from any Python script, and even for parallel computations on large cluster architectures. For information about individual releases, see our CHANGELOG and CONTRIBUTIONS.

License

pyunicorn is BSD-licensed (3 clause).

Reference

Please acknowledge and cite the use of this software and its authors when results are used in publications or published elsewhere. You can use the following reference:

J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths. “Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package”. Chaos 25, 113101 (2015), doi:10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Funding

The development of pyunicorn has been supported by various funding sources, notably the German Federal Ministry for Education and Research (projects GOTHAM and CoSy-CC2), the Leibniz Association (projects ECONS and DominoES), the German National Academic Foundation, and the Stordalen Foundation via the Planetary Boundary Research Network (PB.net) among others.

Getting Started

Installation

Official releases

Stable releases can be installed directly from the Python Package Index (PyPI):

$> pip install pyunicorn

Alternatively, source distributions can be downloaded from the GitHub Releases.

On Windows, please first install the latest version of the Microsoft C++ Build Tools, which is required for compiling Cython modules.

Current development version

In order to use a newer version, please follow the pip instructions for installing from version control or from a local source tree.

Dependencies

pyunicorn is implemented in Python 3 / Cython 3, is tested on Linux, macOS and Windows, and relies on the following packages:

• Required:

  • numpy, scipy

  • python-igraph (for Network)

  • h5netcdf (for Data, NetCDFDictionary)

  • tqdm (for progress bars)

• Optional:

  • Matplotlib, Cartopy (for plotting features)

  • mpi4py (for parallelizing costly computations)

  • Sphinx (for generating documentation)

  • Jupyter Notebook (for tutorial notebooks)

Documentation

For extensive HTML documentation, jump right to the homepage. In a local source tree, HTML and PDF documentation can be generated using Sphinx:

$> pip install .[docs]
$> cd docs; make clean html latexpdf

Tuturials

For some example applications look into the tutorials provided with the documentation. They are designed to be self-explanatory, and are set up as Jupyter notebooks.

Development

Test suite

Before committing changes or opening a pull request (PR) to the code base, please make sure that all tests pass. The test suite is managed by tox and is configured to use system-wide packages when available. Install the test dependencies as follows:

$> pip install -e .[tests]

The test suite can be run from anywhere in the project tree by issuing:

$> tox

To display the defined test environments and target them individually:

$> tox -l
$> tox -e style,lint,test,docs

To test individual files:

$> flake8 src/pyunicorn/core/network.py     # style check
$> pylint src/pyunicorn/core/network.py     # static code analysis
$> pytest tests/test_core/test_network.py   # unit tests