coniii 2.4.3rc0

Convenient Interface to Inverse Ising (ConIII)

Convenient Interface to Inverse Ising

ConIII is a Python package for solving maximum entropy problems with a focus on the pairwise maximum entropy model, also known as the inverse Ising problem. Support for Python 3.8.3 and higher.

If you use ConIII for your research, please consider citing the following:

Lee, E.D. and Daniels, B.C., 2019. Convenient Interface to Inverse Ising (ConIII): A Python 3 Package for Solving Ising-Type Maximum Entropy Models. Journal of Open Research Software, 7(1), p.3. DOI: http://doi.org/10.5334/jors.217.

The paper also contains an overview of the modules. For code documentation, see here.

Installation

This package is available on PyPI. It can be installed by first installing the needed Boost C++ libraries and using pip.

$ conda install -c conda-forge boost==1.74
$ pip install coniii

If you have trouble using pip, then you can always build this package from source. The following code will down download the latest release from GitHub and install the package. Make sure that you are running Python 3.8.3 or higher and have boost v1.74.0 installed.

$ git clone https://github.com/eltrompetero/coniii.git
$ cd coniii
$ ./pypi_compile.sh
$ pip install dist/*.whl

(Note: Using setuptools in the usual way of python setup.py install will not work because eggs are incompatible with cached jit functions generated using numba.)

Setting up exact solution for systems N > 9

If you would like to use the Enumerate solver for system sizes greater than 9 spins, you must run enumerate.py to write those files yourself. This can be run from the install directory. If you do not know where the installation directory is, you can find it by starting a Python terminal and running

>>> import coniii
>>> coniii.__path__

Once inside the install directory, you can run in your bash shell

$ python enumerate.py [N]

where [N] should be replaced by the size of the system. This will write the equations for the Ising model in the {0,1} basis. On the other hand,

$ python enumerate.py [N] 1

specifies that the system should be written for the {-1,1} basis. Note that the package uses the {-1,1} basis by default. For more details, see the __main__ block at the end of the file enumerate.py.

Quick guide (with Jupyter notebook)

A Jupyter notebook with a brief introduction and examples for how to use ConIII is available. An HTML version is here. The notebook is installed into your package directory if you used pip.

To use the notebook, install jupyter.

$ pip install jupyter

or if you are using the Conda package manager

$ conda install jupyter

Then, first copy the notebook file "usage_guide.ipynb" into a directory outside the "coniii" directory. Change to this directory and run

$ jupyter notebook

This should open the notebook in your default web browser.

Quick guide (console)

First, install iPython for a console-based interpreter and start it.

$ pip install ipython

or if you are using the Conda package manager

$ conda install ipython

Then, first copy the notebook file "usage_guide.py" into a directory outside the "coniii" directory. Change to this directory and run

$ ipython

Once inside the iPython interpreter, run

>>> %run usage_guide.py

This will run all the examples sequentially, so you may want to comment out unwanted lines.

Troubleshooting

This package is only maintained for Python 3 and has only been tested for Python 3.8.3. Check which version of Python you are running in your terminal with

$ python --version

ConIII has been tested on the following systems

• Ubuntu 18.04
• Ubuntu 20.04.1

Trouble compiling the Boost extension manually? Check if your Boost library is included in your path. If it is not, then you can add an include directory entry into the EXTRA_COMPILE_ARGS variable in "setup.py" before compiling.

Support

Please file an issue on the GitHub if you have any problems or feature requests. Provide a stack trace or other information that would be helpful in debugging. For example, OS, system configuration details, and the results of unit tests. Unit tests can be run by navigating to the package directory and running

$ pytest -q

The package directory can be found by running inside python

>>> import coniii
>>> coniii.__path__

You may also need to install pytest.

$ pip install pytest

Updating

When updating, please read the RELEASE_NOTES. There may be modifications to the interface including parameter names as we make future versions more user friendly.

Documentation.