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.. |title| replace:: diffpy.snmf .. _title: https://diffpy.github.io/diffpy.snmf

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A python package implementing the stretched NMF algorithm.

diffpy.snmf implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF (ssNMF) algorithms.

This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal on the independent variable axis. For example, for powder diffraction data taken from samples containing multiple chemical phases where the measurements were done at different temperatures and the materials were undergoing thermal expansion.

For more information about the diffpy.snmf library, please consult our online documentation <https://diffpy.github.io/diffpy.snmf>_.

Citation

If you use this program for a scientific research that leads to publication, we ask that you acknowledge use of the program by citing the following paper in your publication:

Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O’Nolan, Brennan Mcbride, Allison Wustrow, James R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge, Stretched Non-negative Matrix Factorization <https://doi.org/10.1038/s41524-024-01377-5>__, npj Comput Mater 10, 193 (2024).

Installation

The preferred method is to use Miniconda Python <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>_ and install from the "conda-forge" channel of Conda packages.

To add "conda-forge" to the conda channels, run the following in a terminal. ::

    conda config --add channels conda-forge

We want to install our packages in a suitable conda environment. The following creates and activates a new environment named diffpy.snmf_env ::

    conda create -n diffpy.snmf_env diffpy.snmf
    conda activate diffpy.snmf_env

To confirm that the installation was successful, type ::

    python -c "import diffpy.snmf; print(diffpy.snmf.__version__)"

The output should print the latest version displayed on the badges above.

If the above does not work, you can use pip to download and install the latest release from Python Package Index <https://pypi.python.org>_. To install using pip into your diffpy.snmf_env environment, type ::

    pip install diffpy.snmf

If you prefer to install from sources, after installing the dependencies, obtain the source archive from GitHub <https://github.com/diffpy/diffpy.snmf/>_. Once installed, cd into your diffpy.snmf directory and run the following ::

    pip install .

Getting Started

You may consult our online documentation <https://diffpy.github.io/diffpy.snmf>_ for tutorials and API references.

Support and Contribute

Diffpy user group <https://groups.google.com/g/diffpy-users>_ is the discussion forum for general questions and discussions about the use of diffpy.snmf. Please join the diffpy.snmf users community by joining the Google group. The diffpy.snmf project welcomes your expertise and enthusiasm!

If you see a bug or want to request a feature, please report it as an issue <https://github.com/diffpy/diffpy.snmf/issues> and/or submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>. You can also post it to the Diffpy user group <https://groups.google.com/g/diffpy-users>_.

Feel free to fork the project and contribute. To install diffpy.snmf in a development mode, with its sources being directly used by Python rather than copied to a package directory, use the following in the root directory ::

    pip install -e .

To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit hooks.

Install pre-commit in your working environment by running conda install pre-commit.
Initialize pre-commit (one time only) pre-commit install.

Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before trying to commit again.

Improvements and fixes are always appreciated.

Before contributing, please read our Code of Conduct <https://github.com/diffpy/diffpy.snmf/blob/main/CODE_OF_CONDUCT.rst>_.

Contact

For more information on diffpy.snmf please visit the project web-page <https://diffpy.github.io/>_ or email Prof. Simon Billinge at sb2896@columbia.edu.