diffpy.snmf 0.1.0

A python package implementing the stretched NMF algorithm.

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.

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, arXiv:2311.15173 [cond-mat.mtrl-sci] (2023).

Installation

The preferred method is to use Miniconda Python 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 python=3
conda activate diffpy.snmf_env

Then, to fully install diffpy.snmf in our active environment, run

conda install diffpy.snmf

Another option is to use pip to download and install the latest release from Python Package Index. To install using pip into your diffpy.snmf_env environment, we will also have to install dependencies

pip install -r https://raw.githubusercontent.com/diffpy/diffpy.snmf/main/requirements/run.txt

and then install the package

pip install diffpy.snmf

If you prefer to install from sources, after installing the dependencies, obtain the source archive from GitHub. Once installed, cd into your diffpy.snmf directory and run the following

pip install .

Support and Contribute

Diffpy user group 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 and/or submit a fix as a PR. You can also post it to the Diffpy user group.

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.

1. Install pre-commit in your working environment by running conda install pre-commit.

2. 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 contribuing, please read our Code of Conduct.

Contact

For more information on diffpy.snmf please visit the project web-page or email Prof. Simon Billinge at [e-mail].