diffpy.srfit 3.3.1rc0

Citation

If you use diffpy.srfit in a scientific publication, we would like you to cite this package as

P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge, Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems, Acta Crystallogr. A 71, 562-568 (2015).

Installation

The best way to install diffpy.srfit is as part of the diffpy.cmi package. Please see https://github.com/diffpy/diffpy.cmi for installation information.

If for some reason you want to install the diffpy.srfit library on its own, 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.srfit_env

conda create -n diffpy.srfit_env diffpy.srfit
conda activate diffpy.srfit_env

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

Fallback Installation

If the above does not work, you can use pip to download and install the latest release from Python Package Index. To install using pip into your diffpy.srfit_env environment, type

pip install diffpy.srfit

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

pip install .

This package also provides command-line utilities. To check the software has been installed correctly, type

diffpy.srfit --version

You can also type the following command to verify the installation.

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

To view the basic usage and available commands, type

diffpy.srfit -h

Getting Started

You may consult our online documentation for tutorials and API references.

Support and Contribute

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.

Feel free to fork the project and contribute. To install diffpy.srfit 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 contributing, please read our Code of Conduct.

Contact

For more information on diffpy.srfit please visit the project web-page or email the maintainers Caden Myers(cjm2304@columbia.edu) and Simon J. L. Billinge(sbillinge@ucsb.edu).

Acknowledgements

diffpy.srfit is built and maintained with scikit-package.

The source code in observable.py was derived from the 1.0 version of the Caltech “Pyre” project.