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diffpy / diffpy.pdfgui

graphical user interface for real space structure refinement to PDF
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.. |title| replace:: diffpy.pdfgui .. _title: https://diffpy.github.io/diffpy.pdfgui

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Graphical user interface program for structure refinements to atomic pair distribution function.

For users who do not have the expertise or necessity for command line analysis, PDFgui is a convenient and easy to use graphical front end for the PDFfit2 refinement program. It is capable of full-profile fitting of the atomic pair distribution function (PDF) derived from x-ray or neutron diffraction data and comes with built in graphical and structure visualization capabilities.

PDFgui is a friendly interface to the PDFfit2 refinement engine, with many powerful extensions. To get started, please open the manual from the help menu and follow the tutorial instructions. A detailed description is available in this paper <http://dx.doi.org/10.1088/0953-8984/19/33/335219>_.

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

Citation

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

    C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin,
    J Bloch, Th Proffen and S J L Billinge, PDFfit2 and PDFgui:
    computer programs for studying nanostructure in crystals, J. Phys.:
    Condens. Matter 19 (2007) 335219. doi:10.1088/0953-8984/19/33/335219

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.pdfgui_env ::

    conda create -n diffpy.pdfgui_env python=3
    conda activate diffpy.pdfgui_env

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

    conda install diffpy.pdfgui

Another option is to use pip to download and install the latest release from Python Package Index <https://pypi.python.org>_. To install using pip into your diffpy.pdfgui_env environment, type ::

    pip install diffpy.pdfgui

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

    pip install .

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.pdfgui. Please join the diffpy.pdfgui users community by joining the Google group. The diffpy.pdfgui 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.pdfgui/issues> and/or submit a fix as a PR <https://github.com/diffpy/diffpy.pdfgui/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.pdfgui 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 <https://github.com/diffpy/diffpy.pdfgui/blob/main/CODE_OF_CONDUCT.rst>_.

Contact

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