diffpy.morph 0.4.0

Citation

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

“diffpy.morph: Python tools for model independent comparisons between sets of 1D functions” by Andrew Yang, Luis Kitsu Iglesias, Michael F. Toney, Samuel D. Marks, Joshua Safin, Vivian R. K. Wall, Katherine Page, Naomi S. Ginsberg, Dillon Hanlon, Nicholas Leonard, Samuel W. Teitelbaum, Timothy B. van Driel, Chia-Hao Liu, Soham Banerjee, Christopher L. Farrow, Pavol Juhas, Emil S. Bozin, Simon J. L. Billinge, to be published.

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.morph_env

conda create -n diffpy.morph_env diffpy.morph
conda activate diffpy.morph_env

To confirm that the installation was successful, type

python -c "import diffpy.morph; print(diffpy.morph.__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. To install using pip into your diffpy.morph_env environment, we will also have to install dependencies

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

and then install the package

pip install diffpy.morph

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

pip install .

Getting Started

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

USING diffpy.morph

For detailed instructions and full tutorial, see our website <www.diffpy.org/diffpy.morph/>.

Once the required software, including diffpy.morph is all installed, open up a terminal and check installation has worked properly by running

source activate diffpy.morph_env      #if the environment isn't already active
diffpy.morph -h                   #get some helpful information
diffpy.morph --version

If installed correctly, this last command should return the version of diffpy.morph that you have installed on your system. To begin using diffpy.morph, run a command like

diffpy.morph <morph file> <target file>

where both files are text files which contain two-column data, such as .gr or .cgr files that are produced by PDFgetX2, PDFgetX3, or PDFgui. File extensions other than .gr or .cgr, but with the same content structure, also work with diffpy.morph.

Enjoy!

Support and Contribute

Diffpy user group is the discussion forum for general questions and discussions about the use of diffpy.morph. Please join the diffpy.morph users community by joining the Google group. The diffpy.morph 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.morph 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.morph please visit the project web-page or email Simon J.L. Billinge group at sb2896@columbia.edu.

Acknowledgements

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