diffpy.cmi 3.1.2

Complex modeling infrastructure: a modular framework for multi-modal modeling of scientific data.

Complex modeling infrastructure: a modular framework for multi-modal modeling of scientific data.

DiffPy.CMI is designed as an extensible complex modeling infrastructure. Users and developers can readily integrate novel data types and constraints into custom workflows. While widely used for advanced analysis of structural data, the framework is general and can be applied to any problem where model parameters are refined to fit calculated quantities to data.

DiffPy.CMI is a community-driven project that supports Unix, Linux, macOS, and Windows platforms. It is designed to be used in Python scripts enabling flexible scripting and automation for advanced and reproducible workflows. Users are encouraged to leverage the software for their modeling needs and to contribute feedback, use cases, and extensions through the project community.

For more information about the diffpy.cmi library, please consult our online documentation.

Citation

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

Juhás, P.; Farrow, C. L.; Yang, X.; Knox, K. R.; Billinge, S. J. L. Complex Modeling: A Strategy and Software Program for Combining Multiple Information Sources to Solve Ill Posed Structure and Nanostructure Inverse Problems. Acta Crystallogr A Found Adv 2015, 71 (6), 562–568. https://doi.org/10.1107/S2053273315014473.

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.cmi_env

conda create -n diffpy.cmi_env diffpy.cmi
conda activate diffpy.cmi_env

To confirm that the installation was successful, type

python -c "import diffpy.cmi; print(diffpy.cmi.__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.cmi_env environment, type

pip install diffpy.cmi

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

pip install .

Getting Started

Use the cmi command-line interface to install and manage modular optional dependencies, known as packs, and to configure or execute user-defined workflows that combine multiple packs with optional post-installation steps, known as profiles. You may consult our online documentation for more information, tutorials, and API references.

The -h flag is available for all cmi commands and subcommands. It’s highly recommended to use it wherever necessary.

To display help for the main CLI, type

cmi -h
cmi --help

Display help for a specific subcommand with,

cmi <subcommand> -h

Open the full online manual in a web browser by typing,

cmi --manual

To print information about available and installed packs, profiles, and examples, type,

cmi info

To print information about packs, profiles, or examples, type

cmi info packs
cmi info profiles
cmi info examples

To install packs or profiles into your environment, type

cmi install <pack-name>
cmi install <profile-name>

To copy an example or list of examples to cwd, type

cmi copy <example-name>
cmi copy <example-name1> <example-name2>

To copy all examples from a pack or list of packs to cwd, type

cmi copy <pack-name>
cmi copy <pack-name1> <pack-name2>

To copy all examples to cwd, type

cmi copy all

To show basic information about your current conda environment, type

cmi env

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.cmi 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.cmi please visit the project web-page or email Simon Billinge at [e-mail].

Acknowledgements

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