:tocdepth: 1

.. _scientific-software:

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Scientific software standards
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Most research code is written once and never reused because it is hard to install, untested, and undocumented. **scikit-package**, developed with Prof. Simon Billinge, gives scientists a path from a script to a tested, documented, public package, one level at a time.

- Packaging standards, project templates, automated reusable workflows, and tutorials
- Five levels of sharing, from a reusable function to a released pip/conda package
- `Documentation <https://scikit-package.github.io/scikit-package>`__ · `Code <https://github.com/scikit-package/scikit-package>`__ · `Paper <https://doi.org/10.1039/d6dd00121a>`__

.. figure:: ../img/research/scikit-package-levels.png
   :width: 75%
   :align: center
   :alt: Diagram of the five levels of sharing code in scikit-package

   **Five levels of sharing code**, from reusing a function within a file (level 1) to releasing a public package with pip/conda distribution, release notes, and hosted documentation (level 5), with the scikit-package command for each level.

**Academic software built with scikit-package**

- PDFfit2 and PDFgui: Computer programs for studying nanostructure in crystals (`J. Phys. Condens. Matter <https://doi.org/10.1088/0953-8984/19/33/335219>`__)
- cifkit: A Python package for coordination geometry and atomic site analysis (`JOSS <https://doi.org/10.21105/joss.07205>`__)
- Composition and structure analyzer/featurizer for explainable machine learning models to predict solid state structures (`Digital Discovery <https://doi.org/10.1039/D4DD00332B>`__)
- Stretched non-negative matrix factorization (`npj Comput. Mater. <https://doi.org/10.1038/s41524-024-01377-5>`__)
- Real-space texture and pole-figure analysis using the 3D pair distribution function on a platinum thin film (`IUCrJ <https://doi.org/10.1107/S2052252522006674>`__)

Co-authored publications
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- **scikit-package: software packaging standards and roadmap for sharing reproducible scientific software.** S. Lee *et al.*, `Digital Discovery <https://doi.org/10.1039/d6dd00121a>`__ (2026).