Uf3

Pre-release

This is a pre-release for v1.0.0 of UF3 which is tentatively planned for November 18, 2023. Many changes have been made since the previous Pypi package update and will be detailed in the v1.0.0 release.

For a comprehensive list of changes please visit the following link: https://github.com/uf3/uf3/compare/v0.3.2...master

**Warning:** Two major bugs were identified that are corrected in the release. The details can be found at pull request https://github.com/uf3/uf3/pull/60 and pull request https://github.com/uf3/uf3/pull/61. These changes will require recomputing all UF3 feature/descriptor files.

This release includes necessary changes to publish `uf3` to PyPi.

Changes
- Installing `uf3` with `pip` now no longer requires the editable option `-e`.


**Full Changelog**: https://github.com/uf3/uf3/compare/v0.3.0...v0.3.2

This release incorporates all changes from the development branch between July 24, 2022, and September 20, 2022.

**The update includes critical bug fixes for models with multi-component systems and is not compatible with previously generated feature data and fitted models.**

Bug Fixes
* Fix multi-component pair and triplet building (PR by henk789 in https://github.com/uf3/uf3/pull/31)
* Two- and three-body interactions across periodic boundary conditions were occasionally assigned incorrect element species. All multi-component models, therefore, require new featurization and new fitting.
* Fix issue with loading wrong model coefficients (PR by henk789 in https://github.com/uf3/uf3/pull/32)
* Loading models from `JSON` files resulted in wrong coefficients. Stored models are unaffected but are now loading correctly. The bug affected the *master* branch since v0.2.0.
* Sort pair tuples correctly during loading (PR by henk789 in https://github.com/uf3/uf3/pull/25)
* Sort pair hashes by electronegativity (PR by henk789 in https://github.com/uf3/uf3/pull/27)


**Full Changelog**: https://github.com/uf3/uf3/compare/v0.2.0...v0.3.0

This release incorporates all changes from the development branch between Dec 9, 2021 and July 23, 2022.
The update includes changes to function names and arguments, so please check the updated examples and changelog.

Additions:
- Per-sample weighting during fitting
- Enforce repulsion at small distances for pair potentials where basis functions are entirely outside of training data domain
- Improved saving/loading classes to/from JSON files (PR 18, PR 20, PR 21 from henk789)
- Three-body visualization with slices
- Three-body visualization with Plotly-based rendering
- Support for forcing leading (small-distance) basis functions to zero in addition to previously-implemented trailing_trim.
- Support for BSplines with negative-valued knots. Note: LAMMPS' pair_style table requires positive-valued knots.
- Additional keywords for finer control of plotting functions.

Changes:
- Remove unused keywords, such as chemical_system for BasisFeaturizer (PR 9 from Robert-Schmid)
- Serialize uncompressed coefficient array for three-body terms
- New default values for regularizers

Fixes:
- Increased decimal precision when writing to file
- Fit with a list of keys rather than requiring both integer slices and keys
- Handle divide-by-zero errors when training with a single atomic configuration
- Speed up python-based ASE calculator for single- and multi-component systems using NDSplines package
- New default color and line-style settings for plotting pair potentials