Gemdat

What's Changed

* Correct label in radial_distribution_between_species by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/350
* Bug fixes by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/355
* Work-around for atoms without label when reading lammps data by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/356
* Add option to change the colormap for shape analysis by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/347
* Add polar plot of orientation vectors by tfamprikis in https://github.com/GEMDAT-repos/GEMDAT/pull/358


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.5.1...1.6.0

What's Changed
* Refactor `radial_distribution_between_species()` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/340
* Fix all mypy issues by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/341
* Fix crash in `Transitions.occupancy` if input sites are disordered by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/342


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.5.0...1.5.1

This is a small update that adds a new plotting method to `gemdat.Trajectory`.

What's Changed
* Add RDFs calculation based on species by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/338
* Fix vibration amplitudes plot by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/336

Maintenance

* Update README.md by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/334
* Fix coverage badge by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/332


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.4.0...1.5.0

This is a small update that adds GROMACS support and fixes a bug in the rendering of plots with a shaded region.

What's Changed
* Add GROMACS support by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/330
* Fix shaded rendering for msd plot by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/331

**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.3.0...1.4.0

The highlights for this release are:

- All plots have been updated for better clarity and are now available as both matplotlib and plotly varieties. You can choose the backend by passing `backend='matplotlib'` or `backend='plotly'` to the plot methods.
- A trajectory reader for LAMMPS data through `Trajectory.from_lammps(...)`
- A new method to calculate a jump graph from the `Jumps` class: `G = jumps.to_graph()`. The edges are tagged with the activation energies.

What's Changed

* Update Orientations api by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/303
* Update captions for plots by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/308
* Add option to show shaded area for std by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/309
* Add plotly plots by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/313
* Add shortcut for calculating and plotting RDFs by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/318
* Add option to switch between plotting backends by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/326
* Add LAMMPS trajectory reader by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/327
* Add plotly plot for shape by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/324
* Add method to create a graph from jumps by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/325

Under the hood

* Refactor Pathway class by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/305

Bug fixes

* Add warning for multiple paths by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/323
* Tweak method names and update default dimensions by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/301
* Fix rdf plotly test by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/320
* Fix ruff config by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/321

Maintanance

* Add zenodo link and how to cite by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/304
* Minor housekeeping changes by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/310
* Move legacy.py out of main library by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/316
* Move to ruff for autoformatting by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/317





**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.2.1...1.3.0

What's Changed
* Fix broken publish action by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/295


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.2.0...1.2.1