Gemdat

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

The highlights for this release are:

- Orientation tracker, with this version of GEMDAT you can track the orientation of a group of atoms (e.g. tetrahedra) in your trajectory and plot them
- Haven ratio calculator

What's Changed

* Added some plotly plots by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/278
* Rename all `displacement_per_site` to `displacement_per_atom` by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/280
* Add orientations tracker by tfamprikis in https://github.com/GEMDAT-repos/GEMDAT/pull/220
* Implement Haven ratio by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/283
* Add option to select MSD algorithm by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/291
* Improve Orientations API by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/293

Under the hood

* Refactor 3d plots module by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/284
* Refactor Volume class to support multiple data types by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/282

Bug fixes

* Fix periodic jumps of matplotlib jumps_3d plot by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/279

Maintanance

* Update actions versions by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/294

New Contributors
* tfamprikis made their first contribution in https://github.com/GEMDAT-repos/GEMDAT/pull/220

**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.1.0...1.2.0

The highlights for this release are:

- The `SitesData` class has been refactored into `Transitions` and `Jumps`, including improved algorithm for jumps calculations. This will make the code more maintainable and easier to extend for the long term.
- Many small api changes to make the code more intuitive and earier to use, for example, many plots are now accessible through class methods
- New methods for calculating and plotting multiple energy paths

What's Changed

* Make orthographic projection for density plot by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/233
* Return structure with occupancy set as Composition by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/246
* Improve MSD calculation by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/248
* Turn Jumps.rates and Jumps.activation energies into dataframes by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/250
* Add peak labels to free energy plots by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/213
* Add option to calculate multiple paths by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/258
* Make user api more intuitive by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/259
* Make user api more accessible by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/264
* Calculate transitions with custom radii per site type by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/265

Under the hood

* Improve jump specification criteria by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/228
* jumps calculation: switched joined prerequisites to independent prerequisites by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/247
* Add method to extend trajectory by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/242
* Refactor sites methods/attrs into other classes by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/251
* Small tweaks to Transitions by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/256

Bug fixes

* Fix number of sites by type by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/238
* Fix wrong `n_floating` bug by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/253
* Fix RDF test by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/255

Maintanance

* Fix documentation build by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/257
* Fix docs build by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/261

**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/1.0.0...1.1.0