Gemdat

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

The highlights for this release are:

- A new logo 🤩
- Tools for site shape analysis
- The dashboard was split off to [its own repo](https://github.com/GEMDAT-repos/gemdat-dashboard)

What's Changed

* Add functions to perform site shape analysis by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/166
* Add mean squared displacement plot by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/195
* Add optional argument to gemdash, to specify trajectory location by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/214
* Logo by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/219
* Allow custom lattice for density plot and `ShapeAnalyzer` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/225
* Add methods to calculate and apply offsets for shape analysis by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/224
* Add function to display sites on shape plot by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/232

Under the hood

* Speed up percolation test by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/188
* Hide warning when loading a cif file through pymatgen by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/223

Bug fixes

* Fix squared radius in shape_analysis by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/190
* Remove double mention by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/209
* Use kBoltzmann from scipy by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/207
* Fix mismatch with i variable in activation_energies by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/194
* Make sure filtering matching happens against a collection, not a string by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/217
* Fix issues and tweak api for ShapeAnalyzer by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/230

Maintanance

* Update CITATION.cff by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/210
* Add Simone to CITATION.cff by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/211
* Move dashboard to its own repo by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/222
* Switch to bump-my-version by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/229
* Use svg covbadge by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/231


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.9.4...1.0.0

This release introduces some new features and improvements:
- minimal energy pathways are introduced
- errors can be calculated (and shown on the dashbord)
- some plots have been converted to plotly and are now interactive

What's Changed
* Tweak density plotting function by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/175
* Make sure the aspect ratio of the density plot is similar to the volume by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/176
* Improving plots by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/177
* Metrics with standard deviation by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/182
* Fix number of colors for plot_points by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/184
* Implement energy landscapes and pathways from simulation by SCiarella in https://github.com/GEMDAT-repos/GEMDAT/pull/178


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.9.3...0.9.4

What's Changed
* add the data of the package to the manifest by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/152
* Enable testing of dashboard inside github action by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/155
* Allow uneven splits with np.array_split by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/162
* Fix known material MnO2 by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/169
* Update volume.py by AstyLavrinenko in https://github.com/GEMDAT-repos/GEMDAT/pull/160
* Add support for loading NPT data with varying lattice by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/171
* Fix hash function by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/172
* Add density plot to dashboard by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/174

New Contributors
* SCiarella made their first contribution in https://github.com/GEMDAT-repos/GEMDAT/pull/168
* AstyLavrinenko made their first contribution in https://github.com/GEMDAT-repos/GEMDAT/pull/160

**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.9.2...0.9.3