Gemdat

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

This is a test

What's Changed
* Add repr to `Trajectory` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/139
* Update workflow to generate `requirements.txt` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/142
* Add PyPI badges to readme by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/143
* Refactor `Volume.to_structure` and revert to padded watershed for pbc by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/141


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.9.1...0.9.2

Added notebooks to the documentation

What's Changed
* Added submodule for notebooks by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/137


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.9.0...0.9.1

A release which has feature parity with the old matlab code, there are still a few issues to be ironed out before a full 1.0.0 release

The code has been refactored for ease-of-use and integrates nicely with pymatgen now.

What's Changed
* Calculate jump rates and activation energy by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/43
* Calculate jump diffusivity by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/48
* Add metrics to dashboard by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/51
* Optimize site search by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/52
* Fix integration test by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/53
* Store units in FloatWithUnit and use `scipy.constants` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/55
* Add implementation for calculating collective jumps by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/56
* Added displacement tests and typing fixes by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/58
* Require pymatgen-2023.7.14 by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/60
* Add jumps vs time histogram by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/61
* Calculate and plot volume by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/63
* added Supercell and material (stub) selection to dashboard by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/64
* dashboard: fixed jump plots by disabling supercell by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/68
* Calculate and plot rdf by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/66
* Add 3D jumps animation by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/70
* Add cifs for known structures by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/74
* add short run to git submodule by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/71
* Apply dashboard supercell fixes by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/76
* Add Radial Distribution Function plots to dashboard by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/82
* Refactor `SitesData` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/81
* Add legacy interface to mimick matlab code by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/84
* Use `Trajectory` in place of `SimulationData` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/85
* Fix plot labels by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/97
* Fix assignment of `atom_sites_to/from` by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/98
* Add filter method to Trajectory by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/99
* Update pymatgen requirement in pyproject.toml by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/100
* Drift correction by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/101
* Refactor displacements by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/102
* Bump pymatgen pin to >= 2023.8.10 by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/104
* Create LICENSE by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/107
* Add `SimulationMetrics` class by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/105
* Tweak dashboard layout by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/108
* Add tests for matplotlib plots by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/109
* Refactor sites into property-like functions by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/110
* Move rdf plot function and add tests by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/112
* Remove plot module by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/114
* Pass user keyword arguments to `vasp.Vasprun` initializer by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/115
* Derive sites from trajectory (or other) density by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/116
* Restructure volume data with dataclass by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/117
* Fix cache memory leak by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/119
* Fix plots by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/120
* Make integration tests more exhaustive by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/121
* Change tree to conventional src/package structure by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/123
* Update documentation by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/122
* Add missing modules to docs by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/127
* Improve *volume to structure* functionality by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/130
* Updating and adding documentation by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/131
* Fixes for release by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/136


**Full Changelog**: https://github.com/GEMDAT-repos/GEMDAT/compare/0.0.1...0.9.0