Gemdat

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

- This is an **alpha** release

The first release of gemdat, the code is still in flux thus do not expect a lot to work yet:

What's Changed
* Adding Actions by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/2
* Set up documentation by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/4
* first few plots working by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/7
* Add displacement plots by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/9
* Add vibrational properties by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/11
* Add tracer properties by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/14
* creating a new structure by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/12
* Add methods to load a material from a CIF file by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/18
* Structure the calculations, data now has a calculate_all function by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/20
* Add implementation for calculating site transitions by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/19
* Add integration tests, refactor tracer data by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/24
* Add SitesData class by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/25
* Adding a Dashboard by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/21
* Dashboard update: offer two ways of selecting a file, simultaniously by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/30
* Revise extras by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/29
* Calculate origin and destination sites for atoms in transition by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/31
* Calculate occupancy per site by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/36
* Load super cell and check lattice compatibility by stefsmeets in https://github.com/GEMDAT-repos/GEMDAT/pull/39
* added publish pipeline by v1kko in https://github.com/GEMDAT-repos/GEMDAT/pull/40