Apax

What's Changed
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/323
* MD perf stats by M-R-Schaefer in https://github.com/apax-hub/apax/pull/325
* added uncertainty checks to jax md by M-R-Schaefer in https://github.com/apax-hub/apax/pull/328
* Update README.md by PythonFZ in https://github.com/apax-hub/apax/pull/329
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/331
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/336
* full ensemble fix, feature model fix by M-R-Schaefer in https://github.com/apax-hub/apax/pull/332
* fix calibration factors not available in calculator by M-R-Schaefer in https://github.com/apax-hub/apax/pull/337
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/339
* added w_init to template, updated default by M-R-Schaefer in https://github.com/apax-hub/apax/pull/334
* cleaned up validation error messages by M-R-Schaefer in https://github.com/apax-hub/apax/pull/333


**Full Changelog**: https://github.com/apax-hub/apax/compare/v0.6.0...v0.7.0

Notable Changes
- Uncertainties in jaxmd
- Interface for adding new models (currently an equivariant MP model is
- Added Post hoc calibration for ASE calculator as function
- Added temperature schedules for
- Various bug fixes and doc updates

Breaking Changes
All functionality of previous versions was preserved. However you might need to adapt your input files.
For training, the model section now requires the field name: gmnn (or other model).
For MD, the temperature field was replaced with the temperature_schedule field.
Check the config template to see an example of a constant temperature simulation.


What's Changed
* use `store="time"` by PythonFZ in https://github.com/apax-hub/apax/pull/303
* save `energy` as scalar by PythonFZ in https://github.com/apax-hub/apax/pull/304
* fix `batch_eval` by PythonFZ in https://github.com/apax-hub/apax/pull/306
* [MDAnalysis fix]: Do not save units by PythonFZ in https://github.com/apax-hub/apax/pull/307
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/310
* updated jax CUDA installation instructions by M-R-Schaefer in https://github.com/apax-hub/apax/pull/301
* Uncertainty Calibration by M-R-Schaefer in https://github.com/apax-hub/apax/pull/302
* Calibration Nodes docs update by M-R-Schaefer in https://github.com/apax-hub/apax/pull/311
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/313
* moved BAL selection node from ips to apax by M-R-Schaefer in https://github.com/apax-hub/apax/pull/315
* added temperature schedules by M-R-Schaefer in https://github.com/apax-hub/apax/pull/318
* Improved schema command by M-R-Schaefer in https://github.com/apax-hub/apax/pull/316
* switch ase batch predict to CachedDataset by M-R-Schaefer in https://github.com/apax-hub/apax/pull/314
* added uncertainty estimation on dump interval for jaxmd by M-R-Schaefer in https://github.com/apax-hub/apax/pull/312
* Model extension by M-R-Schaefer in https://github.com/apax-hub/apax/pull/317
* automatically publish on PyPi by PythonFZ in https://github.com/apax-hub/apax/pull/321
* zbl no longer Nan by M-R-Schaefer in https://github.com/apax-hub/apax/pull/320
* added missing so3krates scaling parameter by M-R-Schaefer in https://github.com/apax-hub/apax/pull/322


**Full Changelog**: https://github.com/apax-hub/apax/compare/v.0.5.0...v0.6.0

v.0.5.0

notable changes:
- New learning rate schedules
- New batch-evaluationb method for the ase calculator
- h5md dataset loading
- new dataset optimized for differently sized structures
- new Bessel-like basis functions
- shallow ensembles for uncertainty estimation and NLL, CRPS loss functions
- added feature model
- switched linting to ruff
- force features for BAL

What's Changed
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/266
* add `repository` link by PythonFZ in https://github.com/apax-hub/apax/pull/267
* EMA, SAM update, cyclic LR schedule by M-R-Schaefer in https://github.com/apax-hub/apax/pull/269
* train_config.py fix default no. contractions by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/272
* NVE bug fix by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/276
* Add MD restart support and fix config loading by PythonFZ in https://github.com/apax-hub/apax/pull/271
* bump znh5md by PythonFZ in https://github.com/apax-hub/apax/pull/278
* implemented apax batch evaluation node by M-R-Schaefer in https://github.com/apax-hub/apax/pull/280
* H5MD data loading by M-R-Schaefer in https://github.com/apax-hub/apax/pull/282
* Per Batch Padded Dataset by M-R-Schaefer in https://github.com/apax-hub/apax/pull/281
* allow for non NTK linear layers in model by M-R-Schaefer in https://github.com/apax-hub/apax/pull/283
* New Basis function interface by M-R-Schaefer in https://github.com/apax-hub/apax/pull/284
* Mlflow fix by M-R-Schaefer in https://github.com/apax-hub/apax/pull/286
* Node fix by M-R-Schaefer in https://github.com/apax-hub/apax/pull/289
* fixed memory leak in pbp ds by M-R-Schaefer in https://github.com/apax-hub/apax/pull/290
* Shallow ensembles by M-R-Schaefer in https://github.com/apax-hub/apax/pull/275
* refactored distance computation, added feature model by M-R-Schaefer in https://github.com/apax-hub/apax/pull/285
* use znh5md v0.3 by PythonFZ in https://github.com/apax-hub/apax/pull/292
* replace isort, flake8 and black with ruff by PythonFZ in https://github.com/apax-hub/apax/pull/294
* Collective changes from my absence by M-R-Schaefer in https://github.com/apax-hub/apax/pull/293
* bump project version, pin orbax and flax versions by M-R-Schaefer in https://github.com/apax-hub/apax/pull/296
* v0.5.0 by M-R-Schaefer in https://github.com/apax-hub/apax/pull/297


**Full Changelog**: https://github.com/apax-hub/apax/compare/v0.4.0...v.0.5.0

What's Changed
* MD end checkpoint & ensemble NPT fix by M-R-Schaefer in https://github.com/apax-hub/apax/pull/225
* merge main by PythonFZ in https://github.com/apax-hub/apax/pull/226
* remove linting CI in favor of pre-commit.ci by PythonFZ in https://github.com/apax-hub/apax/pull/227
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/228
* update dev branch with new CI by M-R-Schaefer in https://github.com/apax-hub/apax/pull/230
* fixed jax nl always allocating in cartesian coords by M-R-Schaefer in https://github.com/apax-hub/apax/pull/229
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/231
* fixed bug where positions where not initialized for gas phase systems by M-R-Schaefer in https://github.com/apax-hub/apax/pull/232
* Batch evaluation by M-R-Schaefer in https://github.com/apax-hub/apax/pull/233
* Remove JaxMD dependency by M-R-Schaefer in https://github.com/apax-hub/apax/pull/234
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/235
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/236
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/237
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/238
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/240
* Fix eval by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/241
* Update io.py by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/243
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/244
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/242
* Input Pipeline rework by M-R-Schaefer in https://github.com/apax-hub/apax/pull/245
* Huber Loss by M-R-Schaefer in https://github.com/apax-hub/apax/pull/249
* Input Autocomplete by M-R-Schaefer in https://github.com/apax-hub/apax/pull/250
* Cache dataset by M-R-Schaefer in https://github.com/apax-hub/apax/pull/248
* unit fix by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/258
* Batch Pbar by M-R-Schaefer in https://github.com/apax-hub/apax/pull/256
* Mlflow by M-R-Schaefer in https://github.com/apax-hub/apax/pull/255
* ZnTrack Nodes by PythonFZ in https://github.com/apax-hub/apax/pull/254
* FIX Neighborlist for periodic structures by M-R-Schaefer in https://github.com/apax-hub/apax/pull/259
* Dataparallel Training by M-R-Schaefer in https://github.com/apax-hub/apax/pull/257
* Moredocs nico by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/261
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/apax-hub/apax/pull/260
* removed disfunctional docs action by M-R-Schaefer in https://github.com/apax-hub/apax/pull/262
* Docs Examples by M-R-Schaefer in https://github.com/apax-hub/apax/pull/217
* update version to 0.4.0 by M-R-Schaefer in https://github.com/apax-hub/apax/pull/263
* spell check by Tetracarbonylnickel in https://github.com/apax-hub/apax/pull/265
* Cummulative 0.4.0 Changes by M-R-Schaefer in https://github.com/apax-hub/apax/pull/264

New Contributors
* pre-commit-ci made their first contribution in https://github.com/apax-hub/apax/pull/228

**Full Changelog**: https://github.com/apax-hub/apax/compare/v0.3.0...v0.4.0

What's Changed
* Update pyproject.toml by PythonFZ in https://github.com/apax-hub/apax/pull/214
* added model loading edge case for `experiment=""` by M-R-Schaefer in https://github.com/apax-hub/apax/pull/216
* Poetry Update and Orbax fix by M-R-Schaefer in https://github.com/apax-hub/apax/pull/218
* added stress triL loss function by M-R-Schaefer in https://github.com/apax-hub/apax/pull/221
* JIT multiple train steps by M-R-Schaefer in https://github.com/apax-hub/apax/pull/220
* Version 0.3.0 changes by M-R-Schaefer in https://github.com/apax-hub/apax/pull/223


**Full Changelog**: https://github.com/apax-hub/apax/compare/v0.2.0...v0.3.0

**Full Changelog**: https://github.com/apax-hub/apax/compare/v0.1.0...v0.2.0