Kliff

Enhancements 🛠

- Refactor test by mjwen in https://github.com/openkim/kliff/pull/125
- Update the ptemcee dependency by yonatank93 in https://github.com/openkim/kliff/pull/137
- Update GH actions to use latest conda-forge kim-api and test on macOS by mjwen in https://github.com/openkim/kliff/pull/143

Documentation 📖

- Recreate docs building codes by mjwen in https://github.com/openkim/kliff/pull/129

Other Changes

- Fix neighbor list bug by mjwen in https://github.com/openkim/kliff/pull/90
- Fix \_WrapperCalculator by mjwen in https://github.com/openkim/kliff/pull/95
- Remove requirements.txt, add info in setup.py by mjwen in https://github.com/openkim/kliff/pull/108
- Add multiple species support of LJ by mjwen in https://github.com/openkim/kliff/pull/112
- Update CI to fix cmake version by mjwen in https://github.com/openkim/kliff/pull/117
- WIP: Implement bootstrap by yonatank93 in https://github.com/openkim/kliff/pull/107

Added

- Uncertainty quantification via MCMC (yonatank93). New tutorial and explanation of
the functionality provided in the doc.
- Issue and PR template

Fixed

- Linear regression model parameter shape
- NN multispecies calculator to use parameters of all models

Updated

- Documentation on installing KLIFF and dependencies

Added

- Add ParameterTransform class to transform parameters into a different space (e.g. log
space) yonatank93
- Add Weight class to set weight for energy/forces/stress. This is not backward
compatible, which changes the signature of the residual function. Previously, in a
residual function, the weights are passed in via the `data` argument, but now, its
passed in via an instance of the Weight class. yonatank93

Fixed

- Fix checking cutoff entry adityakavalur
- Fix energy_residual_fn and forces_residual_fn to weigh different component

Updated

- Change to use precommit GH action to check code format

Fixed

- Fix neighlist (even after v0.3.2, the problem can still happen). Now neighlist is the
same as kimpy

Added

- Enable params_relation_callback() for KIM model

Fixed

- Fix neighbor list segfault due to numerical error for 1D and 2D cases

- add gpu training for NN model; set the `gpu` parameter of a calculator (e.g.
`CalculatorTorch(model, gpu=True)`) to use it
- add pyproject.toml, requirements.txt, dependabot.yml to config repo
- switch to `furo` doc theme
- changed: compute grad of energy wrt desc in batch mode (NN calculator)
- fix: set `fingerprints_filename` and load descriptor state dict when reuse fingerprints
(NN calculator)