Cmdstanpy

Please note that the next non-bugfix release of CmdStanPy will be CmdStanPy 2.0 and will remove existing deprecations

Fixes

* Update community.rst to mention `bibat` by teddygroves in https://github.com/stan-dev/cmdstanpy/pull/737
* Move to pyproject.toml setup by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/735
* Extract format functionality from Model class by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/740
* Add a num_threads helper argument to pathfinder() by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/741
* Fix an issue where pathfinder() could not accept multiple initial values by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/741
* Update docs for release by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/743


**Full Changelog**: https://github.com/stan-dev/cmdstanpy/compare/v1.2.1...v1.2.2

Please note that the next non-bugfix release of CmdStanPy will be CmdStanPy 2.0 and will remove existing deprecations

Fixes

* Switch from np.random.RandomState to default_rng by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/712
* Fix minor doc typos by gil2rok in https://github.com/stan-dev/cmdstanpy/pull/715
* Stan 2.34: Fix parsing of unit_e output files by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/723
* Add new Pathfinder arguments by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/727
* Allow the 'vars' argument to draws_pd to filter new columns by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/718
* Allow warmup iterations when not adapting by WardBrian in https://github.com/stan-dev/cmdstanpy/pull/731

New Contributors
* gil2rok made their first contribution in https://github.com/stan-dev/cmdstanpy/pull/715

**Full Changelog**: https://github.com/stan-dev/cmdstanpy/compare/v1.2.0...v1.2.1

Please note that the next non-bugfix release of CmdStanPy will be CmdStanPy 2.0 and will remove existing deprecations

New Features:
* Allow git:TAG as a version in install_cmdstan. https://github.com/stan-dev/cmdstanpy/pull/679
* [Stan 2.32] Laplace method and other changes. https://github.com/stan-dev/cmdstanpy/pull/669
* Add "chain__", "iter__", and "draw__" columns to draws_pd. https://github.com/stan-dev/cmdstanpy/pull/677
* Allow multiple dicts in inits, fix multichain. https://github.com/stan-dev/cmdstanpy/pull/688
* [Stan 2.33] Move IO munging to external package, refactors. https://github.com/stan-dev/cmdstanpy/pull/681
* [Stan 2.33] Add Pathfinder. 686

Fixes and Minor Changes:
* Correctly fetch ppc64el CmdStan. https://github.com/stan-dev/cmdstanpy/pull/661
* Add version bounds on standalone GQ for non-HMC . https://github.com/stan-dev/cmdstanpy/pull/657
* Fix: escape spaces in call to make. https://github.com/stan-dev/cmdstanpy/pull/662
* Accept np.floating and np.integer for arguments. https://github.com/stan-dev/cmdstanpy/pull/663
* Only check version URL after determining if it was already installed. https://github.com/stan-dev/cmdstanpy/pull/673
* Update documentation on external C++. https://github.com/stan-dev/cmdstanpy/pull/675
* Handle tilde `~` in model paths.. https://github.com/stan-dev/cmdstanpy/pull/671
* Doc: spelling fixes. https://github.com/stan-dev/cmdstanpy/pull/678
* Fix handling of include-paths in compiler options. 689

New Functionality
- Add method `log_prob` to model class (637)
- Extend `generate_quantities` to non-HMC classes (634)

Other changes
- Improve type hints (631)
- Serialize draws when pickled (632)
- Raise an error if `src_info` fails (638)
- Change tests to `pytest` format (639)

_Note_: This is a release candidate. If no issues are reported, the same version will be published as a full release in one week.

New Functionality
- Add method `log_prob` to model class (637)
- Extend `generate_quantities` to non-HMC classes (634)

Other changes
- Improve type hints (631)
- Serialize draws when pickled (632)
- Raise an error if `src_info` fails (638)
- Change tests to `pytest` format (639)

- `install_cmdstan` now downloads the correct CmdStan for non-x86 Linux machines (616).
- Improved reporting of errors during `compile()` (620).
- Fixed some edge cases in mixing arguments of the `optimize()` function (619).
- Fixed how `NaN` and infinite numbers were serialized to JSON (623).
- Removed dependency on `ujson`. For now, all JSON serialization is done with the Python standard library.
- Added a `timeout` parameter to all model methods which can be used to terminate the CmdStan process after the specified time (621).
- A model will now properly recompile if one of the `include`-d files changed since it was last built (627).