CmdStanPy v1.3.0

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

New Features

• Add diagnose method to CmdStanModel. by @tillahoffmann in #734
• add timing information for sampler outputs by @mitzimorris in #779
• Add new create_inits() methods to other stanfit classes by @amas0 in #791

Fixes

• Clean up TQDM usage by @WardBrian in #781
• CmdStan path validation only requires makefile by @WardBrian in #783
• Enable/disable logging helpers by @amas0 in #796
• Implementation of faster MCMC CSV parsing and Stan CSV utilities by @amas0 in #799, #801
• Additional Stan CSV IO updates and refactoring by @amas0 in #806
• Remove Python 3.8 support by @amas0 in #808
• Deprecate metric argument and property, rename to inv_metric by @WardBrian in #804
• Update tests for new cmdstan defaults by @WardBrian in #797
• Stop trying to munge return codes from subprocess by @WardBrian in #809

Documentation

• Fix documentation links by @amas0 in #790
• Add release notes for 1.3.0 by @WardBrian in #813
• Remove defunct read-the-docs script by @WardBrian in #774

New Contributors

• @amas0 made their first contribution in #790
• @EwoutH made their first contribution in #816

Full Changelog: v1.2.5...v1.3.0

CmdStanPy v1.2.4

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

Fixes

• Add rebuild_cmdstan to API doc by @WardBrian in #761
• Fix from_csv failing to load files from CmdStan 2.35+ by @ahartikainen in #764

Full Changelog: v1.2.3...v1.2.4

CmdStanPy v1.2.3

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

Fixes

• Fix tests for CmdStan 2.35 by @WardBrian in #749
• Fix profile file output when running multiple chains in one process by @WardBrian in #751

Full Changelog: v1.2.2...v1.2.3

CmdStanPy 1.2.2

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 #737
• Move to pyproject.toml setup by @WardBrian in #735
• Extract format functionality from Model class by @WardBrian in #740
• Add a num_threads helper argument to pathfinder() by @WardBrian in #741
• Fix an issue where pathfinder() could not accept multiple initial values by @WardBrian in #741
• Update docs for release by @WardBrian in #743

Full Changelog: v1.2.1...v1.2.2

CmdStanPy 1.2.1

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 #712
• Fix minor doc typos by @gil2rok in #715
• Stan 2.34: Fix parsing of unit_e output files by @WardBrian in #723
• Add new Pathfinder arguments by @WardBrian in #727
• Allow the 'vars' argument to draws_pd to filter new columns by @WardBrian in #718
• Allow warmup iterations when not adapting by @WardBrian in #731

New Contributors

• @gil2rok made their first contribution in #715

Full Changelog: v1.2.0...v1.2.1

CmdStanPy 1.2.0

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. #679
• [Stan 2.32] Laplace method and other changes. #669
• Add "chain__", "iter__", and "draw__" columns to draws_pd. #677
• Allow multiple dicts in inits, fix multichain. #688
• [Stan 2.33] Move IO munging to external package, refactors. #681
• [Stan 2.33] Add Pathfinder. #686

Fixes and Minor Changes:

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

CmdStanPy 1.1.0

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)

CmdStanPy 1.1.0rc1

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)

CmdStanPy 1.0.8

CmdStanPy 1.0.8

• 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).

CmdStanPy 1.0.7

CmdStanPy 1.0.7

• Fixed a critical bug in how outputs containing complex numbers were read in by CmdStanPy. If you are using models which output complex numbers, please update immediately to ensure you are getting the correct results.