cmdstanpy

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 https://github.com/stan-dev/cmdstanpy/pull/761
• Fix from_csv failing to load files from CmdStan 2.35+ by @ahartikainen in https://github.com/stan-dev/cmdstanpy/pull/764

Full Changelog: https://github.com/stan-dev/cmdstanpy/compare/v1.2.3...v1.2.4

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 https://github.com/stan-dev/cmdstanpy/pull/749
• Fix profile file output when running multiple chains in one process by @WardBrian in https://github.com/stan-dev/cmdstanpy/pull/751

Full Changelog: https://github.com/stan-dev/cmdstanpy/compare/v1.2.2...v1.2.3

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)

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

• 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.

CmdStanPy 1.0.6

• Fixed a build error in the documentation
• Improved messages when model fails to compile due to C++ errors.

CmdStanPy 1.0.5

• Fixed a typo in cmdstanpy.show_versions()
• Reorganized and updated the documentation
• Reorganized a lot of internal code
• Cleaned up the output of CmdStanMCMC.draws_pd
• Cleaned up the output of CmdStanMCMC.summary
• Removed the logging which occurred when Python exited with cmdstanpy imported.

CmdStanPy 1.0.4

• Fix an issue with the cmdstanpy.install_cmdstan() function where the installation would report that it had failed even when it had not.

CmdStanPy 1.0.3

• Fix an issue where Stan fit objects were not pickle-able when they previously were. Note: We still do not recommend pickling cmdstanpy objects, but rather using functions save_csvfiles and from_csv.

CmdStanPy 1.0.2

• CmdStanPy can now format (and canonicalize) your Stan files with CmdStanModel.format()
• Stan variables can now be accessed from fit objects using the . syntax when no naming conflicts occur. For example, previous code fit.stan_variable("my_cool_variable") can now be written fit.my_cool_variable
• CmdStanPy is more robust to running in threaded environments and tries harder to not overwrite its own output files
• The install_cmdstan script can now be run in interactive mode using --interactive/-i
• CmdStanPy now computes some diagnostics after running HMC and will warn you about post-warmup divergences and treedepth exceptions
• Runtime exceptions in the generated quantities block should be recognized better now.
• The default level of precision to fit.summary() is now 6, as it is when stansummary is used from the command line.\
• Various documentation improvements

CmdStanPy 1.0.1

• Support new optimizations in CmdStan 2.29
• Support complex numbers as both inputs and outputs of Stan programs
• Sped up assembling output by only reading draws at most once
• Fixed an issue where a command failing could change your working directory
• Improve error messages in some cases
• CmdStanPy no longer changes the global root logging level

Note: The minimum supported version for CmdStanPy is now Python 3.7.

After almost 2 years in the beta barrel, we’re proud to release CmdStanPy 1.0. Many thanks to all of our contributors, as well as to all users who’ve submitted feature requests and bug reports!

CmdStanPy provides access to the Stan compiler, inference algorithms, and diagnostics. It supports both development and production workflows and is well-suited for teaching and learning Stan.

Why use CmdStanPy for your next project?

• Use new features: CmdStanPy runs with the latest CmdStan (or any version of CmdStan, including develop)
• Ease of installation: CmdStanPy can automatically install CmdStan and the underlying C++ toolchain.
• Scalable: can fit big models and big datasets – if CmdStan can fit a model and dataset, so can CmdStanPy.
• Cross-platform: runs on Linux, macOS, and Windows.
• Non-restrictive BSD-3 license

Documentation for the latest release is at https://mc-stan.org/cmdstanpy and documentation for older versions can be found on https://cmdstanpy.readthedocs.io/.