Stan 2.39 release notes

cmdstan.txt

 - Fixed an issue where the `log_prob` command was reading unconstrained parameters in the incorrect order in some circumstances. (#1337)

  - Updated tests to account for the new `converged__` column in optimization output. (#1338)

math.txt

 - Improved the embedded Laplace approximation. (#3250, #3286, #3297, #3281)

 - Added `yule_simon_lcdf`, `yule_simon_cdf`, and `yule_simon_rng`. (#3276, #3283, #3285)

 - Added quantile function for student-t distribution. (#3211)

 - Added `trace_dot(A, B)`. (#3310)

 - Improved the robustness of `gamma_lccdf`. (#3275, #3272, #3292, #3296)

 - Set thread QoS to USER_INITIATED on Apple Silicon. (#3278)

 - Updated tests to ensure they properly clean up memory. (#3293)

 - Fixed typos in error messages, code comments. (#3295)

 - Documented parameter 'y' in apply_scalar_binary. (#3284)

 - Jenkins: change how gh-pages branch gets re-built. (#3316)

 - Jenkins: improved error handling of parallel distribution tests. (#3307)

 - Updated OpenCL C++ to use v2025.07.22. (#3298)

 - Updated cpplint to 2.0.2. (#3294)

stan.txt

 - Added timing information to the output of standalone generated quantities. (#3373, #3377)

 - Added a `converged__` column to the output of the optimization algorithms,
   which documents why the optimization algorithm halted. A string explanation
   is also added as a comment. (#3379)

 - Changes for compatibility with Eigen 5.0.1. (#3371)

 - Fixed an issue where memory was being re-allocated unnecessarily. (#3392)

stanc3.txt

 - The embedded Laplace functions are now available. (#1586, #1599)

 - Length-1 tuples can now be declared using a trailing comma, e.g. `tuple(real, ) x = (3.14, );`. This is primarily valuable for using tuples with the embedded laplace approximation feature, which uses tuples to pass arguments to user-defined callbacks. (#1609)

 - Functions ending in `_jacobian` will always be treated as needing access to the jacobian adjustment, and thus will only be usable in `transformed parameters` and other `_jacobian` functions. (#1584)

 - Added the `yule_simon` distribution: `yule_simon_lpmf`, `yule_simon_lcdf`, `yule_simon_lccdf`, `yule_simon_cdf`, and `yule_simon_rng`. (#1607)

 - Improved the uninitialized variable warnings raised by pedantic mode and `--warn-uninitialized`. (#1579)

 - `--debug-generate-data` is now aware of the new `sum_to_zero_vector`, `sum_to_zero_matrix`, `stochastic_row_matrix`, and `stochastic_column_matrix` types. (#1588)

 - Added missing overloads to the `upper_lower` and `offset_multiplier` constraint functions. (#1589)

 - Improved error message wording and location information. (#1585, #1580, #1587, #1604, #1605, #1608, #1611)

 - Various optimization bug fixes. (#1598, #1600, #1602)

 - stancjs: Use js_of_ocaml-ppx for type safety. (#1613)

 - Fixed a bug in the parser that could lead to crashes when auto-formatting files with many `#includes`. (#1615)