@syclik syclik released this Feb 5, 2015 · 4092 commits to develop since this release

Assets 3

v2.6.0 (5 February 2015)

New Features

  • log_mix function for binary mixtures [half of #970]
  • neg_binomial_2 CDF function [#1129]

Language Enhancements

  • allow local-variable integers to be treated as constants,
    allowing, among other things, more general ODE functions [#1131]
  • initialize transformed data and generated quantities the
    same way as transformed parameters [#1099]
  • libstan.a removed and model compilation is 100% header-only [#1095]
  • check for infinite/nan inits from boundary initializations
    with warning [#537]

API/Build/Test Enhancements

  • removed extra variables being generated by validation [#1248]
  • generalize OperandsAndPartials to second order [#676]
  • rationalize error handling, using const char* args for efficiency [#1234]
  • upgrade to Boost version 1.55 library [#1206]
  • generate .hpp instead of .cpp for models [#803]
  • value_of_rec recursive metaprogram to pull values out of higher-order
    autodiff structures; removes order dependency on fwd/rev includes
  • tests now run more efficiently with Python script [#1110]
  • add performance tests to continuous integration to perform
    end-to-end regression testing on speed [#708, #1245]
  • manual index parser for tool automation in interfaces (such as
    auto-complete suggestions) and emacs mode
  • refactor log determinant and fix return type cast in vector arena
    alloc [#1187]
  • update makefile dependencies for auto-generated cpp test files [#1108]
  • move test models into clearly labeled directories (good/bad) [#1016]
  • removing policies from math error checking [#1122]
  • remove usage of Boost's formatting (which can cause runtime
    errors like printf) [#1103]
  • rearrange directory structure of err_handling [#1102]
  • clean up math includes to proper location in source tree [#778]
  • remove Windows newline and write script to catch in future [#1233]
  • remove extra copy of Eigen (3.2.0), leaving just Eigen 3.2.2 [#1206]
  • remove example-models dependency from Git [#1105]

Bug Fixes

  • allow identifiers with prefixes matching keywords [#1177]
  • allow functions to be used in variable declaration constriants [#1151]
  • fix segfault resulting from multivariate normal in optimizer (root
    cause wasn't in optimizer, but in autodiff nesting cleanup) [#1200]
  • fixed return type in language and C++ for append_row of two
    column vectors and append_col of two row vectors [#1241]
  • fixed derivative error for pareto_type_2_log() [#1223]
  • remove unused models from stan distribution (they're now in
    the stan-dev/example-models repo on GitHub) [#1249]
  • squash compiler warnings and fix windows tests (mostly
    signed vs. unsigned, as usual) [#1257]
  • fix memory leak in ODE solver [#1160]
  • fix overflow in gamma_p function to throw instead [#674]
  • make sure multiply_lower_tri_self_transpose returns a symmetric
    matrix [#1121]
  • fix overflow in Poisson RNG to throw instead [#1053]


  • manual updated for 2.6 [#1081]
    • new chapter on software process (thanks to Sebastian Weber
      and Tony Rossini for help)
    • new chapter on sparse and ragged arrays
    • pointers to Julia and MATLAB interfaces (yay!)
    • vectorization of CDFs described
    • fix priors on IRT models
    • added discussion of multiple change points
    • remove range-contstrained scale priors
    • clarified fixed parameter call
    • remove references to "std::vector" in favor of "array"
    • corrected signs for lasso and ridge and discuss truncated gradient
      and absolute zero results
    • extended discussion of Gaussian process priors (thanks
      to Aki Vehtari, Jon Zelner, and Herra Huu)
    • remove bogus paths to models and replace with pointers to
      example-models repo
    • clarified Wishart/inverse Wishart parameterizations w.r.t. BDA3
    • fixed exp_mod_normal definition
    • fix student-t reparameterization
    • fix hurdle distribution definition


Thanks to all the users who contributed code and doc corrections
and comments: Alex Zvoleff, Juan Sebastián Casallas, Gökçen
Eraslan, seldomworks [GitHub handle], Avraham Adler, Sebastian
Weber, Amos Waterland, David Hallvig, Howard Zail, Andre Pfeuffer,
Bobby Jacob, Cody Ross, Krzysztof Sakrejda, Andrew Ellis, John Sutton