release/v4.1.0: updating version numbers

Author: serban-nicusor-toptal

.github/ISSUE_TEMPLATE.md

@@ -25,4 +25,4 @@ If this is a **feature request**, show what you expect to happen if the feature
 
 
 #### Current Version:
-v4.0.1
+v4.1.0

RELEASE-NOTES.txt

@@ -1,5 +1,64 @@
 Stan Math Library Release Notes
 
+======================================================================
+v4.1.0 (2 June 2021)
+======================================================================
+
+ - Added the Cash-Karp numerical integrator to improve numerical integration of ODEs with semi-stiffness and/or rapid oscillations.(#2336)
+ - Added the quantile function.(#2398)
+ - Added custom reverse mode for diag_pre_multiply() and diag_post_multiply() functions.(#2405, #2453)
+ - Optimized `multi_normal_cholesky` for non-autodiff covariance. (#2439)
+ - Updated Sundials to 5.7.0.(#2441)
+ - Improved memory safety of nested paralellism.(#2445)
+ - Updated TBB to 2020.3.(#2447)
+ - Added the `STAN_NO_RANGE_CHECKS` macro which turns off bounds and range checks.(#2423, #2437)
+ - Optimized `gp_*_cov` functions, especially for large amount of data.(#2464)
+ - Fixed compilation errors when using `unsigned` and `long` types with `apply_scalar_unary`.(#2469)
+ - Added the implementation of the loglogistic probability density function.(#2477)
+ - Adds reverse mode specialization for `csr_matrix_times_vector(sparse data, dense parameter).(#2462)
+ - Allow tbb init to set the number of threads by an argument.(#2455)
+ - Fixed a bug with expressions in poisson distribution functions.(#2414)
+ - Fixed the off by one error in set_zero_all_adjoints_nested.(#2399)
+ - Fixed bug with printing Eigen expressions.(#2436)
+ - Refactored operands and partials to avoid extra allocations.(#2418)
+ - Tidied up distributions C++ code.(#2352)
+ - Updated the integrate_1d internal interface updated in preparation for closures(#2397)
+ - Added docs for new contributors with a getting started guide and docs for contributing new distributions.(#2350, #2466)
+ - Added an ODE testing framework.(#2432)
+ - Replaced the finite difference approximation of the Hessian from one that is based on function calls to one that is based on gradients.(#2348)
+ - Updated code generation for expression tests.(#2419)
+ - Fixed a bug in expression tests and benchmark generation, where downloading `stanc.exe` did not work on Windows.(#2480)
+- Varmat:
+    - Add `rep_*` utility functions for new matrix type(#2358)
+    - `var<Matrix>` overloads for digamma, distance, Phi, inv_Phi, Phi_approx, sqrt, tail, tgamma, rows_dot_self, fma, offset_multiplier, bessel first and second kind, beta, binary log loss, ceil, erf, erfc, exp2, expm1, falling_factorial and floor (#2362, #2378, #2396, #2461)
+    - Added lb/ub/lub_constrain specializations.(#2373, #2382, #2387, #2379)
+    - Added script to automatically check stanc3 signatures for varmat compatibility.(#2434)
+- OpenCL:
+    - Fixed OpenCL implementations of distributions mostly not working with row vectors.(#2360)
+    - Added prim and rev OpenCL implementations for `to_matrix`, `to_vector`, `to_row_vector`, `to_array_1d`, `to_array_2d`, `append_array`, `reverse`, `symmetrize_from_lower_tri`, `symmetrize_from_upper_tri` `trace`.(#2377, #2383, #2388)
+    - Added OpenCL functions `rep_matrix`, `rep_vector`, `rep_row_vector`, `rep_array` and `identity_matrix`.(#2388)
+    - Added operator %.()
+    - Reorganized how work is distributed between threads in generated kernels that use colwise reductions (including all distributions), significantly improving GPU preformance.(#2392)
+    - Removed `.triangularTranspose()` member funtion from `matrix_cl` and `TriangularMapCL` enum. `.triangularTranspose()` is replaced by `symmetrize_from_lower_tri()`.(#2393)
+    - Added support for two dimensional reductions to kernel generator.(#2403)
+    - Added OpenCL implementations for functions `log_mix`, `log_softmax`, `log_sum_exp`, `rank`, `sd`, `softmax` and `˙variance`.(#2426)
+    - Added OpenCL implementations for `ub_constrain`, `lb_constrain`, `lub_constrain`, `offset_multiplier_constrain` and `unit_vector_constrain`.(#2427)
+    - Added OpenCL implementation for `prod` function and kernel generator operation for rowwise, colwise and 2d product.(#2433)
+    - Added OpenCL implementations for functions: `bernoulli_cdf`, `bernoulli_lcdf`, `bernoulli_lccdf`, `cauchy_cdf`, `cauchy_lcdf`, `cauchy_lccdf`.(#2446)
+    - Added OpenCL implementations for functions `double_exponential_cdf`, `double exponential_lcd`, `double_exponential_lccdf`˙, `exp_mod_normal_cdf`, `exp_mod_normal_lcdf` and `exp_mod_normal_lccdf`.(#2449)
+    - Added OpenCL implementations for functions `exponential_cdf`, `exponential_lcdf`, `exponential_lccdf`, `frechet_cdf`, `frechet_lcdf` and `frechet_lccdf`.(#2450)
+    - Added OpenCL implementations for functions `gumbel_cdf`, `gumbel_lcdf`, `gumbel_lccdf`, `logistic_cdf`, `logistic_lcdf` and `logistic_lccdf`.(#2451)
+    - Added a new kernel generator operation that allows writing custom OpenCL code.(#2454)
+    - Added OpenCL implementations for functions `pareto_cdf`, `pareto_lccdf`, `pareto_lcdf`, `pareto_type_2_cdf`, `pareto_type_2_lccdf`, and `pareto_type_2_lcdf`.(#2456)
+    - Added OpenCL implementations for functions: `rayleigh_cdf`, `rayleigh_lccdf`, `rayleigh_lcdf`, `skew_double_exponential_cdf`, `skew_double_exponential_lccdf`, `skew_double_exponential_lcdf` and `skew_double_exponential_lpdf`.(#2457)
+    - Added OpenCL implementations for functions `lognormal_cdf`, `lognormal_lccdf`, `lognormal_lcdf`, `normal_cdf`, `normal_lccdf`, `normal_lcdf`.(#2458)
+    - Added OpenCL implementations for functions `std_normal_cdf`, `std_normal_lccdf`, `std_normal_lcdf`, `uniform_cdf`, `uniform_lccdf` and `uniform_lcdf`.(#2459)
+    - Added OpenCL implementations for functions `weibull_cdf`, `weibull_lccdf` and `weibull_lcdf`.(#2460)
+    - Removed unused OpenCL kernels and checks.(#2463)
+    - Added OpenCL prim implementation for functions: `gp_exponential_cov`, `gp_matern32_cov`, `matern_52_cov` and both prim and rev implementation for `gp_dot_prod_cov`.(#2471)
+    - Added reference (`ref_type`) for kernel generator expressions.(#2404)
+    - Added typecast operation to kernel generator.(#2472)
+
 ======================================================================
 v4.0.1 (17 February 2021)
 ======================================================================

doxygen/doxygen.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME           = "Stan Math Library"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.0.1
+PROJECT_NUMBER         = 4.1.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

stan/math/version.hpp

@@ -12,8 +12,8 @@
 #endif
 
 #define STAN_MATH_MAJOR 4
-#define STAN_MATH_MINOR 0
-#define STAN_MATH_PATCH 1
+#define STAN_MATH_MINOR 1
+#define STAN_MATH_PATCH 0
 
 namespace stan {
 namespace math {