Squashed 'pystan/stan/' changes from a74b1ba..3ba4dcc

3ba4dcc Merge pull request #784 from stan-dev/feature/issue-781-v2.4.0
a9e16af updating doc to right date
c46865b Merge branch 'develop' into feature/issue-781-v2.4.0
3ede4d6 release notes for Stan C++ 2.4
2f575ca updating artifacts to v2.4.0
e0b24a7 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
58f6728 Merge pull request #773 from stan-dev/feature/issue-677-check-function-sigs
3d2bfd6 Merge pull request #770 from stan-dev/feature/issue-668-next-manual
655c74a Merge pull request #764 from stan-dev/bufix/issue-763-arm-typo
9901c80 Merge branch 'develop' into feature/issue-677-check-function-sigs
ad4c13c updating makefile to include function signatures as tests and updating git ignore
843fdd6 Merge pull request #775 from stan-dev/feature/cmdstan-issue-21-elapsed-time-printed-twice
77629da Merge pull request #772 from stan-dev/feature/rstan_issue90
c23b270 added missing function sigs tests:
9cc4b41 updating command.hpp to use std::cout for message stream.
d27c898 added rest of missing function signature tests
7482ca6 added missing function sig tests
2922fbe removing extra .cpp file
13e4cf7 Delete .gitignore.orig
2729744 Merge branch 'develop' into feature/issue-677-check-function-sigs
996479e added operator function sig tests
4f4cca7 Some typo fixes for 2.4 manual
e068d4a Merge pull request #769 from alyst/fix_check_cholesky_corr
d748a4c Merge branch 'develop' into feature/issue-677-check-function-sigs
86801c8 split function signature tests into individual tests
8f2d727 moved dims, size, mdivide function sig tests
019d036 added multivariate distribution function sig tests
21e1650 add sort_indices function-sig tests
58e8ecc reserve the size of values vector of the sampling recorder
bc7b717 added to_matrix function sig test
1b509c1 added rest of matrix function signature tests
eb22fd4 release candidate for 2.4 manual, completes issue #668
b1af904 refactored more matrix function sig tests
4e36f1b added matrix function sig tests:
43c4bf8 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-668-next-manual
b712634 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4549f67 added matrix/array function signatures for:
b6818a1 added rest of real function sig tests
4b18a68 updated function signature tests
b29dfc5 Merge pull request #759 from stan-dev/bugfix/issue-734-user-fun-name-var-conflict
57adf86 removed extra files
57874d3 merge develop
0f46a60 Merge branch 'develop' into bugfix/issue-734-user-fun-name-var-conflict
1f9174b refactor check_cholesky_factor_corr test
da165d0 fix check_cholesky_factor_corr()
5812d7d Merge pull request #758 from stan-dev/bugfix/issue-733-function-void-args
43a7072 rewrote logic of void check for user-defined function args to actually fail when it should
cc7a5a7 Merge branch 'bugfix/issue-733-function-void-args' of https://github.com/stan-dev/stan into bugfix/issue-733-function-void-args
c7e1e30 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c7921f6 Merge pull request #767 from alyst/fix_self_transpose_doc
3ded970 fix typo in multiply_lower_tri_self_transpose()
16c3569 updating test model -- had a typo
e5f2fa8 Merge pull request #751 from stan-dev/feature/issue-652-remove-nesterov-optimization
2a293f7 Merge pull request #746 from stan-dev/feature/issue-331-error-message-1-indexed
0cba5ed Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c21a4d0 fixed typo in 12.3 ARM
6911d56 Merge pull request #744 from stan-dev/feature/issue-743-von_mises-pi
2a075ca Merge pull request #716 from stan-dev/feature/issue-413-cholesky-corr-type
4f77b2d adding test for 1-indexed check_corr_matrix message
b03d526 Some typos fixed in programming.tex
c126722 fixes issue #734 by disallowing user-defined function names as variables
404abdc completes fix for issue #733, by printing warning and failing if user-defined functions contain void type arguments
e67855f Merge branch 'develop' of https://github.com/stan-dev/stan into develop
fc4b0df reorder factor_cov_matrix args to match convention, add remaining tests, completes fixes for issue
02044f9 fixed bug in K==2 boundary condition for factor_U, with test
7d45516 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-413-cholesky-corr-type
5928850 Update README.md
2d5b27b Merge branch 'develop' of https://github.com/stan-dev/stan into develop
9ab1917 added trnasform test for range
c21b5f4 updating gitignore
904a5ca removing nesterov option from command.hpp
74a3b84 removing nesterov from argument list
da7635a updating test with a failing test case for the expected behavior
686b0e7 adding unit test for arg_optimize_algo
02c5553 Merge pull request #741 from stan-dev/feature/issue-740-gitignore-testmodels
01dbdbe Merge pull request #750 from stan-dev/feature/issue-749-fix-arg_init
fa54ebc updating arg_init. The test for this is in CmdStan.
3033bb8 changed order of factor_U and removed unused factor_L
aef2ec7 Merge pull request #729 from stan-dev/feature/issue-726-move-executables-to-CmdStan
f549c28 Merge pull request #608 from stan-dev/feature/fix-issue-589-vectorize-multi_normal
d614c3f Update von_mises.hpp
3cc9c5b added a ifdef for ERROR_INDEX
3ab93c9 replaced TWO_PI with 2*stan::math::pi()
e19d4fe removed unused commente code from transform.hpp and upgraded to multiply_lower_tri_self_transpose in corr_matrix_constrain
05ec8c7 Merge branch 'develop' into feature/issue-743-von_mises-pi
745d768 Merge branch 'feature/issue-413-cholesky-corr-type' of https://github.com/stan-dev/stan into feature/issue-413-cholesky-corr-type
aa7fa6c Merge branch 'develop' of https://github.com/stan-dev/stan into develop
a6c1d9c Merge pull request #747 from stan-dev/bugfix/issue-742-ARM-Ch2
18d46e0 fixed R script, updated README, polls.dat now has 1 row per survey
9609e7b Merge branch 'develop' of https://github.com/stan-dev/stan into develop
def020c fixing call to dom_err_vec
9810407 Merge branch 'develop' into feature/issue-331-error-message-1-indexed
872d0a7 fixes #743. Instead of PI, multiplied by 2 and called it TWO_PI
40c4d80 Merge pull request #728 from ariddell/feature/vs2008-iterator
b5c48a5 Merge pull request #719 from jrnold/doc-fix-formatting-reserved-names
5ad470e signatures
db9f996 Merge pull request #587 from stan-dev/feature/lbfgs
2984166 Merge pull request #717 from jrnold/minor-fix-doc-cholesky_corr-cov
0d4f3ce Merge pull request #739 from stan-dev/feature/issue-696-remove-tabs
11d13e4 Merge branch 'develop' into feature/issue-331-error-message-1-indexed
189b14d Merge branch 'develop' into feature/issue-726-move-executables-to-CmdStan
5778d3f Merge pull request #738 from stan-dev/feature/issue-737-check_positive_ordered
8a48996 Merge pull request #732 from stan-dev/bugfix/issue-723-functions-in-23
7551d81 updating .gitignore to ignore generated .cpp files and not ignore .stan within test-models
950686d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
e420f31 removed tabs in stan and test files
5f484a3 Merge branch 'develop' into feature/lbfgs
8a41bc5 Merge pull request #736 from stan-dev/feature/issue-725-remove-main
5bafc65 Merge pull request #727 from stan-dev/feature/issue-382-remove-cout-cerr
cc854dd Merge pull request #709 from stan-dev/feature/ARM
96da563 Merge pull request #687 from stan-dev/feature/issue-675-check-autodiff
99dfeb7 Merge pull request #710 from stan-dev/feature/issue-491-add-litters
225c45b Merge pull request #718 from jrnold/doc-fix-variable-names-conflict
15b21a6 Merge pull request #722 from jrnold/doc-typo-effective-sample-size
56eb15b adding int_fun that .gitignore previously masked
ec60b40 updated all code so it is 1-indexed
3e63de1 adding error_index as a trait
ca7304d adding tests for 1-indexed messages in matrix checks
365420a removing duplicate name in error message
d41a9f2 updating spec and test for check_positive
69ae88c updating spec and test for check_positive_ordered
0b5f3da updating spec and test for check_positive
1f1bea8 updating spec and test for check_positive_ordered
fdb4165 changed call to log_prob in bfgs
77004d8 Merge branch 'develop' into feature/lbfgs
dde8d5d updating with failing tests for 1-indexed error messages
a441904 modified make/tests for bfgs tests
c8751a2 added do_bfgs_optimize test
0d1e811 added bfgs tests
21765f9 added lbfgs_update tests
791273c adding test for 0 vs 1 indexing within dom_err_vec
3e584a5 added template parameter for dom_err_vec to handle indexing
e026ba6 removing --no_main option from makefile
03b9402 removed ability to generate main
e0b6888 adding test to show that 'int main' isn't in the generated code
b7bb18b fixed typo.
127339e added bfgs_update tests
2e7f33a added bfgs_linesearch tests
bf1e3ad Merge branch 'develop' of https://github.com/stan-dev/stan into develop
7841f35 hopefully final patch for issue #723 with model test and moving scope of reset on symbol table to the parser from the compiler
c57e9fa Merge branch 'develop' of https://github.com/stan-dev/stan into bugfix/issue-723-functions-in-23
1cb8d12 Merge pull request #730 from gokceneraslan/patch-1
23a9b8a Merge pull request #721 from jrnold/doc-typo-boolean-operator
9dde314 Typo fix: delcare->declare
5d748a7 removing 'bool include_main' argument from generate_cpp
d3b9c34 removing ability to generate main from the generator
971bce6 adding test for generate_cpp() so it can be refactored safely
78b66a8 Merge pull request #720 from jrnold/doc-typo-in-stan-bnf
6365168 removing bin/stanc and bin/print from Stan
0cb196e Merge pull request #713 from stan-dev/feature/minor-fix-for-pow-infix
5a10d58 Use const_iterator to resolve Visual Studio 2008 compile error
9ac8702 fixes all three points of issue #723
34f6f95 adding function signatures test for multi_normal
9626096 Added missing '.'
197587e functions signature
8f559e3 removed rest of std::cout from tests
c813ac5 removed rest of std::cout from tests
3114347 updated ch24 ARM models
34b60f9 Merge branch 'develop' into feature/ARM
ab0726e updated rest of Ch17 ARM models with R files
9e93747 updated 17.1-17.3 models with R file
781d424 fixed file names so they work with wiki links
0a46240 remove template<> specification on int-only functions
20f0788 added reset for function signatures in the stan compiler
f0b6712 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
5627d4e added rest of ch17 prelim models
5169c2e Merge branch 'develop' into feature/issue-675-check-autodiff
0219e5d removed stan::agrad in Phi_approx
4525287 Merge pull request #686 from stan-dev/feature/issue-527-normal-rounding
7de20f2 Merge pull request #660 from alyst/elt_ops_extend
e54dcf0 functions signatures
3b3a700 multi_studen_t: correct return when we have zero length input (consistent with multi_normal and friends)
137ec70 Fix some mistakes I made while resolving merge conflicts
fb4e1e2 removed easy std::cout calls from tests
7887214 typo in the equation of effective sample size
f28e6d9 fix formatting of some inline code
34d884a missing quotation mark in Stan BNF
14f9992 fix formatting of reserved names
251222f Variable names do not conflict with functions block identifier
564b2cd removed references to choleksy_(cor|cov) types
04c9e4d added 17.3-17.6 preliminary models
50caa6b add 17.2 models and changed naming of 17.1 models
c358750 added preliminary 17.1 stan model code
62eb150 Create radon_wishart.stan
6713ec3 finished merge with current develop
c4bdf0e Merge branch 'feature/issue-413-cholesky-corr-type' of https://github.com/stan-dev/stan into feature/issue-413-cholesky-corr-type
0df39d5 got rid of commented-out lines in exponentiation_expr
460cfae Merge branch 'develop' of https://github.com/stan-dev/stan into develop
061220e Minor fix to operator ^
d440518 fixed item response model typo
5019c2d Merge branch 'develop' into feature/fix-issue-589-vectorize-multi_normal
bdb6f44 functions_signatures
3d916d8 renamed stan files
dbd2638 added bugs_example/vol1/litter files
eb3b7a4 Merge branch 'feature/issue-491-add-litters' of https://github.com/stan-dev/stan into feature/issue-491-add-litters
3a622bb Create litter.stan
d9028a4 Merge branch 'develop' into feature/issue-675-check-autodiff
fb15647 removed prob and math lib dependencies on autodiff
a51eafd Merge branch 'develop' into feature/issue-527-normal-rounding
0e35ee6 moved *SQRT2 om LHS to *INV_SQRT_2 on RHS
9e3dec7 Merge branch 'develop' into feature/ARM
de87714 fixed rest of ARM models
be2dd9a fixed Ch16-20 ARM models
92c6764 fixed Ch9-15 ARM models
a3c8a08 fixed Ch.8 ARM models
cf70d8c Merge pull request #704 from stan-dev/feature/vm_rng
df43c23 fixed ch7 ARM models
ffdc8f7 Merge pull request #694 from stan-dev/bugfix/issue-688-ordered-logistic-rng
0e67234 fixed ch6 ARM models
a1a0509 fixed ch5 ARM models
c266cb9 fixed ch3 and ch4 ARM models
49b566c Merge pull request #663 from stan-dev/feature/issue-644-inv_wishart_rng
3fe43c4 Merge branch 'develop' into feature/ARM
d3e0f2b adding placeholder tests for do_bfgs_optimize.hpp
56a1727 adding placeholder tests for each untested method in lbfgs_update.hpp
02b2865 adding placeholder tests for each untested method in bfgs_update.hpp
9b7e296 adding placeholder tests for each untested method in bfgs_linesearch.hpp
d07ceee adding placeholder tests for each untested method in bfgs.hpp
9f0f105 split out tests into appropriate test files
fbf9bc9 fixed indexing in von_mises chi square test
f34f157 added copyright information
c1435d9 updated model_header.hpp to include fwd mode autodiff files
3cbbd43 updated range of vm_rng in manual
53a7064 fixed von miss rng and added more tests
eafda80 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
a06b21f updated range of return values for von_mises_rng
07160df added doc
6470851 added von_mises rng to function signatures with test
bfadcb1 fixed von_mises_rng and added chi square goodness of fit test
0b40a12 Merge branch 'develop' into feature/vm_rng
221e785 Merge pull request #658 from aadler/patch-1
0c0d2bf Merge branch 'develop' into bugfix/issue-688-ordered-logistic-rng
70ea82e refectored function_sig tests for:
2e79993 refactored distribution function signature tests for:
d6db531 refactored distribution function signature tests for:
8f46224 refactored distribution function signature tests for:
908a121 moved hypergeometric function-sig tests
c3f01f0 refactor beta_binomial function-sig tests
c340761 moved and refactored binomial function_sig tests
8eb6f8a mover bernoulli function signature test
61a1caa update gitignore file
3b657e0 Merge branch 'develop' into feature/issue-675-check-autodiff
355c21c Merge branch 'develop' into feature/issue-527-normal-rounding
1288c9b thanked Matius Simkovic in the acknowledgements
0d1b705 fixed ordered_logistic_rng indexing
de59831 change ordered_logistic_rng test case so it fails with current code
36e0438 merge develop
e710d56 support scalars in elementwise division (./)
cfd864e fixed mdivide_left_tri_low for fvar
f36e80a fixed eigenvalues_sym and eigenvectors_sym tests for fvar
e6bd922 broke apart trace_quad_form tests
db166f8 fixed log_softmax using statements
b8d24e4 split fvar version of trace_quad_form and trace_gen_quad_form from math version
f0ebf4b added manual doc about behavior of normal_cdf functions
52fd791 fixed test name
e8bc3ff added ccdf_log tail tests
e58753e fixed singular_values so it works with higher order autodiff with tests
50de6e3 fixed cholesky_decompose so it works with higher order autodiff with tests
d31c0b9 added includes so eigenvectors_sym works with higher order autodiff with tests
b7f8722 added includes so eigenvalues_sym works with higher order autodiff with tests
3dca5d6 fixed includes for inverse_spd for autodiff types and added tests
7c79834 fixed fwd/inverse includes
5072f5b fixed log_sum_exp so it works with higher order autodiff and added tests
9467ef7 generalized trace_gen_quad_form for autodiff types and added tests
8f72715 fixed includes for quad_form
d199fe0 generalized trace_quad_form for autodiff types and added tests
250f68c added fvar higher order quad_form tests
9c6035e generalized quad_form to handle fvar and var
3dedf8e added fvar tests for rank
5e2c645 added higher order tests for log_softmax
9906117 updated test names
5adb7fc fixed rounding error for normal_cdf, normal_cdf_log with tests
8a7a9c6 fixed test naming for math/matrix head,segment,tail,subcol,subrow
83da591 added fvar tests for segment
478380d added fvar tests for tail
74f3724 added fvar tests for head
646635b added fwd mode tests for sub_col
610fda3 added fwd mode tests for sub_row
172be16 added more third order autodiff tests for:
c4ba8f3 Merge branch 'develop' into feature/issue-675-check-autodiff
ec98978  Put WolfLSZoom() in an anonymous namespace.
4f84eef Test BFGS update structures and optimization termination conditions.
8b3f40f Break out the BFGS initialization function.
88edef2 Basic unit tests for the quasi-newton updates.
b1c67f1 Merge branch 'feature/lbfgs' of https://github.com/stan-dev/stan into feature/lbfgs
1c454f1 Fix bfgs unit test.
cbb23c1 Merge branch 'develop' into feature/lbfgs
aa9a25e  Merge branch 'develop' into feature/issue-644-inv_wishart_rng
357ee57 Merge branch 'develop' into feature/lbfgs
fe75dd3 fixed 3rd order autodiff tests for:
2179c0e fixed 3rd order autodiff tests for matrix functions:
dbd67df added sign and phi_approx tests for higher order autodiff
ca3b4eb added higher order autodiff tests for gamma_p and gamma_q
37f4035 added higher order autodiff tests to binomial_coefficient_log
55d7a91 fixed 3rd order deriv tests for all other functions
a94cfdc fixed 3rd order deriv for functions
51d9ab9 fixed 3rd order deriv tests for atan, atan2, atanh
b89dd6b fixed 3rd order deriv tests for abs, asin, asinh, acos, acosh
5e1afc9 fixed 3rd order deriv tests for operators
01668ce fixed 3rd order deriv test for log1m, log1m_exp, log1p, log1p_exp
f8e1836 Merge pull request #669 from casallas/feature/ARM-patch22.4
e212ecb Fix do_bfgs_optimize.hpp to pass header tests.
a5c743b Merge branch 'develop' into feature/lbfgs
7e17ce3 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-644-inv_wishart_rng
e1a406e Merge branch 'develop' into feature/fix-issue-589-vectorize-multi_normal
a3f7400 inv_wishart_log: fix wrong matrix type
4e9ca8f arm-22: Fix anova_radon_nopred.stan, generate Fig. 22.4
97d517c Make more explicit that scale and outcomes matrices of (inv_)wishart are symmetric and positive-definite
571b96e add mixed type unit tests for multi_student_t
27f3b14 add mixed type unit tests for multi_normal_cholesky and multi_normal_prec
3111408 add mixed type unit tests for multi_normal
a291252 Added mixed double/var tests for multi_normal
e83bd75 multi_normal_cholesky: this test was added again by mistake when soving merging conflicts
1738cff Merge branch 'develop' into feature/fix-issue-589-vectorize-multi_normal
c046e31 (inv_)wishart_log: use only the lower portion of the outcomes and scale matrices and adds tests to check that property
f13b0ab wishart_rng and inv_wishart_rng now only takes the lower part of the scale matrix
9454871 Marcus's suggestion & use TWO_PI
90acfc4 Spoke too soon
a776854 Only once times pi
5259472 Also check number of gradient evaluations.
5b4b172 Refactor code to prevent duplication with (BFGS-based) optimization routines.
1328c72 Fix some code comments in io/reader.hpp
1fb659c Add a unit test of (L-)BFGS based on the standard 2D Rosenbrock function.
f45df8f Change default convergence tolerances so that we get reasonably close to the minima of the Rosenbrock function.
97bbd10 Refactor some BFGS linesearch code into it's own files.
1f0d323 Refactor the quasi-Newton updates into their own files.
4a5427c Ensuring range is 0 to 2pi
afdff88 Change delta to s
6cfa0fc Update von_mises.hpp
8214bcf Organize special rng tests for (inv)wishart
f2bca8b added von_mises_rng with error checks
7b9448c Merge branch 'develop' into feature/lbfgs
980b947 wishart_rng: turn scale into a symmetric matrix and adds an unit test.
3b3b893 Possible fix for both inv_wishart_rng and wishart_rng
f28c5ce inv_wishart_rng: transpose needed here to be consistent with R chol behaviour
44c8ce4 Possible fix for inv_wishart_rng
4b44513 Some more unit tests for multivariate distributions
abec89f Fix issue 305: remove unused multi_normal over matrix outcomes
fd656c5 Add gradient tests to vectorized multivariate distributions (multi_normal and friends)
821f06e elaborate LKJ transformations
6208882 correct explanation of Jeffreys prior
60b67b2 make lkj_corr_cholesky() work the way it is supposed to
08c4884 do not use srand anymore in lkj_corr_test
ec8877b hopefully accelerate do_lkj_constant
b2ad6bb make lkj_corr_log not depend on lkj_corr_cholesky_log
4308d0f updated reference manual Jacobians math steps
9f1b30f cholesky corr type tested and documented
8ad9736 Merge branch 'develop' into feature/lbfgs
b9ae421 merged changes, mostly to validation return types vs. passed refs
e23b196 Document the new convergence options and mention L-BFGS.
46cafed Fixed good and bad values for history_size option.
0e511a3 Fix relative gradient convergence test.
06022f1 Merge branch 'develop' into feature/lbfgs
c1eae30 Consolidate BFGS-based optimization parameters.  Also, add a new convergence criteria.
dd05e45 Added more tests to basic_estimators/normal_multi.stan
84e268b Some other small improvements to multi_normal and other vectorized multivate
d37bd3e Some small improvements to multi_normal and other vectorized multivate
bc9c4b1 Change the relative convergence parameter to be scaled by the machine precision.
5d6bf80 Add a convergence test based on the relative change in the objective function.
fca62ce Check that the strong Wolfe conditions are satisfied in the line search unit test, also correct some function documentation.
a1dab08 Remove BFGS line search support functions from anonymous namespace since we're unit testing them seperately.
54895e8 Check return code of WolfeLineSearch in unit test.
ec0438b Remove unused template parameter and add more function documentation to bfgs.hpp
d95edee Remove unused (and not particularly desirable) back-tracking linesearch method.
3ec4b4f Add some more function documentation for BFGS.
6ad403d Add unit test for WolfeLineSearch().
abe3575 Unit test CubicInterp function.
9f0d378 Add code documentation for the BFGS support functions.
5a2734c Fix some unused variable warnings
8e5c0b7 added doc for vectorized multi_normal_prec, multi_normal_cholesky, multi_student_t
772a974 added doc for vectorized multi_normal and added subsection in vectorization chapter to describe how it works
9d21e54 Changed "response variable" to "random variable" to be consistent with the Stan
d04b8eb vectorization of multi_student_t_log
bdde24d Vectorization of multi_normal, multi_normal_prec and multi_normal_cholesky + tests
94af2a6 Added vectorization to multi_normal_log
e2e1353 test commit
72410f5 Merge branch 'develop' into feature/lbfgs
deb7251 Added basic unit test for L-BFGS.
7000930 Enable L-BFGS in command.hpp
ec8e102 Implementation of L-BFGS.
1648d79 Factor out the Quasi-Newton update into its own representation to prepare for L-BFGS.
55c13ab Restructure BFGS options for reuse in LBFGS.
256e0d6 Switch to maintaining the inverse Hessian in BFGS.
8704e25 Merge pull request #516 from casallas/feature/ARM
b72dd77 restored .gitignore from current develop
6ddeec6 updated sesame_street1 for prior scale (sd, not prec), vectorized, and moved transformed parameters to local model variables
48ef488 removed .gitignore to merge
ad2fc4e 2.3_CI.R: Vectorize CI calculation for fig. 2.3
2ec94ad merged transform.hpp
102841b intermediate state of Cholesky to allow pull of Ben's code
343a95a add test of factor_L
1b7b502 fix factor_L()
2a0389b Merge branch 'feature/corr-cholesky-type' of https://github.com/stan-dev/stan into feature/corr-cholesky-type
f60a39e add factor_U and factor_L functions to transform to CPCs
ca1fc7a added stubs for all of the cholesky corr factors, w/o tests
0c8070c added ch16 and ch18 of ARM from Sergio (stan-users)
d954c79 updated CHR model files
248b47c scaled priors for CHR models
6dec1a2 scaled priors for CHR models
3fe5f39 removed centering from unnecessary models
28d4426 removed samples.csv
5273259 updated CHR model files from Ch20-25
9a22998 modified ch5 and ch9 with Sergio's codes and updated all README files
3c15ef0 updated rest of model files
9eefb73 cleaned up models up to ch15
d6c3527 cleaned up model files up to ch11
6ef5f1b updated ch23 models
880b16b added fixme's for missing data
aabb9a5 fixed graphs in ch23
1855d60 fixed ch9 graphs
3489911 added ch25 README
84563fc added README files for ch19-24
e8fcaad added README files up to ch15
ae265c3 fixed normal prior distributions
787f18f added matt trick to ch20-23
49e5480 added matt trick up to ch15
9ce6b4f added matt trick to ch12/ch13
8925ada added rest of ch23/24 data files
930c475 added ch23 data files
9f42e43 added data files up through ch22
c836285 added ch19 data files
993a3c5 updated/added data files for ch 2-14
8fa7e32 added ch25
7c2f681 added ch24
8cb82c5 added rest of ch23
be46768 added ch22 and part of ch23
a2cd71e added rest of ch21 ARM
838fbe2 added Ch 21.2,21.3,21.5,21.6
8e7c870 added ch20 models
e6fc5e6 added 19.6 models
03be0cd added 19.5 models
1b2299d added ch19.2,19.3,19.4 with models
b7a4abd added ch9 and c11 readme files
65b87aa removed readme markdown
38a288c updated ch3/ch4 readme
85b4636 fixed ch3 readme
11e29a6 updating readme file test
19001bf changed README filetype
ec66d7b adding ch15
10cb892 updated format of README files and added ch8 readme file
2c98eb7 added ch14 models
407f873 fixed models in ch13
205bca6 added 19.4,19.5 stan model code
33b9523 removed excess data files
e16dab0 added ch13 models
f904923 updated ch12 models
ada420d updated ch12 models
abc9d4e added ch19 stan model files
cec4aaa added ch14 data and added note for 8.3
e5f8fbf added most of ch13 ARM
20712ed added .RData to gitignore list
6484b63 fixed 12.6 and 12.8
06762e1 added ch7 readme
c1f096b added ch6 README
3ecf4dc added ch.5 readme file
2d8b96b updated ch12 and ch11
1678836 updated ch9 and ch10
52ada76 updated ch.8
9444da8 updated ch 7
ec05440 updated ch6 models
3b24f44 added new ch3 and ch4 from Sergio (stan-users)
f5137cc cleaned up rest of ch.5
9e2b4bf cleaned up 5.2
38bef8b clean up 5.1
fd44a98 added 12.8 with note
72f8edf added 12.6
1b11113 added 12.6
ab14c48 added 12.4
0e7afe6 added 12.2 and 12.3
45b89bf added part of 8.3
7c6dadf added 8.3 roach model1
9225e57 fixed 7.2
c4f2306 added part of 4.7 model graph
f443a36 fixed minor typos
beeafe0 removed coment in 9.3
2649fcc fix 8.4 graph
1bcb207 removed sm.RData files
da7d316 fixed plot in 9.4
6ec51c8 added 8.3 multiplot
4500a52 updating ch9 ARM
83d5065 fixed ch9 multiplots
c1f4cad cleaned up most of ch9.3
0da25a9 fixed most loops in 9.3
66313e6 added ch11 missing data file
0e5ba22 cleaned up files
67b7148 fixed stat_function loop issue
bd98c07 fixed all of ch7 except 7.2
25e2a78 cleaned up ch4 and ch7
e3ec584 removed calls to sim() in ch5/6
b206b5f removed calls to sim() in ch3
ba41b18 removed calls to sim() in ch4
abbb117 added 10.6
154d6bd added 10.3 (missing data), 10.4
b50af4f added part of 9.5
a041b64 added ARM 9.4
d504c69 fixed Figure 9.6 in ARM 9.3
0bd7510 added graph in ARM 9.3
50b54bd added part of ch9.3
d2b1bd8 added 8.4 ARM
8756c0c added part of 8.3
47bd774 added Ch8.3 file to be added later
4ce185f added Ch 8.2
4775dd9 added 7.4 ARM
6e0f9de added Ch7.1,7.2,7.3 in ARM
918084f switched to library(rstan)
264b312 added missing graph in ARM Ch 3.5
eb204a4 added Ch6 of ARM and cleaned up earlier chapters
2251db8 finished/fixed Ch.5 ARM code
053b08d fixed all of Ch5 ARM except 5.8
0d3e2a2 added most of Ch5 in ARM
f06b50b added ARM Ch5.5
f2001d2 added ARM Ch5.4
f28c342 added Ch5.2 of ARM
2965bea added ARM Ch5.1 R code
65a1c1c added R code for ARM Ch 4.6
c7230dd added R code for Ch4.1-4.5
871cf55 added ARM files for Ch 2
322fe57 added ch 3.7 code with new data files
7889422 added R code using ggplot2 for most of ch3.1-3.6
0bd82fa removing old files
48ae612 added ch12 models (sesame and radon)
3166aa9 fixed sesame model
537b129 added ch10 models
de49553 added rest of ch9 models
0c64420 cleaned up more model directory files
49932be added grades simulation model from ch8
26c9753 added congress model from ch7 and cleaned up other model directories
ea12287 added most of ARM models from ch4-7

git-subtree-dir: pystan/stan
git-subtree-split: 3ba4dcc0f03d02034a02445792b9bdbcd6010019
Update to Stan 2.4.0

Merge commit 'a6ccd53a67b1172ee55bf14ba647546e74047170' into feature/2.4.0
Update wrapping code for Stan 2.4

No substantive changes; mirroring RStan's stan_fit.hpp
TST: Update tests for 2.4.0
TST: Remove unused tox.ini
TST: Try quieting conda to fix travis-ci errors
DOC: update notes on Windows install
DOC: Update docs for 2.4.0
Improve fit summaries with large numbers

This is a temporary fix pending improved code. PyStan still rounds to 1 decimal
place which is not RStan's behavior.
DOC: Add note about fix for fit summaries
DOC: Minor adjustments to README and release instructions
Fix bug where pip -e would not run install_clib

Hopefully closes a long-standing bug where one could not install from source
with ``pip install -e .``
TST: Update travis-ci miniconda
Display fit summary fitting into a reasonable number of columns

This solution seems relatively robust. Many wheels reinvented. Closes #75.
BLD: Allow building of Python wheels with pip and setuptools
TST: Test against OS X and Linux on travis
API: Make LBFGS the default optimizing algorithm
Fix typo in stan args defaults
Release PyStan 2.4.0.1
Revert "Fix bug where pip -e would not run install_clib"

This reverts commit 4ab82fa15240956eebf886c4a64f5fcb80899d31.

Cython and setuptools' monkey patching do not appear to want to cooperate?