Bump version for next release
DOC: Fix typo
Update Stan source to commit 45a2cb1496ee46ffb51a625b75879cd4b582804b

Merge commit 'e46836df6eae10615b668ff6a10cf7d2ee842403' into feature/stan-dev
Squashed 'pystan/stan/' changes from 8de1916..45a2cb1

45a2cb1 Merge pull request #615 from ariddell/feature/chains-adapter-pystan
d74dfee Merge pull request #633 from ariddell/feature/visual-studio-2008
a5831dc Merge pull request #631 from tmalsburg/develop
12b4663 Support MS Visual Studio 2008 std::math idiosyncrasies
85fc356 Fix another typo in an error message.
fe92ace Fixed typo in error message.
02cad93 Merge pull request #621 from stan-dev/feature/issue-597-function-lang
d00fb0b Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
7887358 Merge pull request #627 from stan-dev/bugfix/issue-624-json-compare-unsigned
aeee3d4 fixed and tested conversion routing array indexing ltr_2_rtl (row-major to column major)
9eef0bb required functions ending in _log to return real
3eb6faa added check that no duplicate functions get added, updated model tests and doc to be consistent
7c526d4 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d080d92 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
66d6ed8 Merge pull request #618 from stan-dev/feature/issue-595-json
616c0de Merge pull request #616 from stan-dev/feature/QR
8efc994 adding missing functions-good2 that was hidden by .gitignore
e464095 completes functions for issue #597 and also fixes #422, allowing binary ops in constraints
8ec60d3 functions passing all tests
2df8ea1 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
d54bc6b Merge pull request #620 from aadler/patch-1
d947b16 Update all.bib
45f9481 Update all.bib
de46e08 Update all.bib
e2cbf6f Update all.bib
50f7b77 Update all.bib
2795df1 Update all.bib
17adefe Update all.bib
5d95127 correcting unit test
947aae2 Update all.bib
4200d8b Update all.bib
01b76e5 Update all.bib
c7333f6 Update all.bib
a437851 Merge pull request #617 from aadler/patch-1
a45d82f added class-level doc
4991651 removed spurious comments
d1f4b7f Update programming.tex
15b2530 Update all.bib
2a3b366 Update programming.tex
b6350c2 forgot semicolons
4df1fef Update all.bib
3f89c27 do not #include<boost/multi_array.hpp> since it is not used
4b207b7 forgot to add two headers
61aec00 Allow construction of stan::mcmc::chains using vectors (rather than Eigen)
6d5c3c6 reverted command.hpp to use io::dump
c0d1d73 parser handles unicode escapes, checks for number range errors, more unit tests
7c9677f functions feature complete with doc and tests all passing
5fbaf16 patched generator behavior for function declarations to avoid body
b53e652 fixed template parameter and return type generation errors for int function params
af8d86b clean up QR decomposition stuff
74069a8 added support for return checks for void functions
97e9d8e Merge branch 'feature/QR' of https://github.com/stan-dev/stan into feature/QR
f75d7c0 added include for forward-mode and qr_Q tests now passing
d745fd4 reorganized location of functions chapter
d91833b introduce qr_Q and qr_R functions (fwd-mode broken)
3f801cf Merge branch 'develop' of https://github.com/stan-dev/stan into develop
761038a fixed and tested error handling and messages in functions to match doc in manual
3b8c880 removed C++11 to_string in favor of boost::lexical_cast
3f57fdf fixed char vs. string comparison bug in parser tests and fixed associated tests, all of which reflected bugs in tests, not in parser
2a32ff8 fixed bug in error testing parser mismatch check so now checking again
4b47c8d generated models for all function uses cases now compile with templates
ed38169 all legal scopes of functions and argument scalar types tested
c4fde5e added test model file, updated language section of manual, more functions as statements
477dd34 command reads data in JSON format, added more checks, tests, to json_data
f102305 simplified ast, added _lp and _rng functions and parser constraints
7221e8c unit tests for json_data_handler
8c08678 fix return in matrix/initialize for clean compile, added tests for return of correct type
fe35e67 json data handler and unit tests
1ccc5ed removed redundant bare_type, test return only from functions with error msg otherwise
03e1d9a functions working through mutual recursion; no check on returns yet
bcb3376 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
3dfc813 adding necessary grammars to previous commit
bae8024 basic function example compiling and running
dacb441 Merge pull request #606 from stan-dev/feature/fix-issue-244-scale
9ddc2e3 more unit tests, better parser diagnostics, added json.hpp
7284c47 unit tests for strings, bugs fix
11150e4 more unit tests, fixed parser bugs, added error messages
6acf501 fixed bug in parser, added more unit tests
e0affd5 added json parser with base handler and exception, and tests -- no UTF-8 validation or Unicode escapes
2d1607e removing unnec. includes
218bf11 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c9e9cc0 Group quad_form_diag with quad_form in the manual
4fcdad1 Renamed function scale to quad_form_diag
447a31f Applying changes recommended by Marcus Brubaker
70dc1ac Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
18b87da Some small improvements to diag_pre_multiply and diag_post_multiply
ad0c0dd Added function matrix scale(matrix, vector), relevant unit tests and documentation
90d09ae added validate equal in similar fashion to validade_greater, validate_greater_or_equal, etc
04f36a9 Merge pull request #600 from stan-dev/feature/more_nuts_tests
144fc51 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-597-function-lang
73c0944 Merge pull request #594 from stan-dev/feature/fix-issue591-nb_rng
22d9c08 more principled patch for issue #422 with tests
20a1ae4 adds template for function grammar, fixes issue #422
7efbe16 Merge pull request #601 from stan-dev/feature/travis-ci
134b18a updating travis script
868ef22 updated neg_binomial_rng test to use the neg_binomial_log to generate the expected values
bffc851 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
468003b fully specifying call to boost::math::pdf
0442557 Merge pull request #565 from stan-dev/feature/fix-cross-compilation
9c8a8f7 Merge pull request #555 from stan-dev/feature/neg_bin
753b066 Unit test to check the NUTS slice criterion
c0c5a19 more fixes for cross-compilation on Linux
0a1b086 Merge branch 'feature/fix-cross-compilation' of https://github.com/stan-dev/stan into feature/fix-cross-compilation
7e6b27a adding tests to make sure c++ syntax is correct
f41f6e1 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
b98cbd9 Fix neg_binomial_rng
dc8d8fc renaming test
3a9e0c0 Merge branch 'develop' into feature/fix-cross-compilation
a8fd956 Merge pull request #570 from stan-dev/bugfix/issue-530-no-model-parameters
e96fbc8 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
f1373d2 Merge branch 'develop' into bugfix/issue-530-no-model-parameters: moving test to CmdStan branch bugfix/issue-530-no-model-parameters
0d69427 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
47e9541 Merge pull request #585 from stan-dev/feature/c++11
7ebc325 Fixing unsigned warning.
052030c updated transform param sample to increment_log_prob, removed false positives for linear transforms, tests
3f7959a Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
cf93279 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
add3680 squashing more warnings
415ebf7 squashing warnings
36bccc6 fixing typo in the generator
ce69af0 testing: moving models out of syntax-only
6c61b66 Merge branch 'develop' into feature/c++11
6c82b59 Merge pull request #588 from stan-dev/feature/issue-405-refactor-command
9c3a259 Fix typo in stan/prob/distributions/univariate/discrete.hpp
f7db402 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4740ea1 Expanding documentation for neg_binomial_2 (forgot to finish sentence)
d2f7d5a Expanding documentation for neg_binomial_2
acede17 Small improvements to neg_binomial_2
ecc42dc add sign tests for rev and fwd
0f200ad Merge pull request #582 from aadler/patch-2
0a7bc82 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
0124c62 refactor: split tests into two tests
60e318b refactor: split tests into two tests
7fd5746 refactor: split tests into two tests
bddf084 Merge pull request #573 from stan-dev/feature/issue-571-const-chain
cfc7ffe adding conditional_condition_bad_2.stan model that I missed earlier
b5886b1 set_double_range_upper unsequenced, tests
110e856 set_int_range_upper unsequenced fix, tests
c454f2c set_double_range_lower unsequenced fix, tests
6faadd9 set_int_range_lower unsequenced fix, tests
33215b9 validate_int_expr unsequenced fix, tests
7c1035b add_var unsequenced fix, tests
95f75e8 validate_set_fun_type unsequenced fix, tests
e73672e add_expression_dimss unsequenced fix, tests
361151f logical_negate_expr unsequenced fix, tests
ab67122 negate_expr unsequenced fix, tests
7ae3ae2 elt_division unsequenced fix, tests
0f53e3b elt_multiplication unsequenced fix, tests
35dcd9f left division unsequenced fix, tests
529730d division unsequenced fix, tests
997f17b multiplication function unsequenced fix, tests
7195d0c validate allow sample unsequenced errors fixed, tests
841b42e validate_int_expr2 unsequenced fix, tests
93fc214 add_conditional_condition unsequenced fix, tests
bfbb2a5 merged origin develop
36c39b0 fix neg_binomial_2 in function_signatures
d12a2c3 added rng for neg_binomial_2
d0773f0 Added neg_binomial_2_log
65d23f1 Update appendices.tex
68e73ff Merge branch 'develop' of https://github.com/stan-dev/stan into develop
0dc5c33 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
f189b15 refactor: tested new print_progress method
841befb refactor: abstracted prefix and suffix out of print_progress
1819651 refactor: abstracted std::cout out of print_progress
e118db2 Merge pull request #564 from stan-dev/feature/sort_index
c88259e fixing references to src/test/test-models/compiled in makefile
8d3dea6 refactor: moving individual tests from compile_models_test to cmdstan repository
4b7b705 Merge pull request #576 from apw/patch-1
180d360 fixed unsigned comparison warnings inside tests
b77f473 adding function sigatures tests for sort_indicies
4c2b07f hopefully this fixes the sign errors
7af1295 Revert "A possible way to use to solve sign-compare warnings"
57e6f00 updating gitignore
1f50e2a Fix two typos: "ane" and "rwo".
7dab996 refactor: moving src/test/CmdStan/models/* tests to cmdstan repository
50a8dfe refactor: removing CmdStan specific models
4fbbf2f refactor: moving src/test/CmdStan/gm/argument_configuration_test.cpp to cmdstan repository
160b30b refactor: moving src/test/CmdStan/print_test.cpp to cmdstan repository
5c0a329 refactor: moving src/test/CmdStan/optimization_output_test.cpp to cmdstan repository
960ec89 refactor: moving src/test/CmdStan/fixed_param_test.cpp to cmdstan repository
8aa7742 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
89901eb moving src/test/CmdStan/command_test.cpp to cmdstan repository
1894554 Minor fix for neg_binomial_2_log_log
7092cd7 adding a typedef to the stan model for use in CmdStan
b0c223d moving namespace ui to common
c4a46eb A possible way to use to solve sign-compare warnings
de7fddd Merge branch 'develop' of https://github.com/stan-dev/stan into develop
5c49c3f Merge pull request #569 from stan-dev/bugfix/issue-568-epil
bbfd68c updated formatting to reduce lines to 80 chars and put open curlies on same line as signature
0bcc50f Merge branch 'develop' into feature/neg_bin
ce0e3d8 Change neg_binomial_log_log to neg_binomial_2_log_log
b0b5ea7 templated container out rather than type of std::vector or Eigen::Matrix
950c8ad Merge branch 'feature/sort_index' of https://github.com/stan-dev/stan into feature/sort_index
ff9f6d5 Changed a bunch of chains methods to be either static or const, as appropriate.
070f5da Manual now mentions that algorithm=fixed_param is mandatory when the parameters block is empty.
0040d0c Merge branch 'develop' of https://github.com/stan-dev/stan into bugfix/issue-530-no-model-parameters
a0ba5d8 Changed name of template parameter to avoid compiler bug on Mac OS X 10.7.5.
3fe07b9 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
fbdafe9 Merge pull request #566 from aadler/patch-1
49f7fa4 Update distributions.tex
2668156 Adjustments in rev and fwd diff for the refactoring of sort_indices_* functions
496798e refactor of sort_indices_* functions based on Bob Carpenter's https://github.com/stan-dev/stan/pull/564#issuecomment-35143532
d6560ed refactor: splitting init_* functions out of command.hpp; needs tests
8278ac5 refactor: splitting sample() out of command.hpp; needs tests
ba38e42 refactor: splitting warmup() out of command.hpp; needs tests
3dd43f1 refactor: splitting run_markov_chain(); needs tests
764e0d8 refactor: splitting print_progress() out of command.hpp
7f2f122 Merge pull request #563 from stan-dev/feature/minor-improvs-log_sum_exp
84d5114 revised doc, section titles, and added examples for sort functions
7f65b53 Added functions sort_indices_* to function_signatures.h
d6d51fb Added sort_indices_* functions to the manual
6d6f31a Added sort_indices_* functions
de9acda fix merge conflicts
c1287e4 refactor: splitting do_print() out of command.hpp
5acceee refactor: splitting write_error_msg() out of command.hpp; added unit tests
b630198 refactor: splitting write_model() out of command.hpp; added unit tests
834c6e9 refactor: splitting write_stan() out of command.hpp; added unit tests
9c84b76 refactor: splitting write_csv() out of command.hpp
973315c refactor: splitting write_iteration_csv() out of command.hpp
f47bc12 moved stan/gm/command.hpp to stan/ui/command.hpp; changed namespaces; moved tests
c3fc12a Adds a test to fwd-diff of log1p_exp
8c7c31e Minor fix for log_sum_exp
cdbd499 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
03f1b15 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
403a3da removing artifacts
0918eb6 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d8ee233 Added neg_binomial_log_log to manual
3d89efe Added neg_binomial_log_rng
e7ff805 Added distribution neg_binomial_log_log
1d6cb5c Merge remote-tracking branch 'origin/develop' into bugfix/issue-530-no-model-parameters
df6c9ff Check for algorithm=fixed_param when there are no model parameters.
ead81fc Merge branch 'develop' of https://github.com/stan-dev/stan into develop
51be3e0 ps_point::_fast_vector_copy and ps_point::_fast_matrix_copy now check for zero-byte sources.
2dfaea5 Merge remote-tracking branch 'origin/develop' into bugfix/issue-530-no-model-parameters Getting feature #353.
3d2793e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
11fdbb1 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
5f43578 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
e44a250 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
9d6b122 add make/local
af27ff4 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
46c3a24 's/EXPECT_FLOAT_EQ/EXPECT_NEAR/g'
283001d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c3f1b5c fix the runtest no fail target
c266daf define, test, and use a sign() function
cc362fb get cross-compiling working again
a9af1ff fix test for Windows vs. not Windows
db517b0 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d8904ee Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d0b195a Merge branch 'develop' of https://github.com/stan-dev/stan into develop
383db8d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
a19dc5a Merge branch 'develop' of https://github.com/stan-dev/stan into develop
dddca39 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
b2ff974 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
7664436 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
413e47e Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
c8dc409 updated parser test
9c71b31 add -lc++ on Linux
e93ea1f Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
56aa195 fix ox_mac makefile after merge
5e8f89e Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
5335f14 implement C++11 flag on Linux too
c0465ba Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
7f59d4c Merge branch 'develop' into feature/c++11
767d93e Removed one more comment
7a10155 Final clean-ups and removal of unneccesary files.
faf96a1 Merge branch 'develop' into feature/c++11
9f65843 Merge branch 'feature/c++11' of https://github.com/stan-dev/stan into feature/c++11
68bfc32 Merge branch 'develop' into feature/c++11
b99a2c1 Added a C++11 flag in makefile
71c8e88 Test with g++ on mac
88bd763 Merge branch 'develop' into feature/c++11
a15de58 Removed clang detection
f361cf4 C++11README updated with make test-* results
888ac4e Updated C++11README
fabb3ff c++11 cleanup
ec75b72 Get parser working under c++11

git-subtree-dir: pystan/stan
git-subtree-split: 45a2cb1496ee46ffb51a625b75879cd4b582804b
Use stan::mcmc::chains to do estimated sample size and rhat calculations.

Closes #21
API: optimizing now returns a vector rather than a dictionary

This mirrors an API change in RStan. Closes #80
Check for empty parameters and remove them.

Mirrors remove_empty_pars in RStan.
Mirror minor changes in RStan
Follow RStan's refactoring of stan_fit.hpp
Update wrapping of stanc
Update documentation and tests for new optimizing return format
Update optimizing tests
Fix remove_empty_pars tests
Update PyStan to work with development version of Stan (45a2cb1)

Merge branch 'feature/stan-dev-catchup' into develop
Update copyright
TST: Test Python 3.4 in CI
Squashed 'pystan/stan/' changes from 45a2cb1..a74b1ba

a74b1ba Merge pull request #703 from stan-dev/feature/issue-690-tag-v2.3.0
c5606c3 Merge branch 'develop' into feature/issue-690-tag-v2.3.0
0d9c4e2 updating makefile with clearer language
f02e605 adding stan-reference-2.3.0.pdf to repository for v2.3.0
b0870ac Merge pull request #702 from stan-dev/feature/issue-698-make-error
45a555c updating makefile message for test-models
1fe3a9d updated release notes for 2.3
676b1d3 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
820b052 Merge pull request #693 from stan-dev/feature/issue-692-remove-artifacts
c5f9bb0 removed doc/stan-reference-2.3.0.pdf
8e1a18c Merge pull request #691 from stan-dev/feature/issue-690-tag-v2.3.0
6173aa3 adding doc/stan-reference-2.3.0.pdf as an artifact
bfddfb0 updating RELEASE-NOTES.txt
97553a2 updating version numbers
ccce7a9 Merge pull request #689 from stan-dev/feature/issue-682-remove-warnings-v2.3.0
f2bece4 removed more warnings
2c86c79 Merge branch 'feature/issue-682-remove-warnings-v2.3.0' of https://github.com/stan-dev/stan into feature/issue-682-remove-warnings-v2.3.0
e6e7c5b adding casts to segmeent to reduce warnings
865bddf fixed a bad cast in trying to remove warnings
f96c740 removing more warnings
14aa19d Merge pull request #681 from stan-dev/feature/issue-648-pow-infix-syntax
30cc9e8 Merge pull request #673 from stan-dev/feature/issue-661-reimplement-error-handling
9d2cbd1 Merge branch 'develop' into feature/issue-661-reimplement-error-handling
ff8fa6c cleanup comments
da0ed59 added exponent operator description to user manual
89dd572 Merge pull request #672 from stan-dev/bugfix/670-io-check-too-large-ints
5413d81 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
e9e4825 Merge pull request #602 from stan-dev/feature/fix-issue-575-to-matrix
707cc68 test exponent operator throws exception
e771085 added file for exponent operator unit test
6764e58 added infix exponent operator, unit test
51a1a4e fixed squared_distance tests
3607af2 fix all current tests except square_distance in agrad-rev
28fec49 removed raise_domain_error files
a7cfc26 fixed check_cov_matrix_test in agrad/rev
f1a6c30 clean up error checks in distributions
a8172a3 Merge branch 'feature/issue-661-reimplement-error-handling' of https://github.com/stan-dev/stan into feature/issue-661-reimplement-error-handling
41c2b7f added trait for Eigen:Block. error handling now works better.
e052912 Merge pull request #671 from stan-dev/feature/issue-508-copyright
6ba0de4 reader checks common syntax errors, added unit tests accordingly
d15b896 fixes check_corr_matrix error
af17c3d Fix cyclic inclusion in containers_conversion (3)
fc920f9 Merge branch 'feature/issue-661-reimplement-error-handling' of https://github.com/stan-dev/stan into feature/issue-661-reimplement-error-handling
90ff102 Give LDLT_factor a value_type field.
23f176c more error handling on data read in from Rdata files, plus unit tests
54512db Fix cyclic inclusion in containers_conversion (2)
98b8122 refactored error_checks for multiplicable, matching dims, matching sizes, vector
f68f244 numbers out of range throw exception, added test to check exception to unit tests
3aa6504 Fix cyclic inclusion in containers_conversion
3d8e72f Forgot to remove this (it was included in containers_conversion_test.cpp
224bb05 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
134644e Improvement in code of to_matrix
bf43518 Merge branch 'feature/issue-661-reimplement-error-handling' of https://github.com/stan-dev/stan into feature/issue-661-reimplement-error-handling
dbc4927 added README for Stan Development Team clarification
b234733 more light updates to doc
037f092 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/fix-issue-575-to-matrix
57e381e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c21fdc3 Merge pull request #639 from alyst/fix_censoring_docs
8752d5c Merge branch 'develop' of https://github.com/stan-dev/stan into develop
db2975d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
0687545 fixing current tests
38d8775 Merge branch 'develop' into feature/issue-661-reimplement-error-handling
7bacea1 updating segment.hpp
51f847c updating check_nonzero_size
06f965a adding includes to typeinfo to dom_err and dom_err_vec
d8d0a35 including less from src/stan/meta/traits.hpp
f6599ac refactor validate_* to check_*
c14567b Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-648-pow-infix-syntax
be85dac Merge pull request #350 from mbrubake/feature/add-multi_gp
9863c89 Merge pull request #665 from stan-dev/feature/issue-567-manual-2.3.0
0f846a4 added error_handling files
f6439dd fix merge conflict
e3d0c12 moved errors to math/error_handling/
6c57a8e refactoring: reimplemented error_handling/matrix
fcfd1cf Merge branch 'develop' of https://github.com/stan-dev/stan into develop
6e727a2 cmdstan manual pointer, remove experimental warning for optimize, links to Py/R/Cmd Stan home pages
896593e added acknowledgment for code
03b564a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-567-manual-2.3.0
926d0fa refactoring: tried to find all check_* references that didn't have a final parameter and filled it in. Should not change behavior
c60d867 removing dom_err and dom_err_vec that do not have a result parameter
a3f9262 adding dom_err and dom_err_vec that do not have a result parameter
88c3c50 refactoring: error_handling/check_consistent_sizes.hpp
3cdc807 refactoring: removed second check_bounded function signature
5e42439 refactoring: error_handling/check_consistent_size
b0ca4f3 refactoring: error_handling/check_bounded.hpp
49bbee1 adding implementation for dom_err_vec
12fa51c Revert "Merge pull request #654 from stan-dev/feature/issue-382-remove-std-cout-cerr"
c9ae1b5 Merge pull request #654 from stan-dev/feature/issue-382-remove-std-cout-cerr
0b50b31 adding unit test for dom_err_vec
34a8ce3 refactoring: reimplemented dom_err to pass tests
3374599 adding unit test for dom_err.
95406da refactor: moved existing check_* functions to src/stan/math/error_handling__/
bcdee65 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-567-manual-2.3.0
dd2e3e3 updated manual with latest suggestions
79f55b0 Merge pull request #643 from stan-dev/feature/issue-590-multi_normal_cholesky_rng
10ccdc6 fixed print.cpp
e213c1d Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-567-manual-2.3.0
464d88d removing std::cout from code
2d6dd27 removing std::cout and std::cerr references from src/stan/io/stan_csv_reader.hpp
02a3920 removing comment containing std::cout
402fbe8 using output_stream instead of std::cout
96b0a14 adding ostream reference to init_adapt
1fc86dd removing reference to std::cerr
d73c72d removing std::cout from print.hpp (leaving it in print.cpp)
8147391 updating mcmc_writer_test.cpp
6f4e1a9 Merge pull request #645 from stan-dev/feature/issue-268-quad_form_sym
e18fd16 Merge branch 'develop' into feature/issue-382-remove-std-cout-cerr
4217ecb Merge pull request #651 from stan-dev/feature/sum_recorder
a30136e Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-567-manual-2.3.0
310f324 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4a78fc5 quad_form_sym: minor changes in unit test
133d6dc Merge pull request #649 from stan-dev/feature/issue-557-disable-eigen-asserts
8abca1a Adding include for stdexcept.
0e0c7b0 adding includes to sum_values.hpp
d5ee1e7 fixing test that demonstrates an assert when the compiler flag is not present
7c1d2b7 containers_conversion.hpp: small improvement in readability
b625e91 changing member variables to reference variables
6a9222a updated version for stan-reference
08a88e3 updated doc and finished issue #567
1f0beb6 adding a recorder that sums values. for use in RStan.
48af422 removing use of std::vector at() method. using [] instead
e215f68 removed CmdStan interface doc
bc1bb7c disabling Eigen asserts
4d66091 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
08fc497 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
2908906 add quad_form_sym unit test to validate asymmetry
cb7a300 Enable quad_form_sym
22a15d2 Added unit tests that checks the symmetry of quad_form_sym
4eff038 Adds multi_normal_cholesky_rng
7a976ae Merge pull request #3 from randommm/feature/multi-gp
30b5983 Move multi_gp gradient test to new folder
abbe742 Merge pull request #635 from stan-dev/feature/refactor-common-run_markov_chain
11fd4f9 Merge pull request #2 from stan-dev/feature/issue-350-add-multi-gp
87dc7b3 Merge branch 'develop' into feature/issue-350-add-multi-gp
208d7f6 Merge pull request #636 from stan-dev/feature/cmdstan-issue-4-standalone-doc
75f2c27 fixed src/test/unit
6d1d5e9 fixed test-headers
459c9a9 Merge branch 'feature/add-multi_gp' of git://github.com/mbrubake/stan into feature/issue-359-add-multi-gp
cdfc4f3 enhance censoring docs
825bd98 Merge pull request #629 from stan-dev/feature/doc-neg-bin
ce96877 Merge pull request #634 from stan-dev/hotfix/lkj_bug
ccae077 changed implementation of covariance and correlation to throw exception instead of outputting to std::cerr
14c3f3a removing std::cout and std::cerr from stan/mcmc/*
3b210a0 removed std::cout from the default arguments of test_gradients within model/util.hpp. common/command.hpp already calls it with streams
a910dc7 removed std::cout and std::cin from dump.hpp, added ostream argument to print(), removed default constructor from both dump_reader and dump_writer
dc777fa updating make/manual so it can be used within CmdStan
0e33c30 updating make/manual so it can be used within CmdStan
24f23ec Merge branch 'develop' into feature/refactor-common-run_markov_chain
6f8d42b updated transform test for correct sizes and now passes
7108cc3 added Jacobian test for corr matrix that fails
32240f3 fix Jacobian in read_corr_L()
91d16c8 Improvements to the documentation for the negative binomial distribution
e46824e Fix typo in the function neg_binomial_2 of the manual
d14a568 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
81a2a33 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
742f5bc Merge branch 'develop' of https://github.com/stan-dev/stan into develop
bef066c Merge branch 'develop' of https://github.com/stan-dev/stan into develop
b500305 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
613a629 refactoring: added argument for MessageRecorder to mcmc_writer
81a998a adding a messages recorder
9fa8f74 adding filtered_values recorder
9ebba24 adding no_op and values recorder
7ef72ff refactor: renamed stan::common::io::as_csv to stan::common::recorder::csv
50a9a48 renaming mcmc_writer's print_* methods to write_*
aa67cab adding comment to mcmc_writer
4af20da refactoring mcmc_writer to take different arguments
7553298 adding unit test for as_csv
8759922 moving as_csv to stan::common::io::as_csv
230a882 refactored mcmc_writer to take an as_csv object to write
41693ab added an as_csv class
4638964 adding documentation to mcmc_writer
53361d0 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
6c61d5b Changes and improvements to to_matrix, to_row_vector, to_array_1d, to_array_2d, to_vector. flatten renamed to array_1d.
7520a5d Added to_matrix, to_row_vector, to_array and flatten. Extended to_vector
b5d1853 adding a StartTransitionCallback (useful for RStan) to run_markov_chain, sample, warmup, and the calls from command()
1a702d3 adding prefix, suffix, and osream arguments to stan::common::sample and warmup; added tests
ca93ff4 adding comment to test
17242a1 removed std::cout in print_progress; called the fully specified print_progress in run_markov_chain, removed defaults out of run_markov_chain
d6d20de removed std::cout in print_progress; called the fully specified print_progress in run_markov_chain, removed defaults out of run_markov_chain
c9d00f2 updating test to push in prefix, suffix, and the ostream
cefa310 adding additional arguments to run_markov_chain with defaults.
1e7982e adding additional arguments to run_markov_chain with defaults.
7c61608 adding const to run_markov_chain arguments
8315139 adding test for run_markov_chain that traps the current output for CmdStan
521638d Add agrad unit tests for multi_gp_log.
24c0154 Fix function signature.
c7c6ac5 Fix inverse in manual.
2956273 Add multi_gp to the manual.
f610ddf Enable multi_gp in the language.

git-subtree-dir: pystan/stan
git-subtree-split: a74b1ba8754a990dbd8c182af10dfdb201ba6afc
Updates Stan to 2.3.0

Merge commit '4eb910861d344170163716fb3c77921f801d5c79' into feature/stan2.3
Adapts PyStan to changes in Stan and RStan 2.3

Significant changes include:

- inclusion of the "Fixed_param" sampling algorithm
- stan/common/recorder abstraction layer shared by CmdStan, PyStan, and RStan
Release PyStan 2.3.0.0