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