Merge commit '846908fcf05756ae33b532c5a9ca87a0faf382db'
Squashed 'pystan/stan/' changes from cc82d51..6dfd8a3

6dfd8a3 Merge pull request #279 from stan-dev/feature/issue-278-Xcode5
2ba2d92 added TEMPLATE_DEPTH parameter to makefile under mac only.
90cd985 added more print statements to makefile
63b8132 Merge pull request #261 from stan-dev/feature/issue-259
fbd374e Merge pull request #277 from stan-dev/feature/issue-187-citations
8c7bb72 Merge pull request #274 from stan-dev/feature/issue-248-functions
b2621e1 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-187-citations
5262e92 added citations, checked format
1dd3673 Fix bug introduced in recent cleanup.
45a787c Merge pull request #276 from stan-dev/feature/issue-246
317db83 changing versions from 1.3.0 to 2.0.0
a76ef4d removing unused makefile
a1285f4 removing commented block
967a204 removing undoced functions from function signatures
150589a renaming stan::math::epsilon() to stan::math::machine_precision()
94d79c0 alphabetized function_signatures.h
77942b4 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
09ec865 Merge pull request #263 from stan-dev/feature/issue-257-abs-deprecate
5a120ce Merge pull request #265 from stan-dev/feature/issue-264-makefile-build-target
dd204c8 adding indicator that Stan tools were built
93834cd quoting the path separators
19ca1d0 updating makefile doc
d39d3c3 fixed #264. fixed 'build' target in makefile
4d3d179 Merge branch 'develop' into feature/issue-259
3fa7a70 Clean up BFGS code and messages a bit further.
7a1a5f7 deprecated abs(real), added stan::math version of abs(real); updating manual in manual branch to avoid conflicts
0745a47 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
a4cefe6 Merge pull request #254 from stan-dev/feature/issue-247
142be9a updated return codes for bfgs optimization
2c3b25e pulling out common code
b984f39 BFGS parameter changes.  Add tol_obj, tol_param and tol_grad parameters.  Change stepsize to init_alpha as it better reflects its use.
73deff9 Add return code strings for BFGS optimizer.
9a5f572 outputs optimization to file. fixed by flushing and closing output stream appropriately.
44f1db0 dirichlet: adding bounds tests for vars
6efe2b6 dirichlet: checking theta is a simplex
9788fa7 dirichlet: checking for alpha > 0
55ffcfd dirichlet: checking mismatched sizes
600b8f8 dirichlet: adding test for mismatched sizes
7eb37b0 adding bounds tests for dirichlet; currently fails
00c1538 Merge pull request #252 from stan-dev/feature/issue-214
89d045c Merge pull request #238 from stan-dev/feature/issue-234
c51eeea removed 'graphical model' from C++ level doc
7fc60c3 removed the word 'graphical' from makefiles
aa7b044 Merge pull request #208 from stan-dev/feature/more-informative-init-error-msgs
0f6fc53 removing compiler warnings in models
1b02f93 squashed all compiler warnings in unit tests
539a140 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
49f35cd Merge pull request #237 from stan-dev/feature/issue-216
b84d7e3 Merge pull request #243 from stan-dev/feature/travis-ci
00dd4cf sending notification emails to mc.stanislaw@gmail.com
3a5bd3c Merge pull request #241 from stan-dev/feature/travis-ci
b5b99ef adding .travis.yml to start using Travis CI
4570e5a Merge pull request #235 from stan-dev/feature/issue-230
8d8fbb3 removed warnings from model tests
39862b0 suppressing compiler warnings
08df90b suppressing unused var warning in generated models
74d8086 changing compiler flag to ignore warnings in Boost and Eigen
5058afa Merge branch 'develop' of https://github.com/stan-dev/stan into feature/more-informative-init-error-msgs
b13a275 fixes abs and fabs behavior for NaN for agrad fwd and rev
d824923 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
0a553d6 Merge pull request #224 from stan-dev/feature/issue-217
4e25746 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
45f23f0 fixes issue #230.
be57279 Merge pull request #206 from stan-dev/feature/improve_hmc_doc
58ded0b Remove extraneous s
10261a6 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
0519410 Merge pull request #215 from stan-dev/feature/expand_data_arg
15f8dc1 Handle case when cubic interpolation overflows in BFGS zoom function.  Fixes infinte loop on eight_schools model.
b9527a6 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
66487ce Merge pull request #205 from stan-dev/feature/move_init_stepsize
1d5af55 Merge pull request #189 from dougalsutherland/newton-backtrack
907ac13 Merge pull request #190 from stan-dev/feature/issue-180
0397b26 Merge pull request #198 from stan-dev/feature/issue-193
62763e4 Update to use new data arg format
e9f2662 Merge develop
0bd4dd4 Merge pull request #194 from stan-dev/feature/fix_rng
13657cf Merge pull request #183 from stan-dev/feature/fix-csv-for-matrices
84153bf Merge branch 'develop' of https://github.com/stan-dev/stan into develop
8526cba Merge pull request #207 from stan-dev/feature/issue-202
496aa43 fixed test so it's windows safe
043aa23 Fixed argument_parser_test to account for argv requiring that the first element be the executable name
3a26de3 Expand data arguments; need to merge model_test_fixture fixes and run tests before making a pull request.
3452cec updating run_command
9cf6521 Revert to displaying help when no arguments are given
7ae2def updating model tests
bb5d52b When initialization violates the constraints, print the variable name.
f3f3588 Merge branch 'feature/issue-202' of github.com:stan-dev/stan into feature/issue-202
4e92404 Fix behavior of remove_duplicates when the value of an argument is empty
eb68367 updating unit / model tests
33354a0 Detailed information on adaptation and HMC arguments
8c2825f working on argument_configuration_test
5279d10 updating model_test_fixture to run test-models
e60a3b1 Updated src/test/gm/command_test.cpp and src/test/gm/arguments/argument_parser_test.cpp to pass
48514c1 adding src/test/gm/arguments/test_model to gitignore list
429b033 adding tests that fail
b7e1374 changing quotes to <> for includes
0f72ae3 adding error_codes
a658a18 from Michael: feature/fix_model_test_fixture
8c54d9f Move dynamic stepsize initializationto adaptation initialization.
93d5a1c updated run_command() to return an error code; updated all tests that use run_command()
0753594 updating display of error code in run_command()
754636e Merge branch 'feature/fix-csv-for-matrices' of https://github.com/stan-dev/stan into feature/fix-csv-for-matrices
efb4dfa Additional unit testing for CSV output of matrices.
f0467d3 Fix CSV output of matrices to be in column-major order, consistent with the header output..
e42aa41 Merge pull request #172 from stan-dev/feature/arg_refactor
084711c Merge pull request #199 from stan-dev/feature/issue-197
7d0f2d0 Merge pull request #195 from stan-dev/feature/var-in-io-error
d247559 Tweak last test to work on both *nix and Windows
a541c24 Return reference instead of copy
4e9bde5 fixed dump sign issue as suggested by ksvanhorn in issue #197
4b91b23 made function names reserved names with tests and doc
b367203 fixed neg_binom_rng
07cfd64 When dimensions don't match, print out the variable name involved as well.
2443e9a fixed error in normal distr
df32e12 Fixed malformed argument configuration
19c12f1 Merge branch 'develop' into feature/fix-csv-for-matrices
1ac9b01 Merge branch 'develop' into feature/arg_refactor
71d7346 Actually use explicitly-set RNG seed
1bf129e Added argument configuration examples
fa088b1 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
ee5b78f Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-180
2eccd22 Merge pull request #174 from stan-dev/feature/issue-169
4bad2c7 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-180
c80fa8e added multivariate/discrete error_checks for RNGs
0cc45b3 added error checks for multivariate/continuous RNGs
6ce5897 added error checks for univariate/discrete RNGs
b96653d Update model fixtures to use new argument config
ad2548b Update logistic speed test
646b0b8 Clean up sampler allocation
e483ecb added error_checks for univariate continuous distribution RNGs
53fd98e De-expose RWM which hasn't been implemented yet
d31a43a Print usage after any help/help-all argument
cb51972 Fixed command test
b2b0dc7 Merge pull request #160 from jadams41/feature/doxygen_warnings
6fcfe63 give up on newton backtracking eventually
9503e23 Updated test to use tweaked argument format
fbc05af Mergity-merge develop
7af6f9b Fixed typo in diagnostic argument processing
3d6068f Fix CSV output of matrices to be in column-major order, consistent with the header output..
3d73a05 Tweaked argument validity info, updated docs
555552c Make consistent with previous arg name changes to avoid seg fault
ca0df77 fixed generator to print value of expression instead of translation
fd145e1 File deletion
1f30cad Rename samples argument to reflect that not all methods will output sample information
210b177 Make example argument configurations valid sampling specifications
f15fb6d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
5df3c5c use new arguments in the makefiles under bugs_example
6b2b8d5 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
b75ba2a Fixed some bad cut/paste editting
a62065a Merge pull request #177 from stan-dev/feature/truncation-logcdf
d883119 Merge pull request #1 from stan-dev/feature/doxygen_warnings
bbcdfd4 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
3c35059 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/truncation-logcdf
3a89679 changed truncated models to use cdf, ccdf, log-diff-exp, added tests in parser to validate univariate, updated doc with new translations
4036c60 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
3ce466e Merge pull request #147 from stan-dev/feature/circular
5cfca9f Merge branch 'develop' of https://github.com/stan-dev/stan into develop
89d400a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/circular
013a45d Merge pull request #173 from stan-dev/feature/issue_105
ad3719a Label after caption.  Label after caption.  Label after caption....
a869b45 moved underscores to end of capitalized variable names to avoid conflict with reserved variables in C++
2863ff6 Expanded argument doc
f1f7227 Remove unused save_warmup from output arguments
34f7d4c fix for error messages in parser due to setting _pass to false without throwing an expectation exception
8ea3ada I can't spell....
90f03f6 Add configuration suggestions upon parser failure; clean up some old comments
45376ea Merge branch 'develop' into feature/circular
4734dd6 shifted landscape orientation of example in intro, shortened number of calls to latex in make
19bcf02 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
8e1fb7a Renamed metropolis to Random Walk Metropolis
4056e49 Add script for formatting argument display into LaTeX
8ab240d added indent back for print output because it fits
d0a2da7 reduced print output to footnotesize and removed indent to fit it without landscape
14f81d8 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
22a7e26 Merge in develop
3d22ccc Merge branch 'feature/arg_refactor' of github.com:stan-dev/stan into feature/arg_refactor
a0db945 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
d27d766 Merge pull request #171 from stan-dev/feature/increment_log_prob
e98dc64 Merge branch 'develop' into feature/increment_log_prob
0673f79 Merge pull request #163 from stan-dev/feature/issue-159
2f3c27a Merge branch 'develop' into feature/doxygen_warnings
0b54c6b cleaning up more doxygen warnings
c771d1d Merge remote-tracking branch 'jadams41-github/feature/doxygen_warnings' into feature/doxygen_warnings
5acb9a2 Bug fixes and updated tests
f8904a4 Allow sampling with no warmup or no sampling iterations; update manual and tests.
261f1da Add stepsize argument to BFGS
9c771c6 Argument display tweaks
fc4fe21 Merge pull request #167 from pdmetcalfe/bugfix/gaussian-typo
fa14878 Merge pull request #168 from stan-dev/feature/cholesky_factor_type
fcd56b8 Merge pull request #165 from stan-dev/feature/issue-149
f271557 Update categorical argument test to tweaked behavior
8808600 Update stan_csv_reader_test for new output format
77b5dc9 Manual updates: make verbatim environments smaller, use both Gelman-Hoffman citations, various typos
ecbd51a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/increment_log_prob
6356370 models updated, doc updated, semicolon added to end of increment_log_prob function
e7a4a6b First round of manual updates
9797a48 fixed one more misspelling of Guassian
5f862ab Merge pull request #166 from stan-dev/feature/softmax-unfold
2fb38cb Add model name to command output, update stan_csv_reader and bin/print to accommodate new header format
5042b14 Actually make merge functional
f7282fb Clean up error message
6173a00 Merge develop
3575a41 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
47e3dd9 slight doc cleanup for transform.hpp
fd750f0 updated manual with cholesky_factor_cov type syntax and transform definitions
da05803 added square Cholesky factor declaration form with only one dimension
ec2d4b0 support for rectangular cholesky factors for covariance
05b231d Fix spelling of "gaussian"
8690474 finished merge
3abbc02 Merge pull request #164 from pdmetcalfe/feature/gamma_rate_fix
0a7f4e8 Merge pull request #132 from jrnold/feature/dlm
48955c0 added reader and writer for square Cholesky, which is now feature complete and unit tested
92ca49e added cholesky factor transform to prob/transform.hpp with tests and some extra error handling cleanup
79e98c9 added checks for cholesky and lower triangular
b845f42 added cholesky_factor to ast, grammars, code generator
7ca5b77 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
76ae5be merged with develop, resolved conflict in function_signatures.h
b958f76 removed categorical_log, added vector/matrix log_sum_exp, improved categorical_logit speed when not vectorized
10fc0cb Tweak progress output
6071919 Change default to BFGS
141a5d3 Merge branch 'develop' into feature/circular
8d3e056 fixed bug in merging function signatures
857b514 merge with develop
f5e63d1 File rename
c0edd15 Tweak diagnostic argument names
fba84d4 updated .gitignore, make/tests, and base_hmc_test to not show the improper artifacts as tracked in git
ba5c36e Fix gamma parametrization
ec4640b Compute percent completion without including the current iteration as complete
623ed00 All initialize to work with negative values
425935f more throrough assignment indexing test
0a18ef5 test for new statement grammar indexing
c00e3af generalized optional dimensions to sequence of dimensions to allow double-indexing on LHS of assignment
6e4fed8 finished merge vs. new Boost, fixing matrix includes
12a4018 Merge branch 'develop' into feature/circular
9de9657 all tests passing for softmax functions and categorical distributions
d3f03e9 added log_softmax rev mode
c3f77d7 softmax unfolded rev mode, added log_softmax and unfolded rev mode
95cc29f Merge branch 'develop' into feature/doxygen_warnings
68eb4dd Merge remote-tracking branch 'upstream/develop' into develop
4aa77b1 Break up tests into each base argument, plus interactions with method
deff06b Typo fixes
d9d9236 Seemingly working fix to the previously-freezing Nesterov optimization code
0863a2e removed parameter for lp-- changed @param vector to @param y
a2d0013 removed 1 parameter for commented out section added parameter for rng
0841ef6 removed parameters from commented out section because they were causing problems
1e82d0f removed @param for commented out variables
bfd2cd4 removed parameter for commented variable
d4d7d96 changed @params to @param--removed @param for dummy variable
33049b2 changed v to m so documentation matched code
b0ae89b same as previous commit (.../max.hpp)
57ddc29 changed v to x twice and v to m once--to match code with documentation
6a5e966 changed @param to @tparam in 2 places
69b919f Autocompile test_model for argument configuration tests
afd121b Preliminary working argument configuration test
25247f3 Output probe info to stream instead of files, a few bug fixes on categorical_argument
ab5c987 Use inclusive range of validity
0b2e648 Comment out optimization algorithms for the moment as nesterov freezes upon execution
502d0af changed @tparm to @tparam--most likely typo--changed x to m so documentation matched code
6339f49 added @param for undocumented classes
d68425c Initial testing capabilities
53a9d2e New usage output
375ab39 Add value_type for informative help output, commas to separate lists
1de3de4 Remove short_description
f6019b4 Use executable name instead of model name in help output
905fa71 added test for categorical_argument with a subargument; changed implementation of categorical_argument
e5e84c6 Removed unnecessary docmentation
9429a50 Changed documentation to match the code
b33baa6 Changed documentation to match code
1f1e9f5 Merge branch 'develop' into feature/arg_refactor
5e7d555 changed <code> and </code> to @code and @endcode w/ space b4 @
8147fb0 added semicolons to end of macros to quiet missing semicolon
f1faff9 removed obsolute line to fix warning in new doxygen edition
34a51ce Fixed bug where bad values didn't terminate execution
a9f6119 Separate diagnostic tests into separate method
511a02c Catch method arguments even without a method= prefix
d9ac173 Uncomment verbose help output
c8c97bc Uncomment verbose help output
bc7a137 Make model_name static, use in argument parser for model-specific help
942071b Added unsigned int argument type to match random seed and avoid overflow errors
7850bf1 Exit with failure if the base arguments are specified multiple times, fix typo in parsing optimization arguments
a7a90be Merge branch 'develop' into feature/circular
5f057df switched to using DoubleVectorView in von_mises distr
1392d16 moved von mises in manual
342c9d0 Merge branch 'feature/arg_refactor' of https://github.com/stan-dev/stan into feature/arg_refactor
e6f94ba Making random initialization range customizable
5b0e39f This reverts commit 52a3b862c401bf73f92e63b57487b3ac179d72a4.
feb8567 compressing help option
be52666 reworking test/models/command
badd941 renamed gaussian_dlm_log to gaussian_dlm_obs_log
b81abad updating help print to indicate which arguments need values
fd530c7 updating .gitignore
5091841 adding singleton_argument tests, test-unit runs now
ed4a44e updating unvalued_argument
cc1ac98 updating mcmc_writer_test
4af856c updating valued_argument, singleton_argument
56403fd merging stan_csv_reader.hpp
52a3b86 added function signatures for gaussian_dlm without m0 and C0
33fd0ed replace use of boost::math::tools::promote_args with stan::prob::return_type
3c90ff9 remove usages of eval() since Stan does not use Eigen's expression templates
6230120 remove debugging statements
9f73c6e check for NaN and infinite values in arguments
84a5edc Added tests to check computed variables
2087c2c added von mises distr to manual
a6a112e modified domain of y in von mises distribution and added more tests
5bedc3e modified von_mises distr and added appropriate test
d783eb0 merge develop into feature/circular
256699c Merge branch 'develop' into feature/circular
91f8931 rename gaussian_dlm test
2ef942e allow V and W to be positive semi-definite (including the zero matrix)
80f7c35 add new checks
33c9fd9 added check for symmetric, positive semi-definite matrices
80ec014 added check for square matrices
262ab22 added check for positive semi-definite matrices
489af5a adding test for unvalued_argument
eebee0f updated log-likelihood tests
e064d76 improve documentation for gaussian_dlm_log
059a1ed add size checks for C0, m0
8e6c977 added support for initial values
2b00a39 Merge branch 'develop' into feature/circular
3e2af9f fix typos
c18dc5d clean up code
d4d1710 added docs for gaussian_log_glm
f9c2553 updating tests
787f8ed added test for valued_argument
9c7604c added test for valued_argument
61ee2ee adding test for categorical_argument, fixed some of the behavior, reformatted
e8c503b adding test for argument.hpp, cleaning up code
5210610 adding test for argument.hpp, cleaning up code
ed3d385 reformatting argument_parser.hpp
4a32b92 reformatting argument_parser.hpp
61af8b1 updated DLM test for sizes of matrices
6a63ab1 added example models
8a7ca2c update
5a009e8 Merge remote-tracking branch 'remotes/stan-dev/develop' into feature/dlm
0f4b61e updating model tests to skip another parameter in the output
d98a393 adding default constructor for stan_csv_timing. Windows doesn't set the members to 0
1f37469 fixing the stan_csv_reader for Mac for line endings terminating in \r
a0fe4c7 fixed descriptions environment in functions.tex for to_vector
c1c6a72 manual update for bug in sample program + acknowledgment for same
caf6a07 fixes issue #63.
e594a04 Change ordering of Wno-c++11-long-long to ensure it is respected.
a3ad756 added -Wno-c++11-long-long flag for clang++ in mac
40d15ff added -Wno-c++11-long-long flag for clang++ in linux. Fixes issue #62
3001b26 added missing compiled model tests
3fd564e added to_vector with tests
b73c6e5 Removed debug output line
c23f67b MUse boost::lexical cast for more robust reading of numbers in scientic notation
79b1bae replace inversion of Q with cholesky decomposition and solving
7cac58a unit tests
daed010 fix ref to gaussian_dlm_seq_log
16dc35c rename gaussian_dlm_seq_log back to gaussian_dlm_log
7ca7b27 misc
ecccef7 current progress
793472e Deleted deprecated help argument
a73a2e8 More flexible help display options
08f1b45 update signatures
12b6912 getting sequential version to work
ba81de8 working implementation
2dfffd7 misc
be76239 Merge remote-tracking branch 'remotes/stan-dev/develop' into feature/dlm
d914d15 model compiles
2b181b6 Lots of bug fixes and behavior tweaks to accompany merge of develop
f052b63 Merge branch 'develop' into feature/arg_refactor
93b8785 initial work
88f8ab5 Implemented optimization algorithms and various samplers, added appropriate arguments
ee17934 New arguments, started refilling command.hpp
cf9e557 Added many new arguments
7dfdc51 Recursive arguments
b5688fe Test argument parsers
19c6b0a Argument parsers
a6aaaa3 Added argument parsers
9c45f24 Break lines at 80 characters.
09871d3 Delete whitespace.
b39b250 Initial commit.

git-subtree-dir: pystan/stan
git-subtree-split: 6dfd8a330f32fca1c2c93270cc1b5149c6e52d61
First pass at adapting PyStan to arg refactor
Add note about PyStan being under development
Bump version to mirror Stan
More arg refactor adjustments
Squashed 'pystan/stan/' changes from 6dfd8a3..ae26c9b

e67c42e Merge branch 'release/v2.0.0'
f65533d Merge pull request #287 from stan-dev/issue/release-notes-2.0.0
abbd984 added more acknowledgments to manual
4814953 Merge branch 'release/v2.0.0' of https://github.com/stan-dev/stan into release/v2.0.0
c5647a4 new release notes for 2.0.0
89b4746 adding doc to the source repository
48b0897 adding version numbers back to the makefiles
5b42aa6 Merge pull request #286 from stan-dev/feature/issue-211-stan2-manual
1f3a06c added some extra notes in the preface, added some extra doc for command-line args, and fixed typos in the distributions
bae44e6 Merge pull request #285 from stan-dev/feature/makefile_remove_dist_target
cdf321a removed 'dist' make target
14d3126 Merge branch 'feature/issue-211-stan2-manual' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
55e10bc Merge branch 'develop' of https://github.com/stan-dev/stan into develop
6f13dda fixed a couple typos
b0cb79f added warning about abs, changed links in appendices to new downloads
8f99ac9 Merge pull request #282 from stan-dev/feature/issue-246-website
fa03e2b updated web site
e151f8a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-246-website
eb5b8fb Merge pull request #281 from stan-dev/feature/issue-278-Xcode5
a124d90 Merge branch 'develop' into feature/issue-278-Xcode5
0431506 updating version to match clang++ version (from -dumpversion)
561914d only adding template-depth flags for Mac when the versions match XCode 5
8196052 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-246-website
00c8792 conditionally use '-' for template-depth option for g++ 4.2, 4.3, 4.4
33864b0 added another Matt trick, more acknowledgments
a29c38d Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
faf9e09 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
89ac691 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
2ea9291 Merge branch 'develop' into feature/issue-246-website
2333f7a working on downloads
5c70ac1 updating version from 1.3.0 to v2.0.0
a123e2e added citation for Matt trick
f3a6462 added more descrptions for optimization and initialization
3c8bf61 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
65172db updated manual with optimization and some more formatting
a0a7fbf Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
695a2fd more doc updates for 2.0
e435afe Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
ebcadf2 fixed more issues in manual
122a06b Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
37d01b7 Merge branch 'feature/issue-211-stan2-manual' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
8797495 fixed typos in doc
48ab974 Edits for the command argument doc
267aecb added new bfgs args, added syntactic highlighting to argument hierarchy
aa8827a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
c69af5e updated commands after proofreading and fixed in-press ref
3838504 command skeletons in place
7ee22e4 added formatting to commands with some extra descriptions
f208227 updated for distributions with sampling statements in both definitions and index
79c982f Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
2c3a9d2 updated docs for 2.0 for everything but the new command structure

git-subtree-dir: pystan/stan
git-subtree-split: ae26c9b441002293ce482baf3369caa0a6aedf36
Update Stan source to 2.0.0

This merges commit 'e98b409262abd5fcc107101cd2a262b628d19f8b' (tag: v2.0.0)
into feature/arg_refactor.
Catchup to Stan 2.0.0
Remove optimzing with sample_file param test for now
Remove _dict_from_pystanargs and just store a copy of Python version of args

This may introduce some minor differences between the way PyStan and RStan
display the arguments to Stan to the user. All the arguments passed from Python
to Stan are still visible.
Add _dict_from_pystanargs back, alternate workaround for Cython problem
Merge branch 'feature/arg_refactor' into develop