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Update Stan source to tag v2.19.0 #566

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Mar 29, 2019
Merged

Update Stan source to tag v2.19.0 #566

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baef0a5
feat(stan): Update Stan source to tag v2.19.0
riddell-stan Mar 20, 2019
e8c85bd
fix: update flags, library paths, tests for Stan 2.19
riddell-stan Mar 20, 2019
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8 changes: 4 additions & 4 deletions pystan/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -262,8 +262,8 @@ def __init__(self, file=None, charset='utf-8', model_name="anon_model",
os.path.join(pystan_dir, "stan", "src"),
os.path.join(pystan_dir, "stan", "lib", "stan_math"),
os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "eigen_3.3.3"),
os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "boost_1.66.0"),
os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "sundials_3.1.0", "include"),
os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "boost_1.69.0"),
os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "sundials_4.1.0", "include"),
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Should we add opencl folder here too

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Perhaps we should wait to see what RStan does. Cmdstan 2.19 does not add opencl by default.

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Sounds good. We really need to test it before release.

np.get_include(),
]

Expand Down Expand Up @@ -309,7 +309,7 @@ def __init__(self, file=None, charset='utf-8', model_name="anon_model",
'-ftemplate-depth-256',
'-Wno-unused-function',
'-Wno-uninitialized',
'-std=c++11',
'-std=c++1y',
"-D_hypot=hypot",
"-pthread",
"-fexceptions",
Expand All @@ -321,7 +321,7 @@ def __init__(self, file=None, charset='utf-8', model_name="anon_model",
'-ftemplate-depth-256',
'-Wno-unused-function',
'-Wno-uninitialized',
'-std=c++11',
'-std=c++1y',
] + extra_compile_args

distutils.log.set_verbosity(verbose)
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2 changes: 1 addition & 1 deletion pystan/stan
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Submodule stan updated 707 files
2 changes: 1 addition & 1 deletion pystan/stan_fit.hpp
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Expand Up @@ -1254,7 +1254,7 @@ namespace pystan {
pystan_sample_writer *sample_writer_ptr
= sample_writer_factory(&sample_stream,
comment_stream, "# ",
1,
3,
0,
constrained_param_names.size(),
output_samples + 1,
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1 change: 0 additions & 1 deletion pystan/tests/test_extra_compile_args.py
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Expand Up @@ -15,7 +15,6 @@ def test_extra_compile_args(self):
'-ftemplate-depth-1024',
'-Wno-unused-function',
'-Wno-uninitialized',
'-std=c++11',
]
if sys.platform.startswith("win"):
extra_compile_args.extend([
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2 changes: 1 addition & 1 deletion pystan/tests/test_unconstrain_pars.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,5 @@ def test_unconstrain_pars(self):
data, seed = {}, 1
fit = self.model.fit_class(data, seed)
assertRaisesRegex = self.assertRaisesRegexp if PY2 else self.assertRaisesRegex
with assertRaisesRegex(RuntimeError, 'variable x missing'):
with assertRaisesRegex(RuntimeError, 'Variable x missing'):
fit.unconstrain_pars({})
11 changes: 6 additions & 5 deletions setup.py
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Expand Up @@ -101,8 +101,8 @@ def find_version(*parts):
stan_include_dirs = ['pystan/stan/src',
'pystan/stan/lib/stan_math/',
'pystan/stan/lib/stan_math/lib/eigen_3.3.3',
'pystan/stan/lib/stan_math/lib/boost_1.66.0',
'pystan/stan/lib/stan_math/lib/sundials_3.1.0/include']
'pystan/stan/lib/stan_math/lib/boost_1.69.0',
'pystan/stan/lib/stan_math/lib/sundials_4.1.0/include']
stan_macros = [
('BOOST_DISABLE_ASSERTS', None),
('BOOST_NO_DECLTYPE', None),
Expand All @@ -115,7 +115,7 @@ def find_version(*parts):
'-ftemplate-depth-256',
'-Wno-unused-function',
'-Wno-uninitialized',
'-std=c++11',
'-std=c++1y',
]

if platform.platform().startswith('Win'):
Expand All @@ -125,7 +125,7 @@ def find_version(*parts):
extra_compile_args = [
'/EHsc',
'-DBOOST_DATE_TIME_NO_LIB',
'/std:c++14',
'/std:c++1y',
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I don't think MSVC has c++1y implemented, so c++14 should be used. (or nothing)

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We only use/support gcc on windows, right? (I'm just following cmdstan and what seemed to work on httpstan)

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Yes. This part is a bit legacy and is here if MSVC starts to work at some point.

]
else:
# fix bug in MingW-W64
Expand All @@ -140,16 +140,17 @@ def find_version(*parts):
stanc_sources = [
"pystan/stan/src/stan/lang/ast_def.cpp",
"pystan/stan/src/stan/lang/grammars/bare_type_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/block_var_decls_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/expression07_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/expression_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/functions_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/indexes_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/local_var_decls_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/program_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/semantic_actions_def.cpp",
"pystan/stan/src/stan/lang/grammars/statement_2_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/statement_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/term_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/var_decls_grammar_inst.cpp",
"pystan/stan/src/stan/lang/grammars/whitespace_grammar_inst.cpp",
]

Expand Down