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Update Stan source to v2.19.1 #652

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Oct 22, 2019
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Update Stan source to v2.19.1 #652

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eecb298
feat: Use Stan 2.19.1 source
riddell-stan Oct 21, 2019
0e6f159
Revert "fix: Disable STAN_THREADS test"
riddell-stan Oct 21, 2019
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2 changes: 1 addition & 1 deletion pystan/stan
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Submodule stan updated 64 files
+1 −1 .github/ISSUE_TEMPLATE.md
+1 −1 Jenkinsfile
+0 −24 RELEASE-NOTES.txt
+1 −1 lib/stan_math
+6 −18 make/tests
+1 −1 src/doxygen/doxygen.cfg
+0 −123 src/stan/analyze/mcmc/autocovariance.hpp
+80 −176 src/stan/analyze/mcmc/compute_effective_sample_size.hpp
+0 −72 src/stan/analyze/mcmc/split_chains.hpp
+1 −1 src/stan/io/array_var_context.hpp
+10 −44 src/stan/io/reader.hpp
+1 −1 src/stan/io/stan_csv_reader.hpp
+0 −131 src/stan/lang/function_signatures.h
+1 −4 src/stan/lang/generator/generate_class_decl.hpp
+2 −2 src/stan/lang/generator/generate_constructor.hpp
+1 −1 src/stan/lang/generator/generate_model_name_method.hpp
+2 −11 src/stan/lang/generator/generate_model_typedef.hpp
+4 −3 src/stan/lang/generator/generate_typedef.hpp
+15 −1 src/stan/lang/grammars/semantic_actions_def.cpp
+4 −4 src/stan/lang/grammars/term_grammar_def.hpp
+19 −33 src/stan/lang/rethrow_located.hpp
+0 −18 src/stan/mcmc/chains.hpp
+1 −1 src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp
+57 −58 src/stan/mcmc/hmc/xhmc/base_xhmc.hpp
+1 −1 src/stan/mcmc/sample.hpp
+24 −20 src/stan/model/indexing/lvalue.hpp
+14 −14 src/stan/model/indexing/rvalue.hpp
+0 −611 src/stan/model/model_base.hpp
+0 −215 src/stan/model/model_base_crtp.hpp
+1 −1 src/stan/model/model_functional.hpp
+0 −2 src/stan/model/model_header.hpp
+4 −49 src/stan/model/prob_grad.hpp
+2 −2 src/stan/services/sample/standalone_gqs.hpp
+2 −2 src/stan/version.hpp
+0 −71 src/test/integration/mtu/mcmc.cpp
+0 −2 src/test/integration/mtu/model.cpp
+38 −0 src/test/test-models/bad/ode/adams/bad_t0_var_type.stan
+38 −0 src/test/test-models/bad/ode/adams/bad_t0_var_type_control.stan
+38 −0 src/test/test-models/bad/ode/adams/bad_ts_var_type_control.stan
+38 −0 src/test/test-models/bad/ode/bad_t0_var_type.stan
+38 −0 src/test/test-models/bad/ode/bad_t0_var_type_bdf_control.stan
+38 −0 src/test/test-models/bad/ode/bad_t0_var_type_rk45_control.stan
+38 −0 src/test/test-models/bad/ode/bad_ts_var_type.stan
+38 −0 src/test/test-models/bad/ode/bad_ts_var_type_bdf_control.stan
+38 −0 src/test/test-models/bad/ode/bad_ts_var_type_rk45_control.stan
+0 −102 src/test/test-models/good/function-signatures/math/matrix/gp_regression_test.stan
+0 −64 src/test/test-models/good/integrate_ode_adams.stan
+0 −62 src/test/test-models/good/integrate_ode_bdf.stan
+1 −73 src/test/test-models/good/integrate_ode_rk45.stan
+0 −1,000 src/test/unit/analyze/mcmc/ar1.csv
+0 −61 src/test/unit/analyze/mcmc/autocovariance_test.cpp
+39 −149 src/test/unit/analyze/mcmc/compute_effective_sample_size_test.cpp
+0 −99 src/test/unit/analyze/mcmc/split_chains_test.cpp
+0 −25 src/test/unit/io/reader_test.cpp
+1 −1 src/test/unit/lang/generator/generate_cpp_test.cpp
+26 −3 src/test/unit/lang/parser/ode_test.cpp
+24 −37 src/test/unit/model/indexing/lvalue_test.cpp
+0 −147 src/test/unit/model/model_base_crtp_test.cpp
+0 −203 src/test/unit/model/model_base_test.cpp
+5 −0 src/test/unit/multiple_translation_units1.cpp
+5 −0 src/test/unit/multiple_translation_units2.cpp
+0 −0 src/test/unit/multiple_translation_units_test.cpp
+1 −0 src/test/unit/services/sample/standalone_gqs_test.cpp
+4 −4 src/test/unit/version_test.cpp
1 change: 0 additions & 1 deletion pystan/tests/test_extra_compile_args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,6 @@ def test_extra_compile_args_failure(self):
pystan.StanModel(model_code=model_code, model_name="normal1",
extra_compile_args=extra_compile_args)

@unittest.skip("temporarily disabled due to STAN_THREADS issue in Stan 2.20")
def test_threading_support(self):
# Dont test with Windows with MinGW-w64 (GCC)
if sys.platform.startswith("win"):
Expand Down