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Update Stan to 2.36.0 #256

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merged 4 commits into from
Dec 10, 2024
Merged

Update Stan to 2.36.0 #256

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ff10e77
Bump stan from `9890ac0` to `ef8374d`
dependabot[bot] Dec 10, 2024
5af76ad
Version bumps
WardBrian Dec 10, 2024
1e68db7
Clear cache
WardBrian Dec 10, 2024
2aab913
Don't try to use a version from 3 years ago...
WardBrian Dec 10, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/main.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ on:
workflow_dispatch: {}

env:
CACHE_VERSION: 1
CACHE_VERSION: 2

# only run one copy per PR
concurrency:
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -136,7 +136,7 @@ print-% : ; @echo $* = $($*) ;
STANC_DL_RETRY = 5
STANC_DL_DELAY = 10
STANC3_TEST_BIN_URL ?=
STANC3_VERSION ?= v2.35.0
STANC3_VERSION ?= v2.36.0

ifeq ($(OS),Windows_NT)
OS_TAG := windows
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -17,7 +17,7 @@ Stan is a probabilistic programming language for coding statistical
models. For an introduction to what can be coded in Stan, see the
[*Stan User's Guide*](https://mc-stan.org/docs/stan-users-guide/index.html).

BridgeStan is currently shipping with Stan version 2.35.0
BridgeStan is currently shipping with Stan version 2.36.0

Documentation is available at https://roualdes.github.io/bridgestan/

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2 changes: 1 addition & 1 deletion stan
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Submodule stan updated 78 files
+1 −1 .github/ISSUE_TEMPLATE.md
+15 −0 RELEASE-NOTES.txt
+1 −1 lib/stan_math
+1 −5 makefile
+1 −1 src/doxygen/doxygen.cfg
+43 −0 src/stan/analyze/mcmc/check_chains.hpp
+8 −0 src/stan/analyze/mcmc/compute_effective_sample_size.hpp
+4 −232 src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp
+108 −0 src/stan/analyze/mcmc/ess.hpp
+66 −0 src/stan/analyze/mcmc/mcse.hpp
+62 −0 src/stan/analyze/mcmc/rank_normalization.hpp
+50 −0 src/stan/analyze/mcmc/rhat.hpp
+58 −0 src/stan/analyze/mcmc/split_chains.hpp
+60 −0 src/stan/analyze/mcmc/split_rank_normalized_ess.hpp
+47 −0 src/stan/analyze/mcmc/split_rank_normalized_rhat.hpp
+297 −90 src/stan/io/deserializer.hpp
+73 −0 src/stan/io/serializer.hpp
+67 −58 src/stan/io/stan_csv_reader.hpp
+19 −19 src/stan/mcmc/chains.hpp
+508 −0 src/stan/mcmc/chainset.hpp
+6 −0 src/stan/mcmc/hmc/base_hmc.hpp
+2 −0 src/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp
+2 −1 src/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp
+129 −97 src/stan/model/indexing/rvalue.hpp
+2 −2 src/stan/model/model_base.hpp
+1 −1 src/stan/model/model_base_crtp.hpp
+2 −2 src/stan/model/model_header.hpp
+2 −1 src/stan/services/sample/hmc_nuts_dense_e.hpp
+2 −1 src/stan/services/sample/hmc_nuts_diag_e.hpp
+40 −7 src/stan/services/util/initialize.hpp
+3 −2 src/stan/services/util/validate_dense_inv_metric.hpp
+1 −1 src/stan/version.hpp
+9 −0 src/test/test-models/good/model/accumulate.stan
+6 −0 src/test/test-models/good/services/test_fail.stan
+7 −0 src/test/test-models/good/services/zero_params.stan
+48 −0 src/test/unit/analyze/mcmc/check_chains_test.cpp
+0 −309 src/test/unit/analyze/mcmc/compute_potential_scale_reduction_test.cpp
+53 −0 src/test/unit/analyze/mcmc/ess_basic_test.cpp
+73 −0 src/test/unit/analyze/mcmc/mcse_test.cpp
+85 −0 src/test/unit/analyze/mcmc/rank_normalization_test.cpp
+54 −0 src/test/unit/analyze/mcmc/rhat_basic_test.cpp
+46 −0 src/test/unit/analyze/mcmc/split_chains_test.cpp
+73 −0 src/test/unit/analyze/mcmc/split_rank_normalized_ess_test.cpp
+63 −0 src/test/unit/analyze/mcmc/split_rank_normalized_rhat_test.cpp
+1,057 −0 src/test/unit/analyze/mcmc/test_csv_files/bern1.csv
+1,057 −0 src/test/unit/analyze/mcmc/test_csv_files/bern2.csv
+1,057 −0 src/test/unit/analyze/mcmc/test_csv_files/bern3.csv
+1,057 −0 src/test/unit/analyze/mcmc/test_csv_files/bern4.csv
+18 −0 src/test/unit/analyze/mcmc/test_csv_files/cmdstan-2-35-0-stansummary.csv
+333 −438 src/test/unit/io/deserializer_free_test.cpp
+46 −0 src/test/unit/io/deserializer_stdvector_test.cpp
+42 −0 src/test/unit/io/deserializer_test.cpp
+43 −0 src/test/unit/io/deserializer_var_test.cpp
+38 −0 src/test/unit/io/deserializer_varmat_test.cpp
+327 −336 src/test/unit/io/serializer_test.cpp
+93 −15 src/test/unit/io/stan_csv_reader_test.cpp
+57 −0 src/test/unit/io/test_csv_files/bernoulli_no_samples.csv
+1,057 −0 src/test/unit/io/test_csv_files/bernoulli_thin.csv
+1,039 −0 src/test/unit/io/test_csv_files/bernoulli_variational.csv
+2,057 −0 src/test/unit/io/test_csv_files/bernoulli_warmup.csv
+55 −0 src/test/unit/io/test_csv_files/fixed_param_output.csv
+157 −0 src/test/unit/io/test_csv_files/no_parameters_hmc.csv
+1 −15 src/test/unit/mcmc/chains_test.cpp
+238 −0 src/test/unit/mcmc/chainset_test.cpp
+557 −0 src/test/unit/mcmc/test_csv_files/bernoulli_500.csv
+1,057 −0 src/test/unit/mcmc/test_csv_files/bernoulli_default.csv
+1,057 −0 src/test/unit/mcmc/test_csv_files/bernoulli_thin.csv
+2,057 −0 src/test/unit/mcmc/test_csv_files/bernoulli_warmup.csv
+82 −0 src/test/unit/mcmc/test_csv_files/datagen_output.csv
+557 −0 src/test/unit/mcmc/test_csv_files/eight_schools_1.csv
+557 −0 src/test/unit/mcmc/test_csv_files/eight_schools_2.csv
+2 −0 src/test/unit/model/compile_test.cpp
+17 −0 src/test/unit/services/instrumented_callbacks.hpp
+177 −0 src/test/unit/services/sample/hmc_nuts_dense_e_adapt_no_params_test.cpp
+58 −0 src/test/unit/services/util/fail_init_test.cpp
+10 −11 src/test/unit/services/util/initialize_test.cpp
+17 −0 src/test/unit/services/util/inv_metric_test.cpp
+2 −2 src/test/unit/version_test.cpp
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