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Update Stan to 2.39 #93

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Merged
WardBrian merged 3 commits into from
May 26, 2026
Merged

Update Stan to 2.39 #93

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689b7c7
Update Stan to 2.39
WardBrian May 26, 2026
16089b6
Fix tests
WardBrian May 26, 2026
decb6e5
Typo fix
WardBrian May 26, 2026
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ print-% : ; @echo $* = $($*) ;
STANC_DL_RETRY = 5
STANC_DL_DELAY = 10
STANC3_TEST_BIN_URL ?=
STANC3_VERSION ?= v2.38.0
STANC3_VERSION ?= v2.39.0

ifeq ($(OS),Windows_NT)
OS_TAG := windows
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2 changes: 1 addition & 1 deletion clients/R/R/zzz.R
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Expand Up @@ -10,7 +10,7 @@ HMC_SAMPLER_VARIABLES = c(

PATHFINDER_VARIABLES = c("lp_approx__", "lp__", "path__")

OPTIMIZATION_VARIABLES = c("lp__")
OPTIMIZATION_VARIABLES = c("lp__", "converged__")

LAPLACE_VARIABLES = c("log_p__", "log_g__")

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2 changes: 1 addition & 1 deletion clients/julia/src/model.jl
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Expand Up @@ -34,7 +34,7 @@ const HMC_SAMPLER_VARIABLES = [

const PATHFINDER_VARIABLES = ["lp_approx__", "lp__", "path__"]

const OPTIMIZE_VARIABLES = ["lp__"]
const OPTIMIZE_VARIABLES = ["lp__", "converged__"]

const LAPLACE_VARIABLES = ["log_p__", "log_q__"]

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2 changes: 1 addition & 1 deletion clients/julia/test/test_laplace.jl
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Expand Up @@ -45,7 +45,7 @@
@testset for jacobian in [true, false]
out_opt =
optimize(simple_jacobian_model; jacobian = jacobian, seed = UInt32(12345))
mode_array = out_opt.draws[2:end]
mode_array = out_opt.draws[3:end]
out = laplace_sample(
simple_jacobian_model,
mode_array;
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2 changes: 1 addition & 1 deletion clients/julia/test/test_optimize.jl
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Expand Up @@ -96,7 +96,7 @@

@testset "Model without parameters" begin
out = optimize(empty_model)
@test length(out.names) == 1 # lp
@test length(out.names) == 2 # lp, converged
end


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2 changes: 1 addition & 1 deletion clients/python/tests/test_optimize.py
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Expand Up @@ -107,7 +107,7 @@ def test_bad_init(bernoulli_model):

def test_model_no_params(empty_model):
out = empty_model.optimize()
assert len(out.parameters) == 1 # lp
assert len(out.parameters) == 2 # lp, converged


@pytest.mark.parametrize(
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16 changes: 4 additions & 12 deletions clients/python/tinystan/model.py
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Expand Up @@ -66,19 +66,11 @@ def print_callback(msg, size, is_error):

PATHFINDER_VARIABLES = ["lp_approx__", "lp__", "path__"]

OPTIMIZE_VARIABLES = [
"lp__",
]
OPTIMIZE_VARIABLES = ["lp__", "converged__"]

LAPLACE_VARIABLES = [
"log_p__",
"log_q__",
]
LAPLACE_VARIABLES = ["log_p__", "log_q__"]

FIXED_SAMPLER_VARIABLES = [
"lp__",
"accept_stat__",
]
FIXED_SAMPLER_VARIABLES = ["lp__", "accept_stat__"]


class HMCMetric(Enum):
Expand Down Expand Up @@ -122,7 +114,7 @@ def preprocess_laplace_inputs(
if isinstance(mode, StanOutput):
# handle case of passing optimization output directly
if len(mode.data.shape) == 1:
mode = mode.data[1:]
mode = mode.data[len(OPTIMIZE_VARIABLES) :]
else:
raise ValueError("Laplace can only be used with Optimization output")
# mode = mode.create_inits(chains=1, seed=seed)
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2 changes: 1 addition & 1 deletion stan
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Submodule stan updated 30 files
+1 −0 .github/CONTRIBUTING.md
+1 −1 .github/ISSUE_TEMPLATE.md
+1 −1 README.md
+10 −0 RELEASE-NOTES.txt
+1 −1 lib/stan_math
+1 −1 src/doxygen/doxygen.cfg
+3 −1 src/stan/io/stan_csv_reader.hpp
+2 −2 src/stan/mcmc/hmc/hamiltonians/ps_point.hpp
+2 −2 src/stan/model/indexing/rvalue.hpp
+7 −4 src/stan/services/optimize/bfgs.hpp
+7 −4 src/stan/services/optimize/lbfgs.hpp
+13 −2 src/stan/services/optimize/newton.hpp
+17 −0 src/stan/services/sample/standalone_gqs.hpp
+34 −0 src/stan/services/util/gq_writer.hpp
+1 −1 src/stan/version.hpp
+25 −0 src/test/unit/mcmc/hmc/hamiltonians/ps_point_test.cpp
+8 −6 src/test/unit/services/optimize/bfgs_jacobian_test.cpp
+8 −7 src/test/unit/services/optimize/bfgs_test.cpp
+8 −6 src/test/unit/services/optimize/lbfgs_jacobian_test.cpp
+8 −7 src/test/unit/services/optimize/lbfgs_test.cpp
+8 −6 src/test/unit/services/optimize/newton_jacobian_test.cpp
+14 −12 src/test/unit/services/optimize/newton_test.cpp
+2 −2 src/test/unit/services/pathfinder/eight_schools_test.cpp
+3 −3 src/test/unit/services/pathfinder/normal_glm_test.cpp
+1 −1 src/test/unit/services/sample/standalone_gqs_2390_test.cpp
+1 −1 src/test/unit/services/sample/standalone_gqs_multidim_test.cpp
+1 −1 src/test/unit/services/sample/standalone_gqs_parallel_test.cpp
+1 −1 src/test/unit/services/sample/standalone_gqs_test.cpp
+12 −0 src/test/unit/services/util/gq_writer_test.cpp
+2 −2 src/test/unit/version_test.cpp
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