WardBrian · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026
diff --git a/Makefile b/Makefile
@@ -169,7 +169,7 @@ print-%  : ; @echo $* = $($*) ;
 STANC_DL_RETRY = 5
 STANC_DL_DELAY = 10
 STANC3_TEST_BIN_URL ?=
-STANC3_VERSION ?= v2.39.0
+STANC3_VERSION ?= v2.40.0
 
 ifeq ($(OS),Windows_NT)
  OS_TAG := windows

diff --git a/clients/R/R/compile.R b/clients/R/R/compile.R
@@ -105,10 +105,10 @@ compile_model <- function(stan_file, stanc_args = NULL, make_args = NULL) {
   stancflags <- paste("--include-paths=.", paste(stanc_args, collapse = " "))
 
   flags <- c(
-    paste("-C", get_tinystan_path()),
+    paste("-C", shQuote(get_tinystan_path())),
     make_args,
-    paste0("STANCFLAGS=\"", stancflags, "\""),
-    output
+    paste0("STANCFLAGS=", shQuote(stancflags)),
+    shQuote(output)
   )
 
   suppressWarnings({

diff --git a/clients/typescript/package.json b/clients/typescript/package.json
@@ -70,14 +70,14 @@
     "@babel/preset-env": "^7.26.0",
     "@babel/preset-typescript": "^7.26.0",
     "@godaddy/dmd": "^1.0.4",
-    "@vitest/coverage-v8": "^4.1.0",
+    "@vitest/coverage-v8": "^5.0.1",
     "jsdoc-babel": "^0.5.0",
     "jsdoc-to-markdown": "^9.0.5",
     "prettier": "^3.3.1",
     "tsdown": "^0.22.0",
     "typescript": "^6.0.2",
     "vite": "^8.0.0",
-    "vitest": "^4.1.0"
+    "vitest": "^5.0.1"
   },
   "publishConfig": {
     "access": "public"

diff --git a/clients/typescript/yarn.lock b/clients/typescript/yarn.lock
diff --git a/src/buffer.hpp b/src/buffer.hpp
@@ -155,6 +155,10 @@ class filtered_writer : public stan::callbacks::structured_writer {
     }
   }
 
+  // workaround for
+  // https://github.com/stan-dev/stan/pull/3406#issuecomment-5716227487
+  void write(const std::string &, unsigned long) {}
+
   // other write methods are currently unused by anything we need
   using stan::callbacks::structured_writer::write;
 

diff --git a/src/file.hpp b/src/file.hpp
@@ -51,10 +51,10 @@ inline std::vector<var_ctx_ptr> load_inits(int num_chains,
     }
     return json_inits;
   }
+
   std::string inits(inits_char);
-  std::vector<std::string> init_files;
-  boost::algorithm::split(init_files, inits,
-                          [](char c) { return c == SEPARATOR; });
+  std::vector<std::string> init_files
+      = stan::io::split(inits, std::string_view(&SEPARATOR, 1));
   if (init_files.size() != num_chains) {
     throw std::invalid_argument(
         "Number of parameter initializations provided must be 0, 1, or match "

diff --git a/src/tinystan.cpp b/src/tinystan.cpp
@@ -232,7 +232,7 @@ int tinystan_pathfinder(const TinyStanModel *tmodel, size_t num_paths,
     error::error_logger logger(*tmodel, refresh != 0);
 
     interrupt::tinystan_interrupt_handler interrupt;
-    stan::callbacks::structured_writer dummy_json_writer;
+    io::filtered_writer dummy_json_writer;
 
     bool save_iterations = false;
 
@@ -248,8 +248,7 @@ int tinystan_pathfinder(const TinyStanModel *tmodel, size_t num_paths,
           calculate_lp);
     } else {
       std::vector<stan::callbacks::writer> null_writers(num_paths);
-      std::vector<stan::callbacks::structured_writer> null_structured_writers(
-          num_paths);
+      std::vector<io::filtered_writer> null_structured_writers(num_paths);
       return_code = stan::services::pathfinder::pathfinder_lbfgs_multi(
           model, json_inits, seed, id, init_radius, max_history_size,
           init_alpha, tol_obj, tol_rel_obj, tol_grad, tol_rel_grad, tol_param,

diff --git a/stan b/stan
+1 −1		.github/ISSUE_TEMPLATE.md
+205 −504		Jenkinsfile
+16 −3		RELEASE-NOTES.txt
+1 −1		lib/stan_math
+1 −1		src/doxygen/doxygen.cfg
+4 −1		src/stan/analyze/mcmc/check_chains.hpp
+4 −0		src/stan/analyze/mcmc/ess.hpp
+2 −2		src/stan/analyze/mcmc/mcse.hpp
+11 −7		src/stan/callbacks/json_writer.hpp
+5 −4		src/stan/callbacks/structured_writer.hpp
+17 −15		src/stan/io/json/json_data_handler.hpp
+16 −17		src/stan/io/stan_csv_reader.hpp
+148 −0		src/stan/io/string_utils.hpp
+1 −2		src/stan/services/pathfinder/multi.hpp
+11 −5		src/stan/services/sample/standalone_gqs.hpp
+4 −1		src/stan/services/util/gq_writer.hpp
+7 −4		src/stan/services/util/initialize.hpp
+1 −1		src/stan/version.hpp
+21 −0		src/test/unit/callbacks/json_writer_test.cpp
+0 −1		src/test/unit/callbacks/stream_logger_test.cpp
+1 −2		src/test/unit/callbacks/stream_writer_test.cpp
+1 −2		src/test/unit/callbacks/unique_stream_writer_test.cpp
+2 −2		src/test/unit/callbacks/writer_test.cpp
+0 −1		src/test/unit/io/json/json_data_test.cpp
+0 −1		src/test/unit/io/stan_csv_reader_test.cpp
+0 −1		src/test/unit/model/indexing/index_test.cpp
+9 −13		src/test/unit/services/check_adaptation.hpp
+0 −1		src/test/unit/services/optimize/laplace_jacobian_test.cpp
+0 −1		src/test/unit/services/optimize/laplace_sample_test.cpp
+5 −9		src/test/unit/services/sample/hmc_nuts_diag_e_adapt_test.cpp
+148 −1		src/test/unit/services/sample/standalone_gqs_parallel_test.cpp
+0 −1		src/test/unit/services/sample/standalone_gqs_test.cpp
+100 −0		src/test/unit/services/util/initialize_test.cpp
+1 −2		src/test/unit/util.hpp
+0 −1		src/test/unit/variational/eta_adapt_small_test.cpp
+2 −2		src/test/unit/version_test.cpp