Update Stan to 2.35 (#235)

* Bump stan from `cc7c617` to `9890ac0`

Bumps [stan](https://github.com/stan-dev/stan) from `cc7c617` to `9890ac0`.
- [Release notes](https://github.com/stan-dev/stan/releases)
- [Commits](stan-dev/stan@cc7c617...9890ac0)

---
updated-dependencies:
- dependency-name: stan
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Updates for Stan RNG changes

* mingw32-make is no longer required on Windows, use make where applicable

* Reset cache version

* Format fixes

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Brian Ward <bward@flatironinstitute.org>

.github/workflows/main.yaml

@@ -8,7 +8,7 @@ on:
   workflow_dispatch: {}
 
 env:
-  CACHE_VERSION: 1
+  CACHE_VERSION: 0
 
 # only run one copy per PR
 concurrency:
@@ -58,17 +58,10 @@ jobs:
           path: ./test_models/
           key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
-      - name: Build test models (Unix)
-        if: matrix.os != 'windows-latest' && steps.test-models.outputs.cache-hit != 'true'
+      - name: Build test models
+        if: steps.test-models.outputs.cache-hit != 'true'
         run: |
           make STAN_THREADS=true O=0 test_models -j4
-        shell: bash
-
-      - name: Build test models (Windows)
-        if: matrix.os == 'windows-latest' && steps.test-models.outputs.cache-hit != 'true'
-        run: |
-          mingw32-make.exe STAN_THREADS=true O=0 test_models -j4
-        shell: pwsh
 
   python:
     needs: [build]

Makefile

@@ -136,7 +136,7 @@ print-%  : ; @echo $* = $($*) ;
 STANC_DL_RETRY = 5
 STANC_DL_DELAY = 10
 STANC3_TEST_BIN_URL ?=
-STANC3_VERSION ?= v2.34.0
+STANC3_VERSION ?= v2.35.0
 
 ifeq ($(OS),Windows_NT)
  OS_TAG := windows

R/R/compile.R

@@ -1,5 +1,5 @@
 IS_WINDOWS <- isTRUE(.Platform$OS.type == "windows")
-MAKE <- Sys.getenv("MAKE", ifelse(IS_WINDOWS, "mingw32-make", "make"))
+MAKE <- Sys.getenv("MAKE", "make")
 
 
 verify_bridgestan_path <- function(path) {

README.md

@@ -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 2.34.1
+BridgeStan is currently shipping with Stan version 2.35.0
 
 Documentation is available at https://roualdes.github.io/bridgestan/
 

docs/getting-started.rst

@@ -8,7 +8,7 @@ Requirement: C++ toolchain
 Stan requires a C++ tool chain consisting of
 
 * A C++14 compiler. On Windows, MSCV is *not* supported, so something like MinGW GCC is required.
-* The Gnu :command:`make` utility for \*nix *or* :command:`mingw32-make` for Windows
+* The Gnu :command:`make` utility. On Windows, :command:`make` or :command:`mingw32-make` can be used
 
 Here are complete instructions by platform for installing both, from the CmdStan installation instructions.
 
@@ -63,10 +63,7 @@ a terminal in your BridgeStan folder and running
 
 .. code-block:: shell
 
-    # MacOS and Linux
     make test_models/multi/multi_model.so
-    # Windows
-    mingw32-make.exe test_models/multi/multi_model.so
 
 This will compile the file :file:`test_models/multi/multi.stan` into a shared library object for use with BridgeStan.
 This will require internet access the first time you run it in order

julia/src/compile.jl

@@ -1,6 +1,6 @@
 
 function get_make()
-    get(ENV, "MAKE", Sys.iswindows() ? "mingw32-make.exe" : "make")
+    get(ENV, "MAKE", "make")
 end
 
 

python/bridgestan/compile.py

@@ -29,10 +29,7 @@ def verify_bridgestan_path(path: Union[str, os.PathLike]) -> None:
 IS_WINDOWS = platform.system() == "Windows"
 WINDOWS_PATH_SET = False
 
-MAKE = os.getenv(
-    "MAKE",
-    "make" if not IS_WINDOWS else "mingw32-make",
-)
+MAKE = os.getenv("MAKE", "make")
 
 
 def set_bridgestan_path(path: Union[str, os.PathLike]) -> None:

rust/src/compile.rs

@@ -3,11 +3,7 @@ use log::info;
 use path_absolutize::Absolutize;
 use std::path::{Path, PathBuf};
 
-const MAKE: &str = if cfg!(target_os = "windows") {
-    "mingw32-make"
-} else {
-    "make"
-};
+const MAKE: &str = "make";
 
 /// Compile a Stan Model. Requires a path to the BridgeStan sources (can be
 /// downloaded with [`download_bridgestan_src`](crate::download_bridgestan_src) if that feature

src/bridgestan.cpp

@@ -65,7 +65,7 @@ int bs_param_constrain(const bs_model* m, bool include_tp, bool include_gq,
       // If RNG is not provided (e.g., we are not using include_gq), use a dummy
       // RNG.
       // SAFETY: this can be static because we know the rng is never advanced.
-      static boost::ecuyer1988 dummy_rng(0);
+      static stan::rng_t dummy_rng(0);
 
       if (include_gq)
         throw std::invalid_argument("include_gq=true but rng=nullptr");

src/model_rng.cpp

@@ -5,7 +5,6 @@
 #include <stan/io/empty_var_context.hpp>
 #include <stan/io/var_context.hpp>
 #include <stan/model/model_base.hpp>
-#include <stan/services/util/create_rng.hpp>
 #include <stan/math.hpp>
 #include <stan/math/prim/meta.hpp>
 #include <stan/version.hpp>
@@ -219,7 +218,7 @@ void bs_model::param_unconstrain_json(const char* json,
 
 void bs_model::param_constrain(bool include_tp, bool include_gq,
                                const double* theta_unc, double* theta,
-                               boost::ecuyer1988& rng) const {
+                               stan::rng_t& rng) const {
   Eigen::VectorXd params_unc = Eigen::VectorXd::Map(theta_unc, param_unc_num_);
   Eigen::VectorXd params;
   model_->write_array(rng, params_unc, params, include_tp, include_gq,

src/model_rng.hpp

@@ -2,7 +2,7 @@
 #define MODEL_RNG_H
 
 #include <stan/model/model_base.hpp>
-#include <boost/random/additive_combine.hpp>
+#include <stan/services/util/create_rng.hpp>
 #include <string>
 #include <vector>
 #include <random>
@@ -31,6 +31,11 @@ class bs_model {
    */
   ~bs_model() noexcept;
 
+  bs_model(bs_model const&) = delete;
+  bs_model(bs_model&&) = delete;
+  bs_model operator=(bs_model const&) = delete;
+  bs_model operator=(bs_model&&) = delete;
+
   /**
    * Return the name of the model.  This class manages the memory,
    * so the returned string should not be freed.
@@ -116,7 +121,7 @@ class bs_model {
    */
   void param_constrain(bool include_tp, bool include_gq,
                        const double* theta_unc, double* theta,
-                       boost::ecuyer1988& rng) const;
+                       stan::rng_t& rng) const;
 
   /**
    * Calculate the log density for the specified unconstrain
@@ -251,13 +256,9 @@ class bs_model {
  */
 class bs_rng {
  public:
-  bs_rng(unsigned int seed) : rng_(seed) {
-    // discard first value as workaround for
-    // https://github.com/stan-dev/stan/issues/3167
-    rng_.discard(1);
-  }
+  bs_rng(unsigned int seed) : rng_(0, 1, 0, seed) {}
 
-  boost::ecuyer1988 rng_;
+  stan::rng_t rng_;
 };
 
 #endif