Update to Stan 2.37 (#287)

* Bump stan from `ef8374d` to `1357c13`

Bumps [stan](https://github.com/stan-dev/stan) from `ef8374d` to `1357c13`.
- [Release notes](https://github.com/stan-dev/stan/releases)
- [Commits](stan-dev/stan@ef8374d...1357c13)

---
updated-dependencies:
- dependency-name: stan
  dependency-version: 1357c136bf22e3f0d25ed3529fea55fe76842eac
  dependency-type: direct:production
...

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

* Version bumps

* Add new make flag to catch eigen runtime errors

* resolve Rust lints

* Doc tweaks

---------

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 <brianmward99@gmail.com>

Author: dependabot[bot]

Makefile

@@ -20,9 +20,8 @@ include $(MATH)make/libraries
 # Set -fPIC globally since we're always building a shared library
 override CXXFLAGS += -fPIC -fvisibility=hidden -fvisibility-inlines-hidden
 override CXXFLAGS_SUNDIALS += -fPIC
-override CPPFLAGS += -DBRIDGESTAN_EXPORT
+override CPPFLAGS += -DBRIDGESTAN_EXPORT -DSTAN_OVERRIDE_EIGEN_ASSERT
 
-# set flags for stanc compiler (math calls MIGHT? set STAN_OPENCL)
 ifdef STAN_OPENCL
 	override STANCFLAGS += --use-opencl
 	STAN_FLAG_OPENCL=_opencl
@@ -136,7 +135,7 @@ print-%  : ; @echo $* = $($*) ;
 STANC_DL_RETRY = 5
 STANC_DL_DELAY = 10
 STANC3_TEST_BIN_URL ?=
-STANC3_VERSION ?= v2.36.0
+STANC3_VERSION ?= v2.37.0
 
 ifeq ($(OS),Windows_NT)
  OS_TAG := windows

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 2.36.0
+BridgeStan is currently shipping with Stan version 2.37.0
 
 Documentation is available at https://roualdes.github.io/bridgestan/
 

docs/getting-started.rst

@@ -185,8 +185,9 @@ If you wish to use BridgeStan for an older released version, all you need to do
 3. Also in the ``stan`` submodule, run ``make math-update``
 4. In the top level BridgeStan directory, run ``make clean``
 
-To return to the version of Stan currently used by BridgeStan, you can run ``make stan-update`` from the top level directory
-and remove :makevar:`STANC3_VERSION` from your ``make/local`` file, before running ``make clean`` again.
+To return to the version of Stan currently used by BridgeStan, you can run
+``make stan-update`` from the top level directory and remove :makevar:`STANC3_VERSION` from
+your ``make/local`` file, before running ``make clean`` again.
 
 Using Pre-Existing Stan Installations
 _____________________________________

docs/internals/development.rst

@@ -15,17 +15,23 @@ they have the minimal C++ build tools required for working with BridgeStan.
 C++
 ---
 
-* We use the C++1y standard for compilation (``-std=c++1y`` in both clang and gcc). This is partway between C++11 and C++14, and is what Stan requires.
+* We use the C++17 standard for compilation (``-std=c++17`` in both clang and gcc).
+  This is what Stan requires since version 2.36.
+
+* We try to write standards-compliant code that does not depend on features of specific platforms
+  (except where needed for compatibility).
 
-* We try to write standards-compliant code that does not depend on features of specific platforms (except where needed for compatibility).
   Specifically, we do not use OS-dependent or compiler-dependent C++.
   Our C++ code does not depend on the ``R.h`` or ``Python.h`` headers, for example.
-  On the other hand, adding new signatures to work with a specific language's style of foreign function interface is permitted
-  (an example can be found in the :ref:`R compatibility functions <R-compat>`, which requires a particular pointer-based style).
+  On the other hand, adding new signatures to work with a specific language's style of foreign
+  function interface is permitted (an example can be found in the :ref:`R compatibility functions <R-compat>`,
+  which requires a particular pointer-based style).
 
-* We try to follow the `Google C++ Style Guide <https://google.github.io/styleguide/cppguide.html>`_, but (a) we allow C++ exceptions, and (b) we allow reference arguments.
+* We try to follow the `Google C++ Style Guide <https://google.github.io/styleguide/cppguide.html>`_, but
+  (a) we allow C++ exceptions, and (b) we allow reference arguments.
 
-* We recommend using `Clang format <https://clang.llvm.org/docs/ClangFormat.html>`_ with our config file `.clang-format <https://github.com/roualdes/bridgestan/blob/main/.clang-format>`_.
+* We recommend using `Clang format <https://clang.llvm.org/docs/ClangFormat.html>`_ with our config file
+  `.clang-format <https://github.com/roualdes/bridgestan/blob/main/.clang-format>`_.
 
 Python
 ------

docs/languages/c-api.rst

@@ -1,7 +1,7 @@
 C API
 =====
 
-----
+---
 
 Installation
 ------------

docs/languages/python.rst

@@ -22,7 +22,7 @@ The first time you compile a model, the BridgeStan source code for your current
 will be downloaded and placed in :file:`~/.bridgestan/`.
 If you prefer to use a source distribution of BridgeStan, consult the following section.
 
-Note that the system pre-requisites from the :doc:`Getting Started guide <../getting-started>` 
+Note that the system pre-requisites from the :doc:`Getting Started guide <../getting-started>`
 are still required and will not be automatically installed by this method.
 
 From Source

rust/examples/example.rs

@@ -25,7 +25,7 @@ fn main() {
 
     // The path to the compiled model
     let path = compile_model(&bs_path, &path, &[], &[]).expect("Could not compile Stan model.");
-    println!("Compiled model: {:?}", path);
+    println!("Compiled model: {path:?}");
 
     let lib = open_library(path).expect("Could not load compiled Stan model.");
 
@@ -54,5 +54,5 @@ fn main() {
     let logp = model
         .log_density_gradient(&point[..], true, true, &mut gradient_out[..])
         .expect("Stan failed to evaluate the logp function.");
-    println!("logp: {}\ngrad: {:?}", logp, gradient_out);
+    println!("logp: {logp}\ngrad: {gradient_out:?}");
 }

rust/tests/common.rs

@@ -17,9 +17,9 @@ pub fn get_model<S: AsRef<str>>(name: S) -> (StanLibrary, Option<CString>) {
     let name = name.as_ref();
     let mut base = model_dir();
     base.push(name);
-    let lib = base.join(format!("{}_model.so", name));
+    let lib = base.join(format!("{name}_model.so"));
     if !lib.exists() {
-        panic!("Could not find compiled model {}", name);
+        panic!("Could not find compiled model {name}");
     }
     let lib = open_library(lib).unwrap();
 

rust/tests/model.rs

@@ -196,8 +196,8 @@ fn model_compiling() {
     let name = "stdnormal";
     let mut base = model_dir();
     base.push(name);
-    let lib_path = base.join(format!("{}_model.so", name));
-    let stan_path = base.join(format!("{}.stan", name));
+    let lib_path = base.join(format!("{name}_model.so"));
+    let stan_path = base.join(format!("{name}.stan"));
     remove_file(lib_path).unwrap_or_default();
 
     let bs_path: PathBuf = std::env::var("BRIDGESTAN")