Update to Stan 2.35 (#5)

* Get ready for Stan 2.35 changes

* Update metadata

* Clear cache

* 3.12 fix

* Update main.yaml

Author: WardBrian

.github/windows-env.yml

@@ -5,5 +5,5 @@ channels:
 dependencies:
   - tbb-devel>=2021
   - sundials==6.1.1
-  - cmdstan==2.34.0 # for speed, we don't really need all the mingw stuff this pulls in
+  - cmdstan==2.35.0 # for speed, we don't really need all the mingw stuff this pulls in
   - pip

.github/workflows/main.yaml

@@ -11,8 +11,8 @@ on:
   workflow_dispatch: {}
 
 env:
-  CMDSTAN_VERSION: "2.34.0"
-  CACHE_NUMBER: 1
+  CMDSTAN_VERSION: "2.35.0"
+  CACHE_NUMBER: 0
 
 jobs:
   test-package:
@@ -21,7 +21,8 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.9, "3.10", 3.11, 3.12]
+      fail-fast: false
 
     steps:
       - name: Check out github
@@ -57,7 +58,8 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.9, "3.10", 3.11, 3.12]
+      fail-fast: false
 
     steps:
       - name: Check out github

.gitignore

@@ -8,3 +8,4 @@ __pycache__/
 build/
 .pytest_cache/
 *.egg-info/
+env/

README.md

@@ -8,7 +8,7 @@ This is very similar to *[Exposing Stan user-defined functions using CmdStanR an
 
 This supports all possible Stan functions, including pRNGs and functions which edit the `target` variable.
 These are supported through two objects exposed on all models, `StanRNG` and `StanAccumulator`, which are
-thin wrappers for `boost::ecuyer1988` and `stan::math::accumulator<double>`, respectively.
+thin wrappers for `stan::rng_t` and `stan::math::accumulator<double>`, respectively.
 
 ## Running
 

misc/build.ps1

@@ -17,7 +17,7 @@ $extension = python -c "from distutils import sysconfig; print(sysconfig.get_con
 $pybind_includes = python -m pybind11 --includes
 
 $cxxflags = '-std=c++1y -O3 -D_REENTRANT -DBOOST_DISABLE_ASSERTS -D_BOOST_LGAMMA -DTBB_INTERFACE_NEW -Wno-sign-compare -Wno-deprecated-builtins -Wno-ignored-attributes -shared'
-$cppflags = "-I $conda_library_path\include\ -I $cmdstan_location/stan/src -I $cmdstan_location/stan/lib/rapidjson_1.1.0/ -I $cmdstan_location/stan/lib/stan_math/ -I $cmdstan_location/stan/lib/stan_math/lib/eigen_3.4.0 -I $cmdstan_location/stan/lib/stan_math/lib/boost_1.78.0 $pybind_includes"
+$cppflags = "-I $conda_library_path\include\ -I $cmdstan_location/stan/src -I $cmdstan_location/stan/lib/rapidjson_1.1.0/ -I $cmdstan_location/stan/lib/stan_math/ -I $cmdstan_location/stan/lib/stan_math/lib/eigen_3.4.0 -I $cmdstan_location/stan/lib/stan_math/lib/boost_1.84.0 $pybind_includes"
 
 $linkflags = "-Wl`",/LIBPATH:$conda_library_path\lib\`" -Wl`",/LIBPATH:$cpython_libs`""
 $linklibs = '-ltbb -lsundials_nvecserial -lsundials_cvodes -lsundials_idas -lsundials_kinsol'

misc/build.sh

@@ -14,4 +14,4 @@ else
     extra_args=""
     dll_ext=".so.2"
 fi
-g++ -std=c++1y $extra_args -O3 -D_REENTRANT -DBOOST_DISABLE_ASSERTS -Wno-sign-compare -Wno-ignored-attributes -I "$CMDSTAN"/stan/lib/stan_math/lib/tbb_2020.3/include  -I "$CMDSTAN"/stan/src -I "$CMDSTAN"/lib/rapidjson_1.1.0/ -I "$CMDSTAN"/stan/lib/stan_math/ -I "$CMDSTAN"/stan/lib/stan_math/lib/eigen_3.4.0 -I "$CMDSTAN"/stan/lib/stan_math/lib/boost_1.78.0 -I "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/include -I $CMDSTAN/stan/lib/stan_math/lib/sundials_6.1.1/src/sundials $(python3 -m pybind11 --includes) -shared -fPIC "$model_name".cpp -o "$model_name$(python3-config --extension-suffix)" -Wl,-L,"$CMDSTAN/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"$CMDSTAN/stan/lib/stan_math/lib/tbb" "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a "$CMDSTAN"/stan/lib/stan_math/lib/tbb/libtbb"$dll_ext"
+g++ -std=c++1y $extra_args -O3 -D_REENTRANT -DBOOST_DISABLE_ASSERTS -Wno-sign-compare -Wno-ignored-attributes -I "$CMDSTAN"/stan/lib/stan_math/lib/tbb_2020.3/include  -I "$CMDSTAN"/stan/src -I "$CMDSTAN"/lib/rapidjson_1.1.0/ -I "$CMDSTAN"/stan/lib/stan_math/ -I "$CMDSTAN"/stan/lib/stan_math/lib/eigen_3.4.0 -I "$CMDSTAN"/stan/lib/stan_math/lib/boost_1.84.0 -I "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/include -I $CMDSTAN/stan/lib/stan_math/lib/sundials_6.1.1/src/sundials $(python3 -m pybind11 --includes) -shared -fPIC "$model_name".cpp -o "$model_name$(python3-config --extension-suffix)" -Wl,-L,"$CMDSTAN/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"$CMDSTAN/stan/lib/stan_math/lib/tbb" "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a "$CMDSTAN"/stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a "$CMDSTAN"/stan/lib/stan_math/lib/tbb/libtbb"$dll_ext"

misc/setuptools_version.py

@@ -11,7 +11,7 @@
     cmdstan_path + "/lib/rapidjson_1.1.0/",
     cmdstan_path + "/stan/lib/stan_math/",
     cmdstan_path + "/stan/lib/stan_math/lib/eigen_3.4.0",
-    cmdstan_path + "/stan/lib/stan_math/lib/boost_1.78.0",
+    cmdstan_path + "/stan/lib/stan_math/lib/boost_1.84.0",
     cmdstan_path + "/stan/lib/stan_math/lib/sundials_6.1.1/include",
     cmdstan_path + "/stan/lib/stan_math/lib/sundials_6.1.1/src/sundials",
 ]

pybind_stan_fns/__init__.py

@@ -4,7 +4,6 @@
 import subprocess
 import sys
 import sysconfig
-from distutils import sysconfig as dist_sysconfig
 from pathlib import Path
 
 import cmdstanpy
@@ -47,7 +46,7 @@ def get_pybind_includes():
     ("stan", "lib", "rapidjson_1.1.0"),
     ("stan", "lib", "stan_math"),
     ("stan", "lib", "stan_math", "lib", "eigen_3.4.0"),
-    ("stan", "lib", "stan_math", "lib", "boost_1.81.0"),
+    ("stan", "lib", "stan_math", "lib", "boost_1.84.0"),
 ]
 
 OTHER_INCLUDES = []
@@ -68,7 +67,7 @@ def get_pybind_includes():
     STANC = STANC.with_suffix(".exe")
     CPP_DEFINES.extend(["_BOOST_LGAMMA", "TBB_INTERFACE_NEW"])
     CONDA_PATH = Path(os.environ["CONDA_PREFIX"])
-    OTHER_INCLUDES.append(str(CONDA_PATH / "Library" / "include"))
+    OTHER_INCLUDES.append(os.fspath(CONDA_PATH / "Library" / "include"))
     LDFLAGS = [
         f'-Wl,/LIBPATH:{CONDA_PATH / "Library" / "lib"}',
         f'-Wl,/LIBPATH:{CONDA_PATH / "libs"}',
@@ -93,13 +92,13 @@ def get_pybind_includes():
     CXX = "clang++"
     CXX_FLAGS.extend(["-undefined", "dynamic_lookup"])
 
-CMDSTAN_INCLUDE_PATHS = [str(CMDSTAN.joinpath(*sub)) for sub in CMDSTAN_SUB_INCLUDES]
+CMDSTAN_INCLUDE_PATHS = [os.fspath(CMDSTAN.joinpath(*sub)) for sub in CMDSTAN_SUB_INCLUDES]
 
 CPP_FLAGS = [f"-D{define}" for define in CPP_DEFINES] + [
     f"-I{path}"
     for path in CMDSTAN_INCLUDE_PATHS + OTHER_INCLUDES + get_pybind_includes()
 ]
-EXT_SUFFIX = dist_sysconfig.get_config_var("EXT_SUFFIX")
+EXT_SUFFIX = sysconfig.get_config_var("EXT_SUFFIX")
 LDLIBS = [f"-l{lib}" for lib in LIBRARIES]
 
 
@@ -109,17 +108,17 @@ def expose(file: str):
     # create .cpp file and add pybind specific code
     subprocess.run(
         [
-            str(STANC),
+            os.fspath(STANC),
             "--standalone-functions",
             f"--include-paths={file_path.parent}",
-            f"--o={file_path.parent / file_path.stem}.cpp-pre",
-            str(file_path),
+            f"--o={file_path.parent / file_path.with_suffix('.cpp-pre')}",
+            os.fspath(file_path),
         ],
         check=True,
     )
     preprocess.preprocess(
-        str(file_path.parent / file_path.stem) + ".cpp-pre",
-        out=(str(file_path.parent / file_path.stem) + ".cpp"),
+        os.fspath(file_path.parent / file_path.with_suffix(".cpp-pre")),
+        out=os.fspath(file_path.parent / file_path.with_suffix(".cpp")),
     )
 
     # invoke compiler
@@ -128,8 +127,8 @@ def expose(file: str):
         + CXX_FLAGS
         + CPP_FLAGS
         + [
-            f"-o{file_path.parent / file_path.stem}{EXT_SUFFIX}",
-            f"{file_path.parent / file_path.stem}.cpp",
+            f"-o{file_path.parent / file_path.with_suffix(EXT_SUFFIX)}",
+           os.fspath(file_path.parent / file_path.with_suffix(".cpp")),
         ]
         + LDFLAGS
         + LDLIBS
@@ -138,6 +137,6 @@ def expose(file: str):
 
     if res.returncode:
         raise RuntimeError("Build failed!\n" + " ".join(compile_command) + "\n" + res.stderr)
-    sys.path.append(str(file_path.parent))
+    sys.path.append(os.fspath(file_path.parent))
 
     return importlib.import_module(file_path.stem)

pybind_stan_fns/preprocess.py

@@ -22,7 +22,7 @@ def insert_includes(text):
 PYBIND11_MODULE({model_name}, m)
 {{
 
-  py::class_<boost::ecuyer1988>(m, "StanRNG")
+  py::class_<stan::rng_t>(m, "StanRNG")
       .def(py::init<int>());
 
   using acc = stan::math::accumulator<double>;
@@ -108,8 +108,8 @@ def populate_boilerplate(model_name, text):
             arg_names.append(arg_name.replace("&", "").replace("__", ""))
             arg_tys.append(arg_ty)
 
-            if arg.startswith("boost::ecuyer"):
-                arg_defaults.append("boost::ecuyer1988(1234)")
+            if arg.startswith("stan::rng_t"):
+                arg_defaults.append("stan::rng_t(1234)")
             else:
                 arg_defaults.append("")
 

pyproject.toml

@@ -1,3 +1,21 @@
 [build-system]
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "pybind_stan_fns"
+readme = "README.md"
+version = "0.0.1"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Brian Ward", email = "bward@flatironinstitute.org" }]
+requires-python = ">=3.8"
+dependencies = ["numpy>=1.21.0", "cmdstanpy>=1.0.6", "pybind11"]
+
+[project.urls]
+"Homepage" = "https://github.com/WardBrian/pybind_expose_stan_fns"
+
+[tool.setuptools]
+packages = ["pybind_stan_fns"]
+
+[project.optional-dependencies]
+test = ["pytest"]