fix: use stanio for creating Stan's data JSON (#205)

Author: WardBrian

pyproject.toml

@@ -28,12 +28,13 @@ Homepage = "https://pymc-devs.github.io/nutpie/"
 Repository = "https://github.com/pymc-devs/nutpie"
 
 [project.optional-dependencies]
-stan = ["bridgestan >= 2.6.1"]
+stan = ["bridgestan >= 2.6.1", "stanio >= 0.5.1"]
 pymc = ["pymc >= 5.20.1", "numba >= 0.60.0"]
 pymc-jax = ["pymc >= 5.20.1", "jax >= 0.4.27"]
 nnflow = ["flowjax >= 17.1.0", "equinox >= 0.11.12"]
 dev = [
   "bridgestan >= 2.6.1",
+  "stanio >= 0.5.1",
   "pymc >= 5.20.1",
   "numba >= 0.60.0",
   "jax >= 0.4.27",
@@ -43,6 +44,7 @@ dev = [
 ]
 all = [
   "bridgestan >= 2.6.1",
+  "stanio >= 0.5.1",
   "pymc >= 5.20.1",
   "numba >= 0.60.0",
   "jax >= 0.4.27",

python/nutpie/compile_stan.py

@@ -1,25 +1,16 @@
-import json
 import tempfile
 from dataclasses import dataclass, replace
 from importlib.util import find_spec
 from pathlib import Path
 from typing import Any, Optional
 
-import numpy as np
 import pandas as pd
 from numpy.typing import NDArray
 
 from nutpie import _lib
 from nutpie.sample import CompiledModel
 
 
-class _NumpyArrayEncoder(json.JSONEncoder):
-    def default(self, obj):
-        if isinstance(obj, np.ndarray):
-            return obj.tolist()
-        return json.JSONEncoder.default(self, obj)
-
-
 @dataclass(frozen=True)
 class CompiledStanModel(CompiledModel):
     _coords: Optional[dict[str, Any]]
@@ -39,7 +30,16 @@ def with_data(self, *, seed=None, **updates):
         data.update(updates)
 
         if data is not None:
-            data_json = json.dumps(data, cls=_NumpyArrayEncoder)
+            if find_spec("stanio") is None:
+                raise ImportError(
+                    "stanio is not installed in the current environment. "
+                    "Please install it with something like "
+                    "'pip install stanio' or 'pip install nutpie[stan]'."
+                )
+
+            import stanio
+
+            data_json = stanio.dump_stan_json(data)
         else:
             data_json = None
 
@@ -136,7 +136,7 @@ def compile_stan_model(
         raise ImportError(
             "BridgeStan is not installed in the current environment. "
             "Please install it with something like "
-            "'pip install bridgestan'."
+            "'pip install bridgestan' or 'pip install nutpie[stan]'."
         )
 
     import bridgestan

tests/test_stan.py

@@ -31,7 +31,7 @@ def test_stan_model():
 def test_stan_model_data():
     model = """
     data {
-        real x;
+        complex x;
     }
     parameters {
         real a;
@@ -44,7 +44,7 @@ def test_stan_model_data():
     compiled_model = nutpie.compile_stan_model(code=model)
     with pytest.raises(RuntimeError):
         trace = nutpie.sample(compiled_model)
-    trace = nutpie.sample(compiled_model.with_data(x=np.array(3.0)))
+    trace = nutpie.sample(compiled_model.with_data(x=np.array(3.0j)))
     trace.posterior.a  # noqa: B018