Merge main into modelapi-centralize-action-validation

Resolved conflict by combining:
- Updated import style (separate lines, shutil instead of distutils)
- Added BNGParseError import needed for validate_action method

Author: jrfaeder

bionetgen/core/utils/utils.py

@@ -1,7 +1,8 @@
-import os, subprocess
-from bionetgen.core.exc import BNGParseError, BNGPerlError
-from distutils import spawn
+import os
+import shutil
+import subprocess
 
+from bionetgen.core.exc import BNGParseError, BNGPerlError
 from bionetgen.core.utils.logging import BNGLogger
 
 
@@ -679,7 +680,7 @@ def _try_path(candidate_path):
             return hit
 
     # 3) On PATH
-    bng_on_path = spawn.find_executable("BNG2.pl")
+    bng_on_path = shutil.which("BNG2.pl")
     if bng_on_path:
         tried.append(bng_on_path)
         hit = _try_path(bng_on_path)
@@ -706,7 +707,7 @@ def test_perl(app=None, perl_path=None):
     logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
     # find path to perl binary
     if perl_path is None:
-        perl_path = spawn.find_executable("perl")
+        perl_path = shutil.which("perl")
     if perl_path is None:
         raise BNGPerlError
     # check if perl is actually working

bionetgen/simulator/csimulator.py

@@ -1,11 +1,31 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError
 
+
+def _new_ccompiler():
+    """Return a distutils ccompiler instance, sourced from setuptools.
+
+    distutils was removed from the stdlib in Python 3.12; setuptools vendors
+    the same API as ``setuptools._distutils``. Imported lazily so that
+    ``import bionetgen`` does not require setuptools at runtime — only
+    instantiating ``CSimulator`` does.
+    """
+    try:
+        from setuptools._distutils import ccompiler
+    except ImportError as exc:
+        raise BNGCompileError(
+            None,
+            "CSimulator requires the distutils ccompiler API, which was "
+            "removed from the stdlib in Python 3.12. Install setuptools "
+            "(pip install setuptools) to provide it.",
+        ) from exc
+    return ccompiler.new_compiler()
+
+
 # This allows access to the CLIs config setup
 app = BioNetGen()
 app.setup()
@@ -164,7 +184,7 @@ def __init__(self, model_file, generate_network=False):
         else:
             print(f"model format not recognized: {model_file}")
         # set compiler
-        self.compiler = ccompiler.new_compiler()
+        self.compiler = _new_ccompiler()
         self.compiler.add_include_dir(conf.get("cvode_include"))
         self.compiler.add_library_dir(conf.get("cvode_lib"))
         # compile shared library