From 3e886a55d5b810e09dece94b738952a17c35cc1e Mon Sep 17 00:00:00 2001
From: Bill Hlavacek <bill.hlavacek@gmail.com>
Date: Sun, 10 May 2026 15:12:35 -0600
Subject: [PATCH 1/3] Replace distutils.spawn.find_executable with shutil.which

distutils was removed from the stdlib in Python 3.12 and emits a
DeprecationWarning before then. shutil.which is the modern stdlib
equivalent, takes the same argument, and returns the same result
(absolute path or None).
---
 bionetgen/core/utils/utils.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/bionetgen/core/utils/utils.py b/bionetgen/core/utils/utils.py
index 7d19fd23..604162cc 100644
--- a/bionetgen/core/utils/utils.py
+++ b/bionetgen/core/utils/utils.py
@@ -1,7 +1,8 @@
-import os, subprocess
-from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
+import os
+import shutil
+import subprocess
 
+from bionetgen.core.exc import BNGPerlError
 from bionetgen.core.utils.logging import BNGLogger
 
 
@@ -589,7 +590,7 @@ 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)
@@ -616,7 +617,7 @@ 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

From 3925a0ab637e7aa2d6c2c92f7d5aefc84853b789 Mon Sep 17 00:00:00 2001
From: Bill Hlavacek <bill.hlavacek@gmail.com>
Date: Sun, 10 May 2026 15:12:46 -0600
Subject: [PATCH 2/3] Replace distutils.ccompiler with setuptools._distutils
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

distutils was removed from the stdlib in Python 3.12. setuptools
vendors the same API as setuptools._distutils.

The ccompiler import is wrapped in a lazy _new_ccompiler() helper
called from CSimulator.__init__, so plain 'import bionetgen' does
not require setuptools at runtime — only the cpy simulator path
does, which already requires CVODE installed locally. Missing
setuptools yields a clear BNGCompileError with install guidance.
---
 bionetgen/simulator/csimulator.py | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/bionetgen/simulator/csimulator.py b/bionetgen/simulator/csimulator.py
index 34a6bdcd..b65958aa 100644
--- a/bionetgen/simulator/csimulator.py
+++ b/bionetgen/simulator/csimulator.py
@@ -1,11 +1,30 @@
 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 +183,7 @@ 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

From 514f24720ee4485862ae781f92b356806e75ff5b Mon Sep 17 00:00:00 2001
From: Bill Hlavacek <bill.hlavacek@gmail.com>
Date: Sun, 10 May 2026 15:21:16 -0600
Subject: [PATCH 3/3] Apply black formatting to _new_ccompiler helper

---
 bionetgen/simulator/csimulator.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bionetgen/simulator/csimulator.py b/bionetgen/simulator/csimulator.py
index b65958aa..4e7dd0d5 100644
--- a/bionetgen/simulator/csimulator.py
+++ b/bionetgen/simulator/csimulator.py
@@ -25,6 +25,7 @@ def _new_ccompiler():
         ) from exc
     return ccompiler.new_compiler()
 
+
 # This allows access to the CLIs config setup
 app = BioNetGen()
 app.setup()