From dc45893efb168b92548594e55742d84f7c00a7fe Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Mon, 13 Apr 2026 13:43:17 +0000
Subject: [PATCH 1/2] Refactor CSimulator error handling to use BNGLogger and
 BNGSimulatorError

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 bionetgen/core/exc.py             | 11 +++++++++++
 bionetgen/simulator/csimulator.py | 26 +++++++++++++++++++-------
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/bionetgen/core/exc.py b/bionetgen/core/exc.py
index 11f5307f..f4f25a8a 100644
--- a/bionetgen/core/exc.py
+++ b/bionetgen/core/exc.py
@@ -93,3 +93,14 @@ def __init__(
         self.model = model
         self.message = message
         super().__init__(self.message)
+
+
+class BNGSimulatorError(BNGError):
+    """Error related to simulating a BNG model."""
+
+    def __init__(
+        self,
+        message="There was an issue simulating your BNG model",
+    ):
+        self.message = message
+        super().__init__(self.message)
diff --git a/bionetgen/simulator/csimulator.py b/bionetgen/simulator/csimulator.py
index 34a6bdcd..2a5527e4 100644
--- a/bionetgen/simulator/csimulator.py
+++ b/bionetgen/simulator/csimulator.py
@@ -4,7 +4,8 @@
 from distutils import ccompiler
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
-from bionetgen.core.exc import BNGCompileError
+from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
+from bionetgen.core.utils.logging import BNGLogger
 
 # This allows access to the CLIs config setup
 app = BioNetGen()
@@ -12,6 +13,8 @@
 conf = app.config["bionetgen"]
 def_bng_path = conf["bngpath"]
 
+logger = BNGLogger()
+
 
 class RESULT(ctypes.Structure):
     _fields_ = [
@@ -55,16 +58,24 @@ def set_species_init(self, arr):
         """
         Set the initial species values array
         """
-        # TODO: Transition to BNGErrors and logging
-        assert len(arr) == self.num_spec_init
+        if len(arr) != self.num_spec_init:
+            logger.error(
+                f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
+            )
+            raise BNGSimulatorError(
+                f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
+            )
         self.species_init = np.array(arr, dtype=np.float64)
 
     def set_parameters(self, arr):
         """
         Set the parameter values array
         """
-        # TODO: Transition to BNGErrors and logging
-        assert len(arr) == self.num_params
+        if len(arr) != self.num_params:
+            logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
+            raise BNGSimulatorError(
+                f"Expected {self.num_params} parameters, got {len(arr)}"
+            )
         self.parameters = np.array(arr, dtype=np.float64)
 
     def simulate(self, t_start=0, t_end=100, n_steps=100):
@@ -141,7 +152,7 @@ class CSimulator(BNGSimulator):
     def __init__(self, model_file, generate_network=False):
         # check cvode library paths
         if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
-            print("CVODE include and library paths are not set, compilation won't work")
+            logger.warning("CVODE include and library paths are not set, compilation won't work")
         # let's load the model first
         if isinstance(model_file, str):
             # load model file
@@ -162,7 +173,8 @@ def __init__(self, model_file, generate_network=False):
                 )
             os.chdir(cd)
         else:
-            print(f"model format not recognized: {model_file}")
+            logger.error(f"model format not recognized: {model_file}")
+            raise BNGSimulatorError(f"model format not recognized: {model_file}")
         # set compiler
         self.compiler = ccompiler.new_compiler()
         self.compiler.add_include_dir(conf.get("cvode_include"))

From c0fe1c83c68180e203d393f0afd57e73e47cbf32 Mon Sep 17 00:00:00 2001
From: akutuva21 <akutuva22@gmail.com>
Date: Mon, 13 Apr 2026 10:20:28 -0400
Subject: [PATCH 2/2] chore: PR #92 remove forbidden artifacts and run black

---
 .gitignore                        | 2 ++
 bionetgen/simulator/csimulator.py | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/
diff --git a/bionetgen/simulator/csimulator.py b/bionetgen/simulator/csimulator.py
index 2a5527e4..f99ccd30 100644
--- a/bionetgen/simulator/csimulator.py
+++ b/bionetgen/simulator/csimulator.py
@@ -152,7 +152,9 @@ class CSimulator(BNGSimulator):
     def __init__(self, model_file, generate_network=False):
         # check cvode library paths
         if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
-            logger.warning("CVODE include and library paths are not set, compilation won't work")
+            logger.warning(
+                "CVODE include and library paths are not set, compilation won't work"
+            )
         # let's load the model first
         if isinstance(model_file, str):
             # load model file