From 74e952cea4f79dfa1c3836e1282be4d3f87e0e31 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 13:43:30 +0000
Subject: [PATCH] =?UTF-8?q?=F0=9F=A7=B9=20Transition=20csimulator=20init?=
 =?UTF-8?q?=20asserts=20to=20BNGErrors=20and=20BNGLogger?=
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Replaced plain `assert` statements used during species and parameter initialization in `csimulator.py` with proper error handling.
The code now explicitly checks lengths, logs detailed mismatch info using `BNGLogger`, and raises a newly introduced `BNGSimulatorError`.

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 bionetgen/core/exc.py             |  7 +++++++
 bionetgen/simulator/csimulator.py | 20 +++++++++++++++-----
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/bionetgen/core/exc.py b/bionetgen/core/exc.py
index 11f5307f..a260a1db 100644
--- a/bionetgen/core/exc.py
+++ b/bionetgen/core/exc.py
@@ -93,3 +93,10 @@ def __init__(
         self.model = model
         self.message = message
         super().__init__(self.message)
+
+class BNGSimulatorError(BNGError):
+    """Error related to BNG simulators."""
+
+    def __init__(self, message="There was an issue with the BNG simulator"):
+        self.message = message
+        super().__init__(self.message)
diff --git a/bionetgen/simulator/csimulator.py b/bionetgen/simulator/csimulator.py
index 34a6bdcd..c72cab53 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()
@@ -39,6 +40,7 @@ class CSimWrapper:
     """
 
     def __init__(self, lib_path, num_params=None, num_spec_init=None):
+        self.logger = BNGLogger()
         # we need the result struct to reconstruct the object
         self.return_struct = RESULT
         # load the shared library
@@ -55,16 +57,24 @@ 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:
+            self.logger.error(
+                f"Length of species initialization array ({len(arr)}) does not match expected length ({self.num_spec_init})",
+                loc=f"{__file__} : CSimWrapper.set_species_init()"
+            )
+            raise BNGSimulatorError(f"Expected {self.num_spec_init} initial species, but 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:
+            self.logger.error(
+                f"Length of parameter array ({len(arr)}) does not match expected length ({self.num_params})",
+                loc=f"{__file__} : CSimWrapper.set_parameters()"
+            )
+            raise BNGSimulatorError(f"Expected {self.num_params} parameters, but got {len(arr)}")
         self.parameters = np.array(arr, dtype=np.float64)
 
     def simulate(self, t_start=0, t_end=100, n_steps=100):