Switch deepcopy to dill for model copying

Replaced usage of deepcopy with dill serialization for copying model objects in InitMap. Added dill as a dependency in pyproject.toml to support this change.

Author: JR-1991

pyenzyme/thinlayers/psyces.py

@@ -10,6 +10,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 from joblib import Parallel, delayed
+import dill  # noqa: F401
 import numpy as np
 import pandas as pd
 import os
@@ -526,7 +527,7 @@ def to_pysces_model(self, model: pysces.model):
         Returns:
             pysces.model: The updated model with initial conditions set.
         """
-        model = deepcopy(model)
+        model = dill.loads(dill.dumps(model))
         model.sim_time = np.array(self.time)
         model.__dict__.update(
             {

pyproject.toml

@@ -23,6 +23,7 @@ mdmodels = "^0.2.1"
 joblib = "^1.5.0"
 bokeh = "^3.7.3"
 matplotlib = "^3.10"
+dill = ">=0.3.9,<0.5.0"
 
 [tool.poetry.group.psyces.dependencies]
 pysces = "^1.2.3"