From 8814450c507f0c6779415d2fbcf568acb4e17b89 Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Tue, 14 Feb 2023 15:07:42 -0800
Subject: [PATCH 1/2] timeout works, but does not include compile time in limit

---
 spatialpy/solvers/solver.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py
index c884a6f8..d1591728 100644
--- a/spatialpy/solvers/solver.py
+++ b/spatialpy/solvers/solver.py
@@ -27,7 +27,7 @@
 
 import numpy
 
-from spatialpy.core.spatialpyerror import ModelError, SimulationError, SimulationTimeout
+from spatialpy.core.spatialpyerror import ModelError, SimulationError
 
 def _read_from_stdout(stdout ,verbose=True):
     try:
@@ -536,7 +536,6 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
         :returns: A SpatialPy Result object containing spatial and time series data from simulation.
         :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result)
 
-        :raises SimulationTimeout: Simulation exceeded timeout.
         :raises SimulationError: Simulation execution failed.
         """
         from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel
@@ -587,7 +586,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
                         result.timeout = True
                         # send signal to the process group
                         os.killpg(process.pid, signal.SIGINT)
-                        raise SimulationTimeout("SpatialPy solver timeout exceded.") from err
+
             except OSError as err:
                 print(f"Error, execution of solver raised an exception: {err}")
                 print(f"cmd = {solver_cmd}")

From 667097a43bd7bf2e869dc6f309d079d4dfa8bcdb Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Wed, 15 Feb 2023 15:38:17 -0800
Subject: [PATCH 2/2] Fixes #348

---
 spatialpy/core/result.py    | 13 +++++++++++++
 spatialpy/solvers/solver.py | 14 ++++++--------
 2 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/spatialpy/core/result.py b/spatialpy/core/result.py
index 1753a1d9..9b83348e 100644
--- a/spatialpy/core/result.py
+++ b/spatialpy/core/result.py
@@ -156,6 +156,19 @@ def __init__(self, model=None, result_dir=None):
         self.timeout = False
         self.official_vtk = False
         self.result_dir = result_dir
+        self.listOfResultObjects = [self]
+
+    def __len__(self):
+        return len(self.listOfResultObjects)
+
+    def __getitem__(self, index):
+        return self.listOfResultObjects[index]
+
+    def __setitem__(self, index, item):
+        self.listOfResultObjects[index] = item
+
+    def append(self, item):
+        self.listOfResultObjects.append(item)
 
     def __eq__(self, other):
         if isinstance(other, Result) and self.result_dir and other.result_dir:
diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py
index d1591728..e6ee3115 100644
--- a/spatialpy/solvers/solver.py
+++ b/spatialpy/solvers/solver.py
@@ -534,13 +534,11 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
         :type verbose: bool
 
         :returns: A SpatialPy Result object containing spatial and time series data from simulation.
-        :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result)
+        :rtype: spatialpy.Result.Result 
 
         :raises SimulationError: Simulation execution failed.
         """
         from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel
-        if number_of_trajectories > 1:
-            result_list = []
         # Check if compiled, call compile() if not.
         if not self.is_compiled:
             self.compile(debug=debug, profile=profile)
@@ -601,9 +599,9 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
             result.success = True
             if profile:
                 self.__read_profile_info(result)
-            if number_of_trajectories > 1:
-                result_list.append(result)
-            else:
-                return result
+            if run_ndx == 0:                
+                first_result = result
+            elif number_of_trajectories > 1:
+                first_result.append(result)
 
-        return result_list
+        return first_result