Merge pull request #27 from UC-Davis-molecular-computing/dev

Dev

README.md

@@ -10,6 +10,7 @@ The core of the simulator uses a [batching algorithm](https://arxiv.org/abs/2005
 * [First example protocol](#first-example-protocol)
 * [Larger state protocol](#larger-state-protocol)
 * [Protocol with Multiple Fields](#protocol-with-multiple-fields)
+* [Simulating Chemical Reaction Networks (CRNs)](#simulating-chemical-reaction-networks-crns)
 
 ## Installation
 

ppsim/__version__.py

@@ -1 +1 @@
-version = '0.1.3' # version line; WARNING: do not remove or change this line or comment
+version = '0.1.5' # version line; WARNING: do not remove or change this line or comment

ppsim/simulation.py

@@ -411,7 +411,10 @@ def run(self, run_until: Union[float, ConvergenceDetector] = None,
                 Defaults to True.
         """
         if len(self.snapshots) == 0 and timer is True:
-            self.add_snapshot(TimeUpdate())
+            if type(run_until) is float or type(run_until) is int:
+                self.add_snapshot(TimeUpdate(time_bound=run_until))
+            else:
+                self.add_snapshot(TimeUpdate())
 
         end_time = None
         # stop_condition() returns True when it is time to stop
@@ -499,8 +502,9 @@ def get_next_time():
             snapshot.update()
 
         if len(self.snapshots) == 1 and type(self.snapshots[0]) is TimeUpdate:
+            self.snapshots[0].pbar.close()
             self.snapshots.pop()
-            print()
+            # print()
 
     @property
     def reactions(self) -> str: