diff --git a/bio_compose/__init__.py b/bio_compose/__init__.py index bb1c090..d99e15c 100644 --- a/bio_compose/__init__.py +++ b/bio_compose/__init__.py @@ -16,13 +16,26 @@ def run_simulation(*args, **kwargs) -> SimulationResult: """ - Run a simulation with BioCompose + Run a simulation with BioCompose. Args: - - **args**: Positional arguments: - 1 argument(**smoldyn simulation only**): smoldyn simulation configuration in which time parameters (dt, duration) are already defined. - 3 arguments(**smoldyn simulation only**): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt - 5 arguments(**sbml simulation only**): sbml filepath, simulation start, simulation end, simulation steps, simulator. + *args: Positional arguments: + 1 argument (smoldyn simulation only): + - smoldyn simulation configuration in which time parameters (dt, duration) are already defined. + + 3 arguments (smoldyn simulation only): + - smoldyn configuration file + - smoldyn simulation duration + - smoldyn simulation dt + + 5 arguments (sbml simulation only): + - sbml filepath + - simulation start + - simulation end + - simulation steps + - simulator + + **kwargs: Keyword arguments. Returns: `SimulationResult` instance of simulation results. diff --git a/documentation/build/doctrees/bio_compose.doctree b/documentation/build/doctrees/bio_compose.doctree index 1bd96c5..04306ad 100644 Binary files a/documentation/build/doctrees/bio_compose.doctree and b/documentation/build/doctrees/bio_compose.doctree differ diff --git a/documentation/build/doctrees/environment.pickle b/documentation/build/doctrees/environment.pickle index 34c6a38..3b215d1 100644 Binary files a/documentation/build/doctrees/environment.pickle and b/documentation/build/doctrees/environment.pickle differ diff --git a/documentation/build/html/_modules/bio_compose.html b/documentation/build/html/_modules/bio_compose.html index 8713b06..6d76d18 100644 --- a/documentation/build/html/_modules/bio_compose.html +++ b/documentation/build/html/_modules/bio_compose.html @@ -92,13 +92,26 @@

Source code for bio_compose

 [docs]
 def run_simulation(*args, **kwargs) -> SimulationResult:
     """
-    Run a simulation with BioCompose
+    Run a simulation with BioCompose.
 
     Args:
-        - **args**: Positional arguments:
-            1 argument(**smoldyn simulation only**): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
-            3 arguments(**smoldyn simulation only**): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt
-            5 arguments(**sbml simulation only**): sbml filepath, simulation start, simulation end, simulation steps, simulator.
+        *args: Positional arguments:
+            1 argument (smoldyn simulation only):
+                - smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
+
+            3 arguments (smoldyn simulation only):
+                - smoldyn configuration file
+                - smoldyn simulation duration
+                - smoldyn simulation dt
+
+            5 arguments (sbml simulation only):
+                - sbml filepath
+                - simulation start
+                - simulation end
+                - simulation steps
+                - simulator
+
+        **kwargs: Keyword arguments.
 
     Returns:
         `SimulationResult` instance of simulation results.
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
index 1a699e3..0ce3ad2 100644
--- a/documentation/build/html/bio_compose.html
+++ b/documentation/build/html/bio_compose.html
@@ -662,13 +662,36 @@ 
Submodules
 

 bio_compose.run_simulation(*args, **kwargs) → SimulationResult[source]

-
Run a simulation with BioCompose

+
Run a simulation with BioCompose.

 

 
Parameters:

-
args (-) – Positional arguments:
-1 argument(smoldyn simulation only): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
-3 arguments(smoldyn simulation only): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt
-5 arguments(sbml simulation only): sbml filepath, simulation start, simulation end, simulation steps, simulator.

+
    
+
  • *args – 
    Positional arguments:
+1 argument (smoldyn simulation only):
    
+
    
+
      
+
    • smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
      • 
+
    
+
    
+
    
+
    3 arguments (smoldyn simulation only):
      
+
    • smoldyn configuration file
      • 
+
    • smoldyn simulation duration
      • 
+
    • smoldyn simulation dt
      • 
+
    
+
    
+
    5 arguments (sbml simulation only):
      
+
    • sbml filepath
      • 
+
    • simulation start
      • 
+
    • simulation end
      • 
+
    • simulation steps
      • 
+
    • simulator
      • 
+
    
+
    
+
    
+
    • 
+
  • **kwargs – Keyword arguments.
    • 
+

 

 
Returns:

 
SimulationResult instance of simulation results.