Sum to 1 for all views; implement warnings correctly

Author: James Marshall

mumot/exceptions.py

@@ -1,6 +1,5 @@
 """MuMoT warning, exception and error classes."""
 
-
 class MuMoTWarning(Warning):
     """Class to report MuMoT-specific warnings.
     """

mumot/models.py

@@ -25,6 +25,7 @@
     Function
 )
 from sympy.parsing.latex import parse_latex
+from warnings import warn
 
 from . import (
     controllers,
@@ -1803,8 +1804,7 @@ def _getSingleAgentRules(self):
                 if reactant in allConstantReactants:
                     warningMsg = 'WARNING! Constant reactants appearing on the right-handside are ignored. Every constant reactant on the left-handside (implicitly) corresponds to the same constant reactant on the right-handside.\n'\
                                  f'E.g., in rule ' + str(rule.lhsReactants) + ' -> ' + str(rule.rhsReactants) + ' constant reactants should not appear on the right-handside.'
-                    print(warningMsg)
-                    #raise exceptions.MuMoTWarning(warningMsg)
+                    warn(warningMsg, exceptions.MuMoTWarning)
                     break  # print maximum one warning
 
             # Add to the target of the first non-empty item the new born coming from empty-set or constant reactants

mumot/utils.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 from sympy.parsing.latex import parse_latex
+from warnings import warn
 
 from . import (
     consts,
@@ -101,7 +102,8 @@ def _format_advanced_option(optionName: str, inputValue, initValues, extraParam=
     """
     if optionName == 'initialState':
         (allReactants, _) = extraParam
-        fixSumTo1 = extraParam2[0]
+        #fixSumTo1 = extraParam2[0] # until we have better information, all views should sum to 1, then use system size to scale
+        fixSumTo1 = True
         idleReactant = extraParam2[1]
         initialState = {}
         # handle initialState dictionary (either convert or generate a default one)
@@ -148,8 +150,7 @@ def _format_advanced_option(optionName: str, inputValue, initValues, extraParam=
                 idleValue = initialState[idleReactant][0]
                 if idleValue > 1: 
                     wrn_msg = f"WARNING! the initial value of reactant {idleReactant} has been changed to {new_val}\n"
-                    print(wrn_msg)
-                    #raise exceptions.MuMoTWarning(wrn_msg)
+                    warn(wrn_msg, exceptions.MuMoTWarning)
                     initialState[idleReactant][0] = new_val
                 # the idleValue have range min-max reset to [0,1]
                 initialState[idleReactant][1] = 0
@@ -171,8 +172,7 @@ def _format_advanced_option(optionName: str, inputValue, initValues, extraParam=
                         new_val = max(0, pop[0] + (1 - sumValues))
                         if not _almostEqual(pop[0], new_val):
                             wrn_msg = f"WARNING! the initial value of reactant {reactant} has been changed to {new_val}\n"
-                            print(wrn_msg)
-                            #raise exceptions.MuMoTWarning(wrn_msg)
+                            warn(wrn_msg, exceptions.MuMoTWarning)
                             sumValues -= pop[0]
                             sumValues += new_val
                             initialState[reactant][0] = new_val
@@ -193,8 +193,7 @@ def _format_advanced_option(optionName: str, inputValue, initValues, extraParam=
                                    for reactant in allReactants
                                    if reactant != reactantToFix])
                 wrn_msg = f"WARNING! the initial value of reactant {reactantToFix} has been changed to {new_val}\n"
-                print(wrn_msg)
-                #raise exceptions.MuMoTWarning(wrn_msg)
+                warn(wrn_msg, exceptions.MuMoTWarning)
                 initialState[reactantToFix][0] = new_val
         return [initialState, fixedBool]
         # print("Initial State is " + str(initialState))

mumot/views.py

@@ -32,6 +32,7 @@
     symbols,
 )
 from sympy.parsing.latex import parse_latex
+from warnings import warn
 
 from . import (
     consts,
@@ -3912,8 +3913,7 @@ def _constructorSpecificParams(self, MAParams):
             #    self._errorMessage.value = "Only Moving-Particle netType is available when rules contain the emptyset."
             if not self._netType == consts.NetworkType.DYNAMIC:
                 wrnMsg = "Only Moving-Particle netType is available when rules contain the emptyset or constant reactants."
-                print(wrnMsg)
-                #raise exceptions.MuMoTWarning()
+                warn(wrnMsg, exceptions.MuMoTWarning)
             self._netType = consts.NetworkType.DYNAMIC
             if self._controller:  # updating value and disabling widget
                 if self._controller._widgetsExtraParams.get('netType') is not None:
@@ -3928,8 +3928,7 @@ def _constructorSpecificParams(self, MAParams):
                     wrnMsg = "WARNING! net-param value " + str(self._netParam) + " is invalid for Moving-Particles. Valid range is [0,1] indicating the particles' communication range. \n"
                     self._netParam = 0.1
                     wrnMsg += "New default values is '_netParam'=" + str(self._netParam)
-                    print(wrnMsg)
-                    #raise exceptions.MuMoTWarning(wrnMsg)
+                    warn(wrnMsg, exceptions.MuMoTWarning)
 
     def _build_bookmark(self, includeParams=True) -> str:
         log_str = "bookmark = " if not self._silent else ""