Remove hardcoded path to database in old scripts

- Switch to using rmgpy settings database.directory
- Also removed the git history saving in kineticGroups.py
 script

Author: connie

scripts/evansPolanyi.py

@@ -197,9 +197,10 @@ def onpick(event):
 
     print 'Loading RMG database...'
     from rmgpy.data.rmg import RMGDatabase
+    from rmgpy import settings
     database = RMGDatabase()
-    database.load('input')
-
+    database.load(settings['database.directory'], kineticsFamilies='all', kineticsDepositories='all')
+    
     try:
         depositories = [database.kinetics.depository[label] for label in args.depository]
     except KeyError:

scripts/kineticsGroups.py

@@ -23,17 +23,15 @@
 from rmgpy.kinetics import Arrhenius, ArrheniusEP, KineticsData
 from rmgpy.data.base import getAllCombinations
 from rmgpy.species import Species
-
-from importOldDatabase import getUsername
-user = getUsername()
+from rmgpy import settings
 
 ################################################################################
 
 def loadDatabase():
     print 'Loading RMG database...'
     from rmgpy.data.rmg import RMGDatabase
     database = RMGDatabase()
-    database.load('input')
+    database.load(settings['database.directory'], kineticsFamilies='all', kineticsDepositories='all')
     return database
 
 def convertKineticsToPerSiteBasis(kinetics, degeneracy):
@@ -143,12 +141,8 @@ def generate(args):
         changed = family.groups.generateGroupAdditivityValues(trainingSet, kunits, method=method)
 
         if changed:
-            # Add a note to the history of each changed item indicating that we've generated new group values
-            event = [time.asctime(),user,'action','Generated new group additivity values for this entry.']
-            for entry in family.groups.entries.values():
-                entry.history.append(event)
             # Save the new group values to disk
-            family.saveGroups(os.path.join('input', 'kinetics', 'families', label, 'groups.py'))
+            family.saveGroups(os.path.join(settings['database.directory'], 'kinetics', 'families', label, 'groups.py'))
 
 ################################################################################
 

scripts/kineticsTraining.py

@@ -381,7 +381,8 @@ def generateEntry(reaction, kinetics, index, ci):
 Tmax = 2000
 
 def getPath(family, index):
-    return os.path.join(os.path.dirname(os.path.abspath(__file__)), 'input', 'kinetics', 'families', family, 'training', '{0}.py'.format(index))
+    from rmgpy import settings
+    return os.path.join(settings['database.directory'], 'kinetics', 'families', family, 'training', '{0}.py'.format(index))
 
 def generate(args):
     """
@@ -453,6 +454,7 @@ def evaluate(args):
 if __name__ == '__main__':
 
     import argparse
+    from rmgpy import settings
 
     parser = argparse.ArgumentParser()
     subparsers = parser.add_subparsers(dest='command', help='')
@@ -471,7 +473,7 @@ def evaluate(args):
 
     args = parser.parse_args()
 
-    loadThermoDatabase(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'input', 'thermo'))
+    loadThermoDatabase(os.path.join(settings['database.directory'], 'thermo'))
 
     try:
         args.run(args)