Merge tag '1.0.4.rc1' into develop

version 1.0.4.rc1

CHANGELOG

+version 1.0.4.rc1
+----------------
+* bug fix in IWidget: the label of the configurator was not taken into account
+* bug fix path_to_module function: the list of directories has to be parsed backwards
+* raise an error when none or more than atom matches the mass stored in the LAMMPS config file
+* modified the label for r value
+
 version 1.0.3.e:
 ----------------
 * bug fix relative to REGISTRY update

MDANSE/Core/ClassRegistry.py

@@ -42,13 +42,13 @@ def path_to_module(path,stop=""):
     path, _ = os.path.splitext(path)
     
     splittedPath = path.split(os.sep)
-    
+        
     try:
-        idx = splittedPath.index(stop)
+        idx = splittedPath[::-1].index(stop)
     except ValueError:
         idx = 0
     finally:
-        module = ".".join(splittedPath[idx:])
+        module = ".".join(splittedPath[len(splittedPath)-1-idx:])
             
     return module
         
@@ -110,14 +110,14 @@ class ClassRegistry(object):
         :param packageDir: the package for which all modules should be imported
         :type packageDir: str
         '''
-                
+                        
         for module in glob.glob(os.path.join(packageDir,'*.py')):
-                                             
+            
             moduleDir, moduleFile = os.path.split(module)
      
             if moduleFile == '__init__.py':
                 continue
-            
+
             # Any error that may occur here has to be caught. In such case the module is skipped.    
             try:
                 if macros:

MDANSE/Framework/Jobs/DistanceHistogram.py

@@ -50,7 +50,7 @@ class DistanceHistogram(IJob):
     settings = collections.OrderedDict()    
     settings['trajectory'] = ('mmtk_trajectory',{})
     settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}})
-    settings['r_values'] = ('range', {'valueType':float, 'includeLast':True, 'mini':0.0})
+    settings['r_values'] = ('range', {'label':'r values (nm)','valueType':float, 'includeLast':True, 'mini':0.0})
     settings['atom_selection'] = ('atom_selection', {'dependencies':{'trajectory':'trajectory'}})
     settings['atom_transmutation'] = ('atom_transmutation', {'dependencies':{'trajectory':'trajectory','atom_selection':'atom_selection'}})
     settings['weights']=('weights',{"dependencies":{"atom_selection":"atom_selection"}})

MDANSE/Framework/Jobs/LAMMPS.py

@@ -100,7 +100,12 @@ class LAMMPSConfigFile(dict):
                                                                     
                 for j in range(1, self["n_atom_types"]+1):
                     idx, mass = lines[i+j].strip().split()
-                    el = ELEMENTS.match_numeric_property("atomic_weight", float(mass), tolerance=1.0e-3)
+                    tolerance = 1.0e-3
+                    idx = int(idx)
+                    mass = float(mass)
+                    el = ELEMENTS.match_numeric_property("atomic_weight", mass, tolerance=tolerance)
+                    if len(el) != 1:
+                        raise LAMMPSConfigFileError("The atom %d with defined mass %f could not be assigned with a tolerance of %f. Please modify the mass in the config file to comply with MDANSE internal database" % (idx,mass,tolerance))
                     self["elements"][idx] = el[0]
 
             m = re.match("^bonds$",line, re.I)

MDANSE/GUI/Widgets/IWidget.py

@@ -50,7 +50,7 @@ class IWidget(wx.Panel):
                                 
         self._configurator = configurator
                                                         
-        self._label = ' '.join(name.capitalize().split('_'))
+        self._label = self._configurator.label
                         
         self.initialize()
                         

MDANSE/__pkginfo__.py

-__version__ = "1.0.3.e"
+__version__ = "1.0.4.rc1"
 
-__date__ = "18-11-2016"
+__date__ = "22-11-2016"
 
 __author__ = "Eric Pellegrini"