Added docstrings to MDANSE.Core classes

Added example_data_directory method to Platform class
Bug fix in mdanse console script

MDANSE/Core/ClassRegistry.py

@@ -164,5 +164,4 @@ class ClassRegistry(abc.ABCMeta):
         :type cls: ClassRegistry
         '''
         
-        
         return sorted(cls._registry.keys())
\ No newline at end of file

MDANSE/Core/Configurable.py

-'''
-MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-------------------------------------------------------------------------------------------
-Copyright (C)
-2015- Eric C. Pellegrini Institut Laue-Langevin
-BP 156
-6, rue Jules Horowitz
-38042 Grenoble Cedex 9
-France
-pellegrini[at]ill.fr
-
-This library is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or (at your option) any later version.
+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
-This library is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library; if not, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- 
-Created on Mar 23, 2015
+''' 
+Created on Mar 30, 2015
 
 @author: pellegrini
 '''
 
+import collections
+
 from MDANSE.Core.Error import Error
 
 class ConfigurationError(Error):
+    '''
+    Handles the exception that may occurs when configuring an object that derives from MDANSE.Core.Configurable class.
+    '''
     pass
 
-import collections
-
 class Configurable(object):
+    '''
+    This class allows any object that derives from it to be configurable within the MDANSE framework.
+    
+    Within that framework, the object will also have to define the class attribute 'configurators' as 
+    a MDANSE.Framework.Configurators.ConfiguratorsDict object to complete its configuration.    
+    '''
     
     configurators = collections.OrderedDict()
 
     def __init__(self):
+        '''
+        Constructor
+        '''
         
         self._configuration = {}
         
@@ -47,30 +61,41 @@ class Configurable(object):
         
     def __getitem__(self, name):
         """
-        Returns a configuration item given its name
+        Returns a configuration item given its name.
+        
+        :param name: the name of the configuration item
+        :type name: str 
+        
         If not found raise a ConfigurationError. 
         """
         
-        if self.configurators.has_key(name):
-            return self._configuration.setdefault(name,{})
+        if not self.configurators.has_key(name):
+            raise ConfigurationError("The item %r is not valid for this configuration." % name)
         
-        raise ConfigurationError("The item %r is not valid for this configuration." % name)
+        return self._configuration.setdefault(name,{})
         
     def setup(self,parameters):
-        """
-        Setup the configuration given a set of parameters
-        """
+        '''
+        Setup the configuration according to a set of input parameters.
+        
+        :param parameters: the input parameters
+        :type parameters: dict
+        '''
                 
+        # Cleans the previous configuration
         self._configuration.clear()
 
         self._configured=False
                 
         # If no configurator has to be configured, just return
         if not self.configurators:
+            self._configured=True
             return
         
         if isinstance(parameters,dict):
+            # Loop over the configuration items          
             for k,v in self.configurators.items():
+                # If no input parameter has been set for this item, use its default value.
                 if not parameters.has_key(k):
                     parameters[k] = v.default
         else:
@@ -104,6 +129,12 @@ class Configurable(object):
         self._configured=True
 
     def __str__(self):
+        '''
+        Returns the informations about the current configuration in text form.
+        
+        :return: the informations about the current configuration in text form
+        :rtype: str
+        '''
         
         if not self._configured:
             return "Not yet configured"

MDANSE/Core/Platform.py

@@ -210,6 +210,14 @@ class Platform(object):
         
         return os.getpid()
 
+    def example_data_directory(self):
+        """Returns the path for mdanse data.
+        
+        @return: the path for mdanse package.
+        @rtype: string
+        """
+        
+        return os.path.dirname(self.package_directory())
 
     def package_directory(self):
         """Returns the path for mdanse package.

MDANSE/Framework/Configurators/MMTKTrajectoryConfigurator.py

@@ -44,7 +44,7 @@ class MMTKNetCDFTrajectoryConfigurator(InputFileConfigurator):
     
     type = 'mmtk_trajectory'
     
-    _default = ''
+    _default = os.path.join(PLATFORM.example_data_directory(),'Data','Trajectories','MMTK','waterbox_in_periodic_universe.nc')
                         
     def configure(self, configuration, value):
                 

Scripts/mdanse

@@ -244,11 +244,11 @@ class CommandLineParser(optparse.OptionParser):
         filename = os.path.abspath('template_%s.py' % name.lower())
         # Try to save the template for the job.
         try:
-            jobs[name].save_job(filename)    
+            jobs[name].save(filename)    
         # Case where an error occured when writing the template.
         except IOError:
             raise CommandLineParserError("Could not write the job template as %r" % filename)
-        # If the job class has no save_job method, thisis not a valid nMolDyn job.
+        # If the job class has no save method, thisis not a valid nMolDyn job.
         except KeyError:
             raise CommandLineParserError("The job %r is not a valid MDANSE job" % name)
         # Otherwise, print some information about the saved template.