Merge branch 'hotfix-1.0.3.c'

CHANGELOG

-version 1.0:
-   - first release 
+version 1.0.3.c:
+----------------
+* bug fix when saving user definitions
+* bug fix with the initial size of the user definitions plugins
+* updated the job template writing
+* small refactoring of the save job template command line option
+* removed unused imports
+* removed white spaces
+
+version 1.0.3.b:
+----------------
+* bug fix with JobControllerPanel in case of crashing jobs
+* regression fixed due to trials to get rid of relative imports MDANSE/Externals/pubsub package
+
+version 1.0.3.a:
+----------------
+* updated `MDANSE/__pkginfo__.py` module
 

MDANSE/Framework/Jobs/IJob.py

@@ -472,17 +472,17 @@ class IJob(Configurable):
             f.write(
 '''import collections
 
+from MDANSE import REGISTRY
+
 from MDANSE.Framework.Jobs.IJob import IJob
 
-class %s(IJob):
+class %(classname)s(IJob):
     """
     You should enter the description of your job here ...
     """
-    
-    type = %r
-    
-    # You should enter the label under which your job will be referenced from the gui.
-    label = %r
+        
+    # You should enter the label under which your job will be viewed from the gui.
+    label = %(label)r
 
     # You should enter the category under which your job will be references.
     category = ('My jobs',)
@@ -532,7 +532,9 @@ class %s(IJob):
         
         # The trajectory is closed
         self.configuration['trajectory']['instance'].close()        
-''' % (classname,shortname,classname))
+
+REGISTRY[%(shortname)r] = %(classname)s
+''' % {'classname':classname,'label':'label of the class','shortname':shortname})
         
         except IOError:
             return None

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -157,5 +157,4 @@ class MeanSquareDisplacement(IJob):
         
         self.configuration['trajectory']['instance'].close()
         
-REGISTRY['msd'] = MeanSquareDisplacement
-     
+REGISTRY['msd'] = MeanSquareDisplacement
\ No newline at end of file
\ No newline at end of file

MDANSE/Framework/__init__.py

@@ -8,12 +8,3 @@ from MDANSE.Framework.OutputVariables import *
 from MDANSE.Framework.Projectors import *
 from MDANSE.Framework.QVectors import *
 from MDANSE.Framework.Selectors import *
-
-import os
-
-from MDANSE import PLATFORM,REGISTRY
- 
-macrosDirectories = sorted([x[0] for x in os.walk(PLATFORM.macros_directory())][0:])
- 
-for d in macrosDirectories:
-    REGISTRY.update(d)

MDANSE/GUI/MainFrame.py

@@ -31,7 +31,6 @@ Created on Apr 14, 2015
 '''
 
 import collections
-import operator
 import os
 import sys
 import webbrowser

MDANSE/GUI/Plugins/AtomSelectionPlugin.py

@@ -166,11 +166,11 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
 
         PUBLISHER.subscribe(self.msg_select_atoms_from_viewer, 'msg_select_atoms_from_viewer')
 
-        UserDefinitionPlugin.__init__(self,parent,size=(800,500))
+        UserDefinitionPlugin.__init__(self,parent,size=(600,600))
                 
     def build_panel(self):
-                                                
-        self._mainPanel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
+                      
+        self._mainPanel = wx.ScrolledWindow(self, wx.ID_ANY)
         self._mainPanel.SetScrollbars(20,20,50,50)
 
         sizer = wx.BoxSizer(wx.VERTICAL)
@@ -251,10 +251,7 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
         self._mainSizer = wx.BoxSizer(wx.VERTICAL)                                                                              
         self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)        
         self.SetSizer(self._mainSizer)            
-        
-        self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
-        self._mgr.Update()
-                                                                                      
+                                                                                              
         self.Bind(wx.EVT_TREE_SEL_CHANGED, self.on_display_keyword_values, self.filterTree)
         self.Bind(wx.EVT_LISTBOX, self.on_insert_keyword_values, self.values)
   
@@ -268,9 +265,9 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
         
     def plug(self):
         
-        self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
+        self._parent._mgr.GetPane(self).Float().Floatable(True).Dockable(True).CloseButton(True)
         
-        self.parent.mgr.Update()
+        self._parent._mgr.Update()
         
         self.set_trajectory(self.dataproxy.data)
 

MDANSE/GUI/Plugins/AtomsListPlugin.py

@@ -33,7 +33,6 @@ Created on Jun 30, 2015
 import os
 
 import wx
-import wx.aui as wxaui
 
 from MDANSE import LOGGER, REGISTRY
 from MDANSE.GUI.Plugins.UserDefinitionPlugin import UserDefinitionPlugin
@@ -85,7 +84,7 @@ class AtomsListPlugin(UserDefinitionPlugin):
         
         self._selection = []
                                 
-        UserDefinitionPlugin.__init__(self,parent,size=(800,500))
+        UserDefinitionPlugin.__init__(self,parent,size=(600,600))
                                                 
     def build_panel(self):
 
@@ -139,9 +138,6 @@ class AtomsListPlugin(UserDefinitionPlugin):
         self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)        
         self.SetSizer(self._mainSizer)            
         
-        self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
-        self._mgr.Update()
-
         self.Bind(wx.EVT_SPINCTRL,self.on_define_list_size,self._nAtomsSpinCtrl)                
         self.Bind(wx.EVT_TREE_BEGIN_DRAG,self.on_add_atom,self._molecules)
         self.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.on_add_atom)

MDANSE/GUI/Plugins/JobPlugin.py

@@ -54,7 +54,7 @@ class JobPlugin(ComponentPlugin):
                 
         self._job = REGISTRY["job"][self._type]()
         
-        ComponentPlugin.__init__(self, parent, size=wx.Size(800,400), *args, **kwargs)
+        ComponentPlugin.__init__(self, parent, size=wx.Size(800,600), *args, **kwargs)
                 
     def build_panel(self):
         
@@ -148,9 +148,9 @@ class JobPlugin(ComponentPlugin):
 
     def plug(self):
                 
-        self._parent._mgr.GetPane(self).Float().Center().Floatable(True).Dockable(True).CloseButton(True).BestSize((800,600))
+        self._parent._mgr.GetPane(self).Float().Center().Floatable(True).Dockable(True).CloseButton(True)
                 
-        self._parent.mgr.Update()
+        self._parent._mgr.Update()
                     
         PUBLISHER.sendMessage("msg_set_data", message=self)
                         
@@ -162,14 +162,14 @@ class JobFrame(wx.Frame):
     
     def __init__(self, parent, jobType, datakey=None):
                 
-        wx.Frame.__init__(self, parent, wx.ID_ANY, size = (800,800), style=wx.DEFAULT_DIALOG_STYLE|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX|wx.RESIZE_BORDER)
+        wx.Frame.__init__(self, parent, wx.ID_ANY, style=wx.DEFAULT_DIALOG_STYLE|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX|wx.RESIZE_BORDER)
 
         self._jobType = jobType
 
         job = REGISTRY['job'][self._jobType]
         
         self.SetTitle(job.label)
-        
+                
         data = REGISTRY['input_data'][job.ancestor[0]](datakey,True)
 
         self.datakey = data.name
@@ -178,6 +178,8 @@ class JobFrame(wx.Frame):
             DATA_CONTROLLER[data.name] = data
                         
         plugin = REGISTRY['plugin'][self._jobType](self)
+
+        self.SetSize(plugin.GetSize())
         
         PUBLISHER.sendMessage("msg_set_data", message=plugin)
                         
@@ -186,6 +188,6 @@ if __name__ == "__main__":
     filename = os.path.join(os.path.dirname(PLATFORM.package_directory()),'Data','Trajectories','MMTK','protein_in_periodic_universe.nc')
     
     app = wx.App(False)
-    f = JobFrame(None,'dl_poly',filename)
+    f = JobFrame(None,'dacf',filename)
     f.Show()
     app.MainLoop()            
\ No newline at end of file

MDANSE/GUI/Plugins/PartialChargesPlugin.py

@@ -33,7 +33,6 @@ Created on Jul 2, 2015
 import os
 
 import wx
-import wx.aui as wxaui
 import wx.grid as wxgrid
 
 from MMTK import AtomCluster, Molecule
@@ -55,7 +54,7 @@ class PartialChargesPlugin(UserDefinitionPlugin):
     
         self._selectedAtoms = []
                         
-        UserDefinitionPlugin.__init__(self, parent)
+        UserDefinitionPlugin.__init__(self, parent,size=(600,600))
                         
     def build_panel(self):
 
@@ -69,12 +68,9 @@ class PartialChargesPlugin(UserDefinitionPlugin):
 
         self._mainPanel.SetSizer(sizer)
                                                 
-        self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
-        self._mgr.Update()
-
     def plug(self):
                 
-        self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
+        self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True)
         
         self.parent.mgr.Update()
         

MDANSE/GUI/Plugins/QVectorsPlugin.py

@@ -191,9 +191,6 @@ class QVectorsPlugin(UserDefinitionPlugin):
         sizer.Add(generateButton, 0, wx.ALL|wx.EXPAND, 5)
 
         self._mainPanel.SetSizer(sizer)
-
-        self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
-        self._mgr.Update()
                                  
         self.Bind(wxaui.EVT_AUINOTEBOOK_PAGE_CLOSE, self.on_close_tab, self._notebook)
         self.Bind(wx.EVT_BUTTON, self.on_generate_q_vectors, generateButton)

MDANSE/GUI/Plugins/UserDefinitionPlugin.py

@@ -30,10 +30,10 @@ Created on Sep 22, 2015
 '''
 
 import wx
+import wx.aui as wxaui
 
 from MDANSE import LOGGER, REGISTRY
 from MDANSE.Framework.UserDefinitionStore import UD_STORE
-
 from MDANSE.GUI import PUBLISHER
 from MDANSE.GUI.Plugins.ComponentPlugin import ComponentPlugin
 
@@ -43,10 +43,14 @@ class UserDefinitionPlugin(ComponentPlugin):
     
     def __init__(self,parent,*args,**kwargs):
         
-        ComponentPlugin.__init__(self,parent,size=(800,500))
+        ComponentPlugin.__init__(self,parent,*args,**kwargs)
         
         self.add_ud_panel()
-                
+        
+        self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
+
+        self._mgr.Update()
+                                
     def add_ud_panel(self):
 
         udPanel = wx.Panel(self._mainPanel,wx.ID_ANY)
@@ -82,10 +86,10 @@ class UserDefinitionPlugin(ComponentPlugin):
             return
                         
         if UD_STORE.has_definition(self._target,self._type,name):
-            LOGGER('There is already a user-definition with that name.','error',['dialog'])
+            LOGGER('There is already an user-definition with that name.','error',['dialog'])
             return
-                  
-        UD_STORE.set_definition(self._target,self.type,name,value)
+                          
+        UD_STORE.set_definition(self._target,self._type,name,value)
                  
         PUBLISHER.sendMessage("msg_set_ud",message=None)
         

MDANSE/GUI/Widgets/UserDefinitionWidget.py

@@ -57,6 +57,8 @@ class UserDefinitionDialog(wx.Dialog):
         
         self.SetTitle(self._plugin.label)
         
+        self.SetSize(self._plugin.GetSize())
+        
         self._plugin.set_trajectory(trajectory)
                 
         PUBLISHER.sendMessage("msg_set_data", message=self._plugin)

MDANSE/__init__.py

@@ -52,3 +52,8 @@ from MMTK import Database
 
 # The default database is still the MMTK one
 Database.path.append(os.path.join(PLATFORM.package_directory(), 'Data'))
+ 
+macrosDirectories = sorted([x[0] for x in os.walk(PLATFORM.macros_directory())][0:])
+ 
+for d in macrosDirectories:
+    REGISTRY.update(d)

MDANSE/__pkginfo__.py

-__version__ = "1.0.3.b"
+__version__ = "1.0.3.c"
 
-__date__ = "07-11-2016"
+__date__ = "08-11-2016"
 
 __author__ = "Eric Pellegrini"
 

Scripts/mdanse

@@ -233,7 +233,7 @@ class CommandLineParser(optparse.OptionParser):
             
         if len(parser.rargs) == 0:
             print "Registered interfaces:"
-            for interfaceName in REGISTRY.get_interfaces():
+            for interfaceName in REGISTRY.interfaces:
                 print "\t- %s" % interfaceName
         elif len(parser.rargs) == 1:
             val = parser.rargs[0]                    
@@ -333,9 +333,10 @@ class CommandLineParser(optparse.OptionParser):
         from MDANSE.Framework.Jobs.IJob import IJob        
 
         if nargs != 2:
-            raise CommandLineParserError("Invalid number of arguments for %r option" % opt_str)
+            print "Two arguments required resp. the name and the shortname of the class to be templated"
+            return
 
-        shortname,classname = parser.rargs
+        classname,shortname = parser.rargs
 
         try:
             IJob.save_template(shortname,classname)