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Commit a5878bca authored by eric pellegrini's avatar eric pellegrini
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Merge branch 'hotfix-1.0.3.c'

parents f2ab7711 9d9458bb
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CHANGELOG
View file @ a5878bca
version 1.0: version 1.0.3.c:
- first release ----------------
* 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
View file @ a5878bca
...@@ -472,17 +472,17 @@ class IJob(Configurable): ...@@ -472,17 +472,17 @@ class IJob(Configurable):
f.write( f.write(
'''import collections '''import collections
from MDANSE import REGISTRY
from MDANSE.Framework.Jobs.IJob import IJob from MDANSE.Framework.Jobs.IJob import IJob
class %s(IJob): class %(classname)s(IJob):
""" """
You should enter the description of your job here ... You should enter the description of your job here ...
""" """
type = %r # You should enter the label under which your job will be viewed from the gui.
label = %(label)r
# You should enter the label under which your job will be referenced from the gui.
label = %r
# You should enter the category under which your job will be references. # You should enter the category under which your job will be references.
category = ('My jobs',) category = ('My jobs',)
...@@ -532,7 +532,9 @@ class %s(IJob): ...@@ -532,7 +532,9 @@ class %s(IJob):
# The trajectory is closed # The trajectory is closed
self.configuration['trajectory']['instance'].close() self.configuration['trajectory']['instance'].close()
''' % (classname,shortname,classname))
REGISTRY[%(shortname)r] = %(classname)s
''' % {'classname':classname,'label':'label of the class','shortname':shortname})
except IOError: except IOError:
return None return None
......
MDANSE/Framework/Jobs/MeanSquareDisplacement.py
View file @ a5878bca
...@@ -157,5 +157,4 @@ class MeanSquareDisplacement(IJob): ...@@ -157,5 +157,4 @@ class MeanSquareDisplacement(IJob):
self.configuration['trajectory']['instance'].close() 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
View file @ a5878bca
...@@ -8,12 +8,3 @@ from MDANSE.Framework.OutputVariables import * ...@@ -8,12 +8,3 @@ from MDANSE.Framework.OutputVariables import *
from MDANSE.Framework.Projectors import * from MDANSE.Framework.Projectors import *
from MDANSE.Framework.QVectors import * from MDANSE.Framework.QVectors import *
from MDANSE.Framework.Selectors 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
View file @ a5878bca
...@@ -31,7 +31,6 @@ Created on Apr 14, 2015 ...@@ -31,7 +31,6 @@ Created on Apr 14, 2015
''' '''
import collections import collections
import operator
import os import os
import sys import sys
import webbrowser import webbrowser
......
MDANSE/GUI/Plugins/AtomSelectionPlugin.py
View file @ a5878bca
...@@ -166,11 +166,11 @@ class AtomSelectionPlugin(UserDefinitionPlugin): ...@@ -166,11 +166,11 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
PUBLISHER.subscribe(self.msg_select_atoms_from_viewer, 'msg_select_atoms_from_viewer') 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): 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) self._mainPanel.SetScrollbars(20,20,50,50)
sizer = wx.BoxSizer(wx.VERTICAL) sizer = wx.BoxSizer(wx.VERTICAL)
...@@ -251,10 +251,7 @@ class AtomSelectionPlugin(UserDefinitionPlugin): ...@@ -251,10 +251,7 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
self._mainSizer = wx.BoxSizer(wx.VERTICAL) self._mainSizer = wx.BoxSizer(wx.VERTICAL)
self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5) self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self._mainSizer) 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_TREE_SEL_CHANGED, self.on_display_keyword_values, self.filterTree)
self.Bind(wx.EVT_LISTBOX, self.on_insert_keyword_values, self.values) self.Bind(wx.EVT_LISTBOX, self.on_insert_keyword_values, self.values)
...@@ -268,9 +265,9 @@ class AtomSelectionPlugin(UserDefinitionPlugin): ...@@ -268,9 +265,9 @@ class AtomSelectionPlugin(UserDefinitionPlugin):
def plug(self): 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) self.set_trajectory(self.dataproxy.data)
......
MDANSE/GUI/Plugins/AtomsListPlugin.py
View file @ a5878bca
...@@ -33,7 +33,6 @@ Created on Jun 30, 2015 ...@@ -33,7 +33,6 @@ Created on Jun 30, 2015
import os import os
import wx import wx
import wx.aui as wxaui
from MDANSE import LOGGER, REGISTRY from MDANSE import LOGGER, REGISTRY
from MDANSE.GUI.Plugins.UserDefinitionPlugin import UserDefinitionPlugin from MDANSE.GUI.Plugins.UserDefinitionPlugin import UserDefinitionPlugin
...@@ -85,7 +84,7 @@ class AtomsListPlugin(UserDefinitionPlugin): ...@@ -85,7 +84,7 @@ class AtomsListPlugin(UserDefinitionPlugin):
self._selection = [] self._selection = []
UserDefinitionPlugin.__init__(self,parent,size=(800,500)) UserDefinitionPlugin.__init__(self,parent,size=(600,600))
def build_panel(self): def build_panel(self):
...@@ -139,9 +138,6 @@ class AtomsListPlugin(UserDefinitionPlugin): ...@@ -139,9 +138,6 @@ class AtomsListPlugin(UserDefinitionPlugin):
self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5) self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self._mainSizer) 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_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_BEGIN_DRAG,self.on_add_atom,self._molecules)
self.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.on_add_atom) self.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.on_add_atom)
......
MDANSE/GUI/Plugins/JobPlugin.py
View file @ a5878bca
...@@ -54,7 +54,7 @@ class JobPlugin(ComponentPlugin): ...@@ -54,7 +54,7 @@ class JobPlugin(ComponentPlugin):
self._job = REGISTRY["job"][self._type]() 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): def build_panel(self):
...@@ -148,9 +148,9 @@ class JobPlugin(ComponentPlugin): ...@@ -148,9 +148,9 @@ class JobPlugin(ComponentPlugin):
def plug(self): 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) PUBLISHER.sendMessage("msg_set_data", message=self)
...@@ -162,14 +162,14 @@ class JobFrame(wx.Frame): ...@@ -162,14 +162,14 @@ class JobFrame(wx.Frame):
def __init__(self, parent, jobType, datakey=None): 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 self._jobType = jobType
job = REGISTRY['job'][self._jobType] job = REGISTRY['job'][self._jobType]
self.SetTitle(job.label) self.SetTitle(job.label)
data = REGISTRY['input_data'][job.ancestor[0]](datakey,True) data = REGISTRY['input_data'][job.ancestor[0]](datakey,True)
self.datakey = data.name self.datakey = data.name
...@@ -178,6 +178,8 @@ class JobFrame(wx.Frame): ...@@ -178,6 +178,8 @@ class JobFrame(wx.Frame):
DATA_CONTROLLER[data.name] = data DATA_CONTROLLER[data.name] = data
plugin = REGISTRY['plugin'][self._jobType](self) plugin = REGISTRY['plugin'][self._jobType](self)
self.SetSize(plugin.GetSize())
PUBLISHER.sendMessage("msg_set_data", message=plugin) PUBLISHER.sendMessage("msg_set_data", message=plugin)
...@@ -186,6 +188,6 @@ if __name__ == "__main__": ...@@ -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') filename = os.path.join(os.path.dirname(PLATFORM.package_directory()),'Data','Trajectories','MMTK','protein_in_periodic_universe.nc')
app = wx.App(False) app = wx.App(False)
f = JobFrame(None,'dl_poly',filename) f = JobFrame(None,'dacf',filename)
f.Show() f.Show()
app.MainLoop() app.MainLoop()
\ No newline at end of file
MDANSE/GUI/Plugins/PartialChargesPlugin.py
View file @ a5878bca
...@@ -33,7 +33,6 @@ Created on Jul 2, 2015 ...@@ -33,7 +33,6 @@ Created on Jul 2, 2015
import os import os
import wx import wx
import wx.aui as wxaui
import wx.grid as wxgrid import wx.grid as wxgrid
from MMTK import AtomCluster, Molecule from MMTK import AtomCluster, Molecule
...@@ -55,7 +54,7 @@ class PartialChargesPlugin(UserDefinitionPlugin): ...@@ -55,7 +54,7 @@ class PartialChargesPlugin(UserDefinitionPlugin):
self._selectedAtoms = [] self._selectedAtoms = []
UserDefinitionPlugin.__init__(self, parent) UserDefinitionPlugin.__init__(self, parent,size=(600,600))
def build_panel(self): def build_panel(self):
...@@ -69,12 +68,9 @@ class PartialChargesPlugin(UserDefinitionPlugin): ...@@ -69,12 +68,9 @@ class PartialChargesPlugin(UserDefinitionPlugin):
self._mainPanel.SetSizer(sizer) 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): 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() self.parent.mgr.Update()
......
MDANSE/GUI/Plugins/QVectorsPlugin.py
View file @ a5878bca
...@@ -191,9 +191,6 @@ class QVectorsPlugin(UserDefinitionPlugin): ...@@ -191,9 +191,6 @@ class QVectorsPlugin(UserDefinitionPlugin):
sizer.Add(generateButton, 0, wx.ALL|wx.EXPAND, 5) sizer.Add(generateButton, 0, wx.ALL|wx.EXPAND, 5)
self._mainPanel.SetSizer(sizer) 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(wxaui.EVT_AUINOTEBOOK_PAGE_CLOSE, self.on_close_tab, self._notebook)
self.Bind(wx.EVT_BUTTON, self.on_generate_q_vectors, generateButton) self.Bind(wx.EVT_BUTTON, self.on_generate_q_vectors, generateButton)
......
MDANSE/GUI/Plugins/UserDefinitionPlugin.py
View file @ a5878bca
...@@ -30,10 +30,10 @@ Created on Sep 22, 2015 ...@@ -30,10 +30,10 @@ Created on Sep 22, 2015
''' '''
import wx import wx
import wx.aui as wxaui
from MDANSE import LOGGER, REGISTRY from MDANSE import LOGGER, REGISTRY
from MDANSE.Framework.UserDefinitionStore import UD_STORE from MDANSE.Framework.UserDefinitionStore import UD_STORE
from MDANSE.GUI import PUBLISHER from MDANSE.GUI import PUBLISHER
from MDANSE.GUI.Plugins.ComponentPlugin import ComponentPlugin from MDANSE.GUI.Plugins.ComponentPlugin import ComponentPlugin
...@@ -43,10 +43,14 @@ class UserDefinitionPlugin(ComponentPlugin): ...@@ -43,10 +43,14 @@ class UserDefinitionPlugin(ComponentPlugin):
def __init__(self,parent,*args,**kwargs): def __init__(self,parent,*args,**kwargs):
ComponentPlugin.__init__(self,parent,size=(800,500)) ComponentPlugin.__init__(self,parent,*args,**kwargs)
self.add_ud_panel() 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): def add_ud_panel(self):
udPanel = wx.Panel(self._mainPanel,wx.ID_ANY) udPanel = wx.Panel(self._mainPanel,wx.ID_ANY)
...@@ -82,10 +86,10 @@ class UserDefinitionPlugin(ComponentPlugin): ...@@ -82,10 +86,10 @@ class UserDefinitionPlugin(ComponentPlugin):
return return
if UD_STORE.has_definition(self._target,self._type,name): 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 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) PUBLISHER.sendMessage("msg_set_ud",message=None)
......
MDANSE/GUI/Widgets/UserDefinitionWidget.py
View file @ a5878bca
...@@ -57,6 +57,8 @@ class UserDefinitionDialog(wx.Dialog): ...@@ -57,6 +57,8 @@ class UserDefinitionDialog(wx.Dialog):
self.SetTitle(self._plugin.label) self.SetTitle(self._plugin.label)
self.SetSize(self._plugin.GetSize())
self._plugin.set_trajectory(trajectory) self._plugin.set_trajectory(trajectory)
PUBLISHER.sendMessage("msg_set_data", message=self._plugin) PUBLISHER.sendMessage("msg_set_data", message=self._plugin)
......
MDANSE/__init__.py
View file @ a5878bca
...@@ -52,3 +52,8 @@ from MMTK import Database ...@@ -52,3 +52,8 @@ from MMTK import Database
# The default database is still the MMTK one # The default database is still the MMTK one
Database.path.append(os.path.join(PLATFORM.package_directory(), 'Data')) 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
View file @ a5878bca
__version__ = "1.0.3.b" __version__ = "1.0.3.c"
__date__ = "07-11-2016" __date__ = "08-11-2016"
__author__ = "Eric Pellegrini" __author__ = "Eric Pellegrini"
Scripts/mdanse
View file @ a5878bca
...@@ -233,7 +233,7 @@ class CommandLineParser(optparse.OptionParser): ...@@ -233,7 +233,7 @@ class CommandLineParser(optparse.OptionParser):
if len(parser.rargs) == 0: if len(parser.rargs) == 0:
print "Registered interfaces:" print "Registered interfaces:"
for interfaceName in REGISTRY.get_interfaces(): for interfaceName in REGISTRY.interfaces:
print "\t- %s" % interfaceName print "\t- %s" % interfaceName
elif len(parser.rargs) == 1: elif len(parser.rargs) == 1:
val = parser.rargs[0] val = parser.rargs[0]
...@@ -333,9 +333,10 @@ class CommandLineParser(optparse.OptionParser): ...@@ -333,9 +333,10 @@ class CommandLineParser(optparse.OptionParser):
from MDANSE.Framework.Jobs.IJob import IJob from MDANSE.Framework.Jobs.IJob import IJob
if nargs != 2: 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: try:
IJob.save_template(shortname,classname) IJob.save_template(shortname,classname)
......
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