Regenerated the jobs unit tests according to recent changes in API.

Bug fixes related to those unit tests.
Improved the AtomsList dialog to keep track the order in which the atoms
are selected.

MDANSE/Framework/Configurable.py

@@ -61,25 +61,30 @@ class Configurable(object):
         Constructor
         '''
                
-        self._configuration = self.build_configuration()
+        self._configuration = collections.OrderedDict()
                                      
         self._configured=False
         
-    @classmethod
-    def build_configuration(cls):
+        self.build_configuration()
+        
+    def build_configuration(self):
         
-        configuration = collections.OrderedDict()
+        self._configuration.clear()
 
-        for name,(typ,kwds) in cls.settings.items():
+        for name,(typ,kwds) in self.settings.items():
             
             try:
-                configuration[name] = REGISTRY["configurator"][typ](name, **kwds)
+                self._configuration[name] = REGISTRY["configurator"][typ](name, **kwds)
             # Any kind of error has to be caught
             except:
                 raise ConfigurationError("Invalid type for %r configurator" % name)
+            
+    def set_settings(self,settings):
         
-        return configuration
+        self.settings = settings
         
+        self.build_configuration()
+                
     def __getitem__(self, name):
         """
         Returns a configuration item given its name.
@@ -112,6 +117,8 @@ class Configurable(object):
         '''
                 
         self._configured=False
+        
+        self.build_configuration()
                                 
         # If no configurator has to be configured, just return
         if not self._configuration:

MDANSE/Framework/Configurators/AtomsListConfigurator.py

@@ -87,11 +87,9 @@ class AtomsListConfigurator(IConfigurator):
             molecule,atoms=value
 
         self["value"] = value
-
-        indexes = [find_atoms_in_molecule(trajConfig['instance'].universe,molecule, at, True) for at in atoms]
-          
-        self['atoms'] = zip(*indexes)      
         
+        self['atoms'] = find_atoms_in_molecule(trajConfig['instance'].universe,molecule, atoms, True)
+                        
         self['n_values'] = len(self['atoms'])
                                     
     def get_information(self):

MDANSE/Framework/Configurators/OutputFilesConfigurator.py

@@ -49,7 +49,7 @@ class OutputFilesConfigurator(IConfigurator):
     
     type = 'output_files'
     
-    _default = ('.', "output", ["netcdf"])
+    _default = ("output", ["netcdf"])
                     
     def __init__(self, name, formats=None, **kwargs):
         '''

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -107,7 +107,7 @@ class AngularCorrelation(IJob):
         """
 
         e1, e2 = self.configuration['axis_selection']['atoms'][index]
-        
+                
         e1 = read_atoms_trajectory(self.configuration["trajectory"]["instance"],
                                    e1,
                                    first=self.configuration['frames']['first'],

MDANSE/Framework/Jobs/IJob.py

@@ -315,7 +315,7 @@ class IJob(Configurable):
         f.write('#!%s\n\n' % sys.executable)
 
         f.write('import unittest\n')
-        f.write('from Tests.UnitTest import UnitTest\n')
+        f.write('from Tests.UnitTests.UnitTest import UnitTest\n')
         f.write('from MDANSE import REGISTRY\n\n')
                 
         f.write('class Test%s(UnitTest):\n\n' % cls.type.upper())

MDANSE/Framework/Jobs/SpatialDensity.py

@@ -136,23 +136,20 @@ class SpatialDensity(IJob):
         
         directCell = numpy.array(self.configuration['trajectory']['instance'].universe.basisVectors()).astype(numpy.float64)
         reverseCell = numpy.array(self.configuration['trajectory']['instance'].universe.reciprocalBasisVectors()).astype(numpy.float64)
+
         # The configuration is made contiguous.
-        
         conf = self.configuration['trajectory']['instance'].universe.contiguousObjectConfiguration()
 
         origins = numpy.zeros((self.configuration['reference_basis']['n_values'],3), dtype = numpy.float64)
         bases = numpy.zeros((self.configuration['reference_basis']['n_values'],3,3), dtype = numpy.float64)
         
         indexes = numpy.array(self.configuration['target_molecule']['indexes']).astype(numpy.int32)
-        
+                
         for i, basis in enumerate(self.configuration['reference_basis']['atoms']):
-            originIndexes, xIndexes, yIndexes = basis
-            origins[i,:] = center_of_mass(conf.array[originIndexes], None)
             
-            x = center_of_mass(conf.array[xIndexes,:], None)
-            y = center_of_mass(conf.array[yIndexes,:], None)
-
-            bases[i,:,:] = numpy.array(build_cartesian_axes(origins[i,:],x,y)).T
+            origin, x, y = basis
+            
+            bases[i,:,:] = numpy.array(build_cartesian_axes(conf.array[origin,:],conf.array[x,:],conf.array[y,:])).T
         
         hist = numpy.zeros_like(self.hist, dtype=numpy.int32)
         

MDANSE/Framework/Plugins/JobPlugin.py

@@ -199,10 +199,8 @@ if __name__ == "__main__":
 
     from MDANSE.GUI import DATA_CONTROLLER
     from MDANSE.GUI.WorkingPanel import WorkingPanel
-    
-    root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))))
-    
-    filename = os.path.join(root,'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)
     f = JobFrame(None,'msd',filename)

MDANSE/Framework/Widgets/AtomsListWidget.py

@@ -38,6 +38,37 @@ from MDANSE import LOGGER
 from MDANSE.Framework.Widgets.UserDefinitionWidget import UserDefinitionsDialog, UserDefinitionWidget
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict
 
+class AtomNameDropTarget(wx.TextDropTarget):
+
+    def __init__(self, molTree,atList):
+        
+        wx.TextDropTarget.__init__(self)
+        self._molecules = molTree
+        self._atoms = atList
+        self._currentMolecule = None
+
+    def OnDropText(self, x, y, data):
+
+        listedAtoms = [self._atoms.GetItem(idx).GetText() for idx in range(self._atoms.GetItemCount())]
+                
+        if data in listedAtoms:
+            return
+
+        atTreeItem = self._molecules.GetSelection()
+        molTreeItem = self._molecules.GetItemParent(atTreeItem)
+        
+        molname = self._molecules.GetItemText(molTreeItem)
+        
+        if self._atoms.GetItemCount() > 0:
+            if (molname != self._currentMolecule):
+                d = wx.MessageDialog(self._atoms, "The dragged atoms does not belong to the same molecule than the current selection.", style=wx.ICON_ERROR|wx.STAY_ON_TOP|wx.CENTRE)
+                d.ShowModal()
+                return
+        else:
+            self._currentMolecule = molname
+                
+        self._atoms.Append([data])
+                
 class AtomsListDialog(UserDefinitionsDialog):
     
     def __init__(self, parent, trajectory, nAtoms):
@@ -57,44 +88,52 @@ class AtomsListDialog(UserDefinitionsDialog):
         self.type = "%d_atoms_list" % self._nAtoms
         
         UserDefinitionsDialog.__init__(self, parent, target, wx.ID_ANY, title="%d Atoms selection dialog" % nAtoms,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
-                        
+        
+        self.SetSize((400,400))
+                                
     def build_dialog(self):
 
         panel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
         panel.SetScrollbars(20,20,50,50)
         
         sizer = wx.BoxSizer(wx.VERTICAL)
-        
-        sb = wx.StaticBox(panel, wx.ID_ANY, label = "Atom selection")
-        sbSizer = wx.StaticBoxSizer(sb, wx.HORIZONTAL)
-        
+                
         gbSizer = wx.GridBagSizer(5,5)
         
         label1 = wx.StaticText(panel, wx.ID_ANY, label="Molecules")
-        label2 = wx.StaticText(panel, wx.ID_ANY, label="Atoms")
+        label2 = wx.StaticText(panel, wx.ID_ANY, label="Selected atoms")
 
         gbSizer.Add(label1, (0,0), flag=wx.EXPAND)
         gbSizer.Add(label2, (0,1), flag=wx.EXPAND)
     
-        self._molecules = wx.ListBox(panel, wx.ID_ANY, style = wx.LB_SINGLE|wx.LB_NEEDED_SB)
+        self._molecules = wx.TreeCtrl(panel, wx.ID_ANY, style=wx.TR_DEFAULT_STYLE|wx.LB_HSCROLL|wx.LB_NEEDED_SB^wx.TR_HIDE_ROOT)
         self._molecularContents = get_chemical_objects_dict(self._trajectory.universe)
-        self._molecules.SetItems(sorted(self._molecularContents.keys()))        
+        
+        root = self._molecules.AddRoot('')
+        
+        for mname in sorted(self._molecularContents.keys()):
+            molnode = self._molecules.AppendItem(root,mname)
+            atomsList = self._molecularContents[mname][0].atomList()
+            atomNames = sorted(set([at.name for at in atomsList]))
+            for aname in atomNames:
+                self._molecules.AppendItem(molnode,aname)
 
-        self._atoms = wx.ListBox(panel, wx.ID_ANY, style = wx.LB_MULTIPLE|wx.LB_NEEDED_SB)
+        self._atoms = wx.ListCtrl(panel, wx.ID_ANY, style=wx.LC_LIST)
         
+        dt = AtomNameDropTarget(self._molecules,self._atoms)
+        self._atoms.SetDropTarget(dt)
+                
         gbSizer.Add(self._molecules, (1,0), flag=wx.EXPAND)
         gbSizer.Add(self._atoms    , (1,1), flag=wx.EXPAND)
         
         gbSizer.AddGrowableRow(1)
         gbSizer.AddGrowableCol(0)
         gbSizer.AddGrowableCol(1)
-        
-        sbSizer.Add(gbSizer, 1, wx.EXPAND|wx.ALL, 5)
 
         setButton  = wx.Button(panel, wx.ID_ANY, label="Set")
         self._resultsTextCtrl  = wx.TextCtrl(panel, wx.ID_ANY, style=wx.TE_READONLY|wx.TE_MULTILINE)
 
-        sizer.Add(sbSizer,1,wx.EXPAND|wx.ALL,5)
+        sizer.Add(gbSizer, 1, wx.EXPAND|wx.ALL, 5)
         sizer.Add(setButton,0,wx.EXPAND|wx.ALL,5)
         sizer.Add(self._resultsTextCtrl,1,wx.EXPAND|wx.ALL,5)
 
@@ -103,21 +142,55 @@ class AtomsListDialog(UserDefinitionsDialog):
         self._mainSizer.Add(panel, 1, wx.EXPAND|wx.ALL, 5)
                 
         self.Bind(wx.EVT_BUTTON, self.on_set_user_definition, setButton)
-        self.Bind(wx.EVT_LISTBOX, self.on_select_molecule, self._molecules)
-        self.Bind(wx.EVT_LISTBOX, self.on_select_atom, self._atoms)
+        self.Bind(wx.EVT_TREE_BEGIN_DRAG,self.on_drag_atom_name,self._molecules)
+        self.Bind(wx.EVT_LIST_KEY_DOWN,self.on_delete_atom_name,self._atoms)
 
+    def on_delete_atom_name(self,event):
+        
+        keycode = event.GetKeyCode()
+        if keycode != wx.WXK_DELETE:
+            return
+        
+        item = self._atoms.GetFirstSelected()        
+        selectedItems = []
+        while item != -1:
+            selectedItems.append(item)
+            item = self._atoms.GetNextSelected(item)
+            
+        if not selectedItems:
+            return
+        
+        selectedItems.reverse()
+        for it in selectedItems:
+            self._atoms.DeleteItem(it)
+            
+    def on_drag_atom_name(self,event):
+                        
+        item = event.GetItem()
+        
+        parentItem = self._molecules.GetItemParent(item)
+        if parentItem == self._molecules.GetRootItem():
+            return            
+                        
+        text = self._molecules.GetItemText(item)        
+        tdo = wx.TextDataObject(text)
+        tds = wx.DropSource(self._molecules)
+        tds.SetData(tdo)
+        tds.DoDragDrop(wx.Drag_CopyOnly)                        
+        
     def set_user_definition(self):
 
         self._selection = []
 
-        if len(self._selectedAtoms) != self._nAtoms:
+        if self._atoms.GetItemCount() != self._nAtoms:
             LOGGER('You must select %d atoms.' % self._nAtoms,'error',['dialog'])
             return
 
-        molecule = str(self._molecules.GetStringSelection())
-        atoms = tuple(str(self._atoms.GetString(idx)) for idx in self._selectedAtoms)
-
-        self._selection = find_atoms_in_molecule(self._trajectory.universe,molecule, atoms, True)
+        atTreeItem = self._molecules.GetSelection()
+        molTreeItem = self._molecules.GetItemParent(atTreeItem)        
+        molecule = self._molecules.GetItemText(molTreeItem)        
+        self._selectedAtoms = [self._atoms.GetItem(idx).GetText() for idx in range(self._atoms.GetItemCount())]
+        self._selection = find_atoms_in_molecule(self._trajectory.universe,molecule, self._selectedAtoms, True)
                         
     def on_set_user_definition(self,event=None):
 
@@ -129,28 +202,10 @@ class AtomsListDialog(UserDefinitionsDialog):
             
         self._resultsTextCtrl.AppendText('Number of selected %d-tuplets: %d\n' % (self._nAtoms,len(self._selection)))
         for idxs in self._selection:
-            line = "   ;   ".join(["Atom %d : %s" % (i,v) for i,v in enumerate(idxs)])
+            line = "  ;  ".join(["Atom %5d : %s" % (v,self._selectedAtoms[i]) for i,v in enumerate(idxs)])
             self._resultsTextCtrl.AppendText(line)
             self._resultsTextCtrl.AppendText('\n')
         
-    def on_select_atom(self, event):
-        
-        selection = self._atoms.GetSelections()
-                
-        if len(selection) > self._nAtoms:
-            self._atoms.DeselectAll()
-            for idx in self._selectedAtoms:
-                self._atoms.SetSelection(idx,True)
-        else:
-            self._selectedAtoms = selection
-                            
-    def on_select_molecule(self, event):
-        
-        atomsList = self._molecularContents[event.GetString()][0].atomList()
-        atomNames = sorted(set([at.name for at in atomsList]))
-        
-        self._atoms.SetItems(atomNames)
-            
     def validate(self):
 
         if not self._selection:
@@ -174,7 +229,7 @@ class AtomListWidget(UserDefinitionWidget):
     def on_new_user_definition(self,event):
         
         atomsListDlg = AtomsListDialog(self,self._trajectory,self._configurator._nAtoms)
-        
+                
         atomsListDlg.ShowModal()
             
         atomsListDlg.Destroy()
@@ -183,11 +238,13 @@ if __name__ == "__main__":
     
     from MMTK.Trajectory import Trajectory
     
-    t = Trajectory(None,"../../../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc","r")
+    from MDANSE import PLATFORM
+            
+    t = Trajectory(None,os.path.join(os.path.dirname(PLATFORM.package_directory()),"Data","Trajectories","MMTK","nagma_in_periodic_universe.nc"),"r")
     
     app = wx.App(False)
                 
-    p = AtomsListDialog(None,t,2)
+    p = AtomsListDialog(None,t,3)
                 
     p.ShowModal()
     

MDANSE/GUI/ComboWidgets/ConfigurationPanel.py

@@ -10,7 +10,7 @@ class ConfigurationPanel(wx.Panel):
         
         wx.Panel.__init__(self, parent, wx.ID_ANY)
         
-        self._configurable = configurable
+        self._configurable = configurable()
         
         self._widgets = {}
         
@@ -20,15 +20,15 @@ class ConfigurationPanel(wx.Panel):
         
         self.panelSizer = wx.BoxSizer(wx.VERTICAL)
 
-        configuration = self._configurable.build_configuration()
+        self._configurable.build_configuration()
 
         for cfgName in self._configurable.settings.keys():
             
-            widget = configuration[cfgName].widget
+            widget = self._configurable.configuration[cfgName].widget
                         
             widgetClass = REGISTRY["widget"][widget]
                         
-            self._widgets[cfgName] = widgetClass(self, cfgName, configuration[cfgName])
+            self._widgets[cfgName] = widgetClass(self, cfgName, self._configurable.configuration[cfgName])
             
             self.panelSizer.Add(self._widgets[cfgName], 0, wx.ALL|wx.EXPAND, 5)
                   

MDANSE/GUI/DataTreePanel.py

@@ -172,4 +172,4 @@ class DataTreePanel(wx.Panel):
         
         dropSource.SetData(data)
         
-        dropSource.DoDragDrop(wx.Drag_AllowMove)
+        dropSource.DoDragDrop(wx.Drag_CopyOnly)

MDANSE/Mathematics/Geometry.py

@@ -53,15 +53,14 @@ def build_cartesian_axes(origin, p1, p2, dtype = numpy.float64):
     
     origin = numpy.array(origin, dtype = dtype)
     p1 = numpy.array(p1, dtype = dtype)
-    p2 = numpy.array(p2, dtype = dtype)
-    
+    p2 = numpy.array(p2, dtype = dtype)    
     
     v1 = p1 - origin
     v2 = p2 - origin
-    
+        
     n1 = (v1 + v2)
     n1 /= numpy.linalg.norm(n1)
-    
+        
     n3 = numpy.cross(v1,n1)
     n3 /= numpy.linalg.norm(n3)
     

MDANSE/MolecularDynamics/Trajectory.py

@@ -132,6 +132,9 @@ def partition_universe(universe,groups):
     return coll
 
 def read_atoms_trajectory(trajectory, atoms, first, last=None, step=1, variable="configuration", dtype=numpy.float64):
+    
+    if not isinstance(atoms,(list,tuple)):
+        atoms = [atoms]
         
     if last is None:
         last = len(trajectory)
@@ -141,8 +144,6 @@ def read_atoms_trajectory(trajectory, atoms, first, last=None, step=1, variable=
     serie = numpy.zeros((nFrames,3), dtype=dtype)
 
     for at in atoms:
-        if not isinstance(at,Atom):
-            at = int(at)
         serie += trajectory.readParticleTrajectory(at, first, last, step, variable).array
                 
     serie /= len(atoms)

Tests/FunctionalTests/Jobs/Test_ac.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestAC(UnitTest):
 
     def test(self):
         parameters = {}
-        parameters['axis_selection'] = {'endpoint1': ('OW',), 'endpoint2': ('HW',), 'molecule': 'Water'}
+        parameters['axis_selection'] = ('Water', ('OW', 'HW'))
         parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
+        parameters['output_files'] = ('output', ['netcdf'])
         parameters['per_axis'] = False
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['ac'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        job = REGISTRY['job']['ac']()
+        job.run(parameters,False)
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()

Tests/FunctionalTests/Jobs/Test_apm.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestAPM(UnitTest):
@@ -11,11 +11,11 @@ class TestAPM(UnitTest):
         parameters['axis'] = ['a', 'b']
         parameters['frames'] = (0, 10, 1)
         parameters['name'] = 'DMPC'
-        parameters['output_files'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
+        parameters['output_files'] = ('output', ['netcdf'])
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/dmpc_in_periodic_universe.nc'
-        job = REGISTRY['job']['apm'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        job = REGISTRY['job']['apm']()
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()

Tests/FunctionalTests/Jobs/Test_btt.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestBTT(UnitTest):
@@ -10,10 +10,10 @@ class TestBTT(UnitTest):
         parameters = {}
         parameters['atom_selection'] = 'all'
         parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
+        parameters['output_files'] = ('output', ['netcdf'])
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['btt'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        job = REGISTRY['job']['btt']()
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()

Tests/FunctionalTests/Jobs/Test_castep.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestCASTEP(UnitTest):
@@ -9,9 +9,9 @@ class TestCASTEP(UnitTest):
     def test(self):
         parameters = {}
         parameters['castep_file'] = '../../../Data/Trajectories/CASTEP/PBAnew.md'
-        parameters['output_file'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
-        job = REGISTRY['job']['castep'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        parameters['output_file'] = ('output', ['netcdf'])
+        job = REGISTRY['job']['castep']()
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()

Tests/FunctionalTests/Jobs/Test_ccf.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestCCF(UnitTest):
@@ -12,14 +12,14 @@ class TestCCF(UnitTest):
         parameters['frames'] = (0, 10, 1)
         parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
         parameters['normalize'] = False
-        parameters['output_files'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
+        parameters['output_files'] = ('output', ['netcdf'])
         parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0, 5, 0.1)})
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
         parameters['transmutated_atoms'] = None
         parameters['weights'] = 'b_coherent'
-        job = REGISTRY['job']['ccf'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        job = REGISTRY['job']['ccf']()
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()

Tests/FunctionalTests/Jobs/Test_charmm.py

 #!/usr/bin/python
 
 import unittest
-from Tests.UnitTest import UnitTest
+from Tests.UnitTests.UnitTest import UnitTest
 from MDANSE import REGISTRY
 
 class TestCHARMM(UnitTest):
@@ -10,10 +10,10 @@ class TestCHARMM(UnitTest):
         parameters = {}
         parameters['dcd_file'] = '../../../Data/Trajectories/CHARMM/2vb1.dcd'
         parameters['fold'] = False
-        parameters['output_file'] = ('/users/pellegrini/workspace/MDANSE/Tests/FunctionalTests/Jobs', 'output', ['netcdf'])
+        parameters['output_file'] = ('output', ['netcdf'])
         parameters['pdb_file'] = '../../../Data/Trajectories/CHARMM/2vb1.pdb'
-        job = REGISTRY['job']['charmm'](status=False)
-        self.assertNotRaises(job.run, parameters)
+        job = REGISTRY['job']['charmm']()
+        self.assertNotRaises(job.run, parameters, status=False)
 
 def suite():
     loader = unittest.TestLoader()