The configurable object is now set as a keyword to avoid crash when

calling build_doc and get_default_parameters class method

MDANSE/Framework/Configurable.py

@@ -77,7 +77,7 @@ class Configurable(object):
         for name,(typ,kwds) in self.settings.items():
             
             try:
-                self._configuration[name] = REGISTRY["configurator"][typ](self, name, **kwds)
+                self._configuration[name] = REGISTRY["configurator"][typ](name, configurable=self,**kwds)
             # Any kind of error has to be caught
             except:
                 raise ConfigurationError("Invalid type for %r configurator" % name)
@@ -187,7 +187,7 @@ class Configurable(object):
         :param cls: the configurable class for which documentation should be built
         :type cls: an instance of MDANSE.Framework.Configurable.Configurable derived class
         
-        :return: the documnetation about the configurable class
+        :return: the documentation about the configurable class
         :rtype: str
         '''
               

MDANSE/Framework/Configurators/AtomsListConfigurator.py

@@ -47,7 +47,7 @@ class AtomsListConfigurator(IConfigurator):
     
     _default = None
                     
-    def __init__(self, configurable, name, nAtoms=2, **kwargs):
+    def __init__(self, name, nAtoms=2, **kwargs):
         '''
         Initializes the configurator.
 
@@ -57,7 +57,7 @@ class AtomsListConfigurator(IConfigurator):
         :type nAtoms: int
         '''
         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._nAtoms = nAtoms
         

MDANSE/Framework/Configurators/ComplexNumberConfigurator.py

@@ -42,7 +42,7 @@ class ComplexNumberConfigurator(IConfigurator):
     
     _default = 0
     
-    def __init__(self, configurable, name, mini=None, maxi=None, choices=None, **kwargs):
+    def __init__(self, name, mini=None, maxi=None, choices=None,**kwargs):
         '''
         Initializes the configurator.
         
@@ -57,7 +57,7 @@ class ComplexNumberConfigurator(IConfigurator):
         '''
 
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._mini = float(mini) if mini is not None else None
 

MDANSE/Framework/Configurators/FloatConfigurator.py

@@ -41,7 +41,7 @@ class FloatConfigurator(IConfigurator):
     
     _default = 0
     
-    def __init__(self, configurable, name, mini=None, maxi=None, choices=None, **kwargs):
+    def __init__(self, name, mini=None, maxi=None, choices=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -56,7 +56,7 @@ class FloatConfigurator(IConfigurator):
         '''
 
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._mini = float(mini) if mini is not None else None
 

MDANSE/Framework/Configurators/FramesConfigurator.py

@@ -48,7 +48,7 @@ class FramesConfigurator(RangeConfigurator):
     
     type = 'frames'
     
-    def __init__(self, configurable, name, **kwargs):
+    def __init__(self, name, **kwargs):
         '''
         Initializes the configurator.
         
@@ -56,7 +56,7 @@ class FramesConfigurator(RangeConfigurator):
         :type name: str
         '''
 
-        RangeConfigurator.__init__(self, configurable, name, sort=True, **kwargs)
+        RangeConfigurator.__init__(self, name, sort=True, **kwargs)
              
     def configure(self, value):
         '''

MDANSE/Framework/Configurators/GroupingLevelConfigurator.py

@@ -62,7 +62,7 @@ class GroupingLevelConfigurator(SingleChoiceConfigurator):
     
     _default = "atom"
     
-    def __init__(self, configurable, name, choices=None, **kwargs):
+    def __init__(self, name, choices=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -77,7 +77,7 @@ class GroupingLevelConfigurator(SingleChoiceConfigurator):
         else:
             choices = list(set(LEVELS.keys()).intersection(choices))
 
-        SingleChoiceConfigurator.__init__(self, configurable, name, choices=choices, **kwargs)
+        SingleChoiceConfigurator.__init__(self, name, choices=choices, **kwargs)
         
     def configure(self,value):
         '''

MDANSE/Framework/Configurators/IConfigurator.py

@@ -97,7 +97,7 @@ class IConfigurator(dict):
     
     _doc_ = "undocumented"
                             
-    def __init__(self, configurable, name, dependencies=None, default=None, label=None, widget=None):
+    def __init__(self, name, **kwargs):
         '''
         Initializes a configurator object.
         
@@ -117,15 +117,15 @@ class IConfigurator(dict):
 
         self._name = name
         
-        self._configurable = configurable
+        self._configurable = kwargs.get('configurable',None)
                 
-        self._dependencies = dependencies if dependencies is not None else {}
+        self._dependencies = kwargs.get('dependencies',{})
 
-        self._default = default if default is not None else self.__class__._default
+        self._default = kwargs.get('default',self.__class__._default) 
 
-        self._label = label if label is not None else " ".join(name.split('_')).strip()
+        self._label = kwargs.get('label'," ".join(name.split('_')).strip())
 
-        self._widget = widget if widget is not None else self.type
+        self._widget = kwargs.get('widget',self.type)
             
     @property
     def default(self):
@@ -192,6 +192,10 @@ class IConfigurator(dict):
 
         :note: this is an abstract method.
         '''
+
+    def set_configurable(self,configurable):
+        
+        self._configurable = configurable
                                                 
     def check_dependencies(self, configured):
         '''

MDANSE/Framework/Configurators/InputFileConfigurator.py

@@ -44,7 +44,7 @@ class InputFileConfigurator(IConfigurator):
     
     _default = ""
     
-    def __init__(self, configurable, name, wildcard="All files|*.*",**kwargs):
+    def __init__(self, name, wildcard="All files|*.*",**kwargs):
         '''
         Initializes the configurator object.
         
@@ -56,7 +56,7 @@ class InputFileConfigurator(IConfigurator):
         '''
         
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._wildcard = wildcard
                 

MDANSE/Framework/Configurators/IntegerConfigurator.py

@@ -41,7 +41,7 @@ class IntegerConfigurator(IConfigurator):
     
     _default = 0
     
-    def __init__(self, configurable, name, mini=None, maxi=None, choices=None, **kwargs):
+    def __init__(self, name, mini=None, maxi=None, choices=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -56,7 +56,7 @@ class IntegerConfigurator(IConfigurator):
         '''
         
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._mini = int(mini) if mini is not None else None
 

MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py

@@ -50,7 +50,7 @@ class InterpolationOrderConfigurator(SingleChoiceConfigurator):
     
     _default = "no interpolation"
         
-    def __init__(self, configurable, name, orders=None,**kwargs):
+    def __init__(self, name, orders=None,**kwargs):
         '''
         Initializes the configurator.
         
@@ -61,7 +61,7 @@ class InterpolationOrderConfigurator(SingleChoiceConfigurator):
         if orders is None:
             orders = ["no interpolation","1st order","2nd order","3rd order","4th order","5th order"] 
                 
-        SingleChoiceConfigurator.__init__(self, configurable, name, choices=orders, **kwargs)
+        SingleChoiceConfigurator.__init__(self, name, choices=orders, **kwargs)
 
     def configure(self, value):
         '''

MDANSE/Framework/Configurators/McStasParametersConfigurator.py

@@ -60,7 +60,7 @@ class McStasParametersConfigurator(IConfigurator):
                 'sample_rotation_deg': 45.0,
                 'detector_height_m': 3.0}        
     
-    def __init__(self, configurable, name, exclude=None, **kwargs):
+    def __init__(self, name, exclude=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -71,7 +71,7 @@ class McStasParametersConfigurator(IConfigurator):
         '''
         
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._exclude = exclude if exclude is not None else []
         

MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py

@@ -43,7 +43,7 @@ class MultipleChoicesConfigurator(IConfigurator):
     
     _default = []
             
-    def __init__(self, configurable, name, choices=None, nChoices=None, **kwargs):
+    def __init__(self, name, choices=None, nChoices=None, **kwargs):
         '''
         Initializes the configurator.
 
@@ -55,7 +55,7 @@ class MultipleChoicesConfigurator(IConfigurator):
         :type nChoices: int or None
         '''
         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._choices = choices
         

MDANSE/Framework/Configurators/NetCDFInputFileConfigurator.py

@@ -49,7 +49,7 @@ class NetCDFInputFileConfigurator(InputFileConfigurator):
     
     _default = ''
         
-    def __init__(self, configurable, name, variables=None, **kwargs):
+    def __init__(self, name, variables=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -60,7 +60,7 @@ class NetCDFInputFileConfigurator(InputFileConfigurator):
         '''        
 
         # The base class constructor.
-        InputFileConfigurator.__init__(self, configurable, name, **kwargs)
+        InputFileConfigurator.__init__(self, name, **kwargs)
         
         self._variables = variables if variables is not None else []
            

MDANSE/Framework/Configurators/OutputDirectoryConfigurator.py

@@ -44,7 +44,7 @@ class OutputDirectoryConfigurator(IConfigurator):
     
     _default = os.getcwd()
 
-    def __init__(self, configurable, name, new=False, **kwargs):
+    def __init__(self, name, new=False, **kwargs):
         '''
         Initializes the configurator.
         
@@ -54,7 +54,7 @@ class OutputDirectoryConfigurator(IConfigurator):
         :type new: bool
         '''        
                 
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._new = new
 

MDANSE/Framework/Configurators/OutputFilesConfigurator.py

@@ -52,7 +52,7 @@ class OutputFilesConfigurator(IConfigurator):
     
     _default = (os.path.join(tempfile.gettempdir(),"output"), ["netcdf"])
                     
-    def __init__(self, configurable, name, formats=None, **kwargs):
+    def __init__(self, name, formats=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -62,7 +62,7 @@ class OutputFilesConfigurator(IConfigurator):
         :type formats: list of str
         '''
                         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
 
         self._formats = formats if formats is not None else OutputFilesConfigurator._default[2]
     

MDANSE/Framework/Configurators/PythonScriptConfigurator.py

@@ -42,7 +42,7 @@ class PythonScriptConfigurator(InputFileConfigurator):
     
     _default = ''
         
-    def __init__(self, configurable, name, variables=None, **kwargs):
+    def __init__(self, name, variables=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -53,7 +53,7 @@ class PythonScriptConfigurator(InputFileConfigurator):
         '''        
 
         # The base class constructor.
-        InputFileConfigurator.__init__(self, configurable, name, **kwargs)
+        InputFileConfigurator.__init__(self, name, **kwargs)
         
         self._variables = variables if variables is not None else []
            

MDANSE/Framework/Configurators/RangeConfigurator.py

@@ -45,7 +45,7 @@ class RangeConfigurator(IConfigurator):
 
     _default = (0,10,1)
 
-    def __init__(self, configurable, name, valueType=int, includeLast=False, sort=False, toList=False, mini=None, maxi=None, **kwargs):
+    def __init__(self, name, valueType=int, includeLast=False, sort=False, toList=False, mini=None, maxi=None, **kwargs):
         '''
         Initializes the configurator.
         
@@ -65,7 +65,7 @@ class RangeConfigurator(IConfigurator):
         :type maxi: int, float or None
         '''
                         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._valueType = valueType
         

MDANSE/Framework/Configurators/SingleChoiceConfigurator.py

@@ -41,7 +41,7 @@ class SingleChoiceConfigurator(IConfigurator):
     
     _default = []
             
-    def __init__(self, configurable, name, choices=None, **kwargs):
+    def __init__(self, name, choices=None, **kwargs):
         '''
         Initializes the configurator.
 
@@ -51,7 +51,7 @@ class SingleChoiceConfigurator(IConfigurator):
         :type choices: list
         '''
         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._choices = choices if choices is not None else []
 

MDANSE/Framework/Configurators/StringConfigurator.py

@@ -43,7 +43,7 @@ class StringConfigurator(IConfigurator):
     
     _default = ""
 
-    def __init__(self, configurable, name, evalType=None, acceptNullString=True, **kwargs):
+    def __init__(self, name, evalType=None, acceptNullString=True, **kwargs):
         '''
         Initializes the configurator.
         
@@ -55,7 +55,7 @@ class StringConfigurator(IConfigurator):
         :type acceptNullString: bool
         '''
         
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._evalType = evalType
         

MDANSE/Framework/Configurators/VectorConfigurator.py

@@ -45,7 +45,7 @@ class VectorConfigurator(IConfigurator):
     
     _default = [1.0,0.0,0.0]
     
-    def __init__(self, configurable, name, valueType=int, normalize=False, notNull=False, dimension=3, **kwargs):
+    def __init__(self, name, valueType=int, normalize=False, notNull=False, dimension=3, **kwargs):
         '''
         Initializes the configurator.
         
@@ -62,7 +62,7 @@ class VectorConfigurator(IConfigurator):
         '''
 
         # The base class constructor.
-        IConfigurator.__init__(self, configurable, name, **kwargs)
+        IConfigurator.__init__(self, name, **kwargs)
         
         self._valueType = valueType
         

MDANSE/Framework/Configurators/WeightsConfigurator.py

@@ -46,7 +46,7 @@ class WeightsConfigurator(SingleChoiceConfigurator):
     
     _default = "equal"
            
-    def __init__(self, configurable, name, **kwargs):
+    def __init__(self, name, **kwargs):
         '''
         Initializes the configurator.
 
@@ -54,7 +54,7 @@ class WeightsConfigurator(SingleChoiceConfigurator):
         :type name: str
         '''
                 
-        SingleChoiceConfigurator.__init__(self, configurable, name, choices=ELEMENTS.numericProperties, **kwargs)
+        SingleChoiceConfigurator.__init__(self, name, choices=ELEMENTS.numericProperties, **kwargs)
 
     def configure(self, value):
         '''

MDANSE/Framework/Jobs/IJob.py

@@ -260,6 +260,7 @@ class IJob(Configurable):
             #. parameters (dict): optional. If not None, the parameters with which the job file will be built.
         """
         
+        
         f = open(jobFile, 'w')
                    
         # The first line contains the call to the python executable. This is necessary for the file to

Tests/FunctionalTests/Jobs/Test_ccf.py

@@ -9,14 +9,14 @@ class TestCCF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
         parameters['normalize'] = False
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0, 5, 0.1)})
+        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 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']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_cn.py

@@ -9,12 +9,12 @@ class TestCN(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['r_values'] = (0, 10, 1)
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None
         job = REGISTRY['job']['cn']()
         self.assertNotRaises(job.run, parameters, status=False)
 

Tests/FunctionalTests/Jobs/Test_dcsf.py

@@ -9,13 +9,13 @@ class TestDCSF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0, 5, 0.1)})
+        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 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']['dcsf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_disf.py

@@ -9,15 +9,15 @@ class TestDISF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['projection'] = None
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0, 5, 0.1)})
+        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 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_incoherent'
         job = REGISTRY['job']['disf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_dp.py

@@ -9,13 +9,13 @@ class TestDP(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['axis'] = 'c'
         parameters['dr'] = 0.01
         parameters['frames'] = (0, 10, 1)
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None
         parameters['weights'] = 'equal'
         job = REGISTRY['job']['dp']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_eisf.py

@@ -9,14 +9,14 @@ class TestEISF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['projection'] = None
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0, 5, 0.1)})
+        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 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_incoherent'
         job = REGISTRY['job']['eisf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_gacf.py

@@ -9,6 +9,7 @@ class TestGACF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['normalize'] = False
@@ -16,7 +17,6 @@ class TestGACF(UnitTest):
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
         parameters['trajectory_variable'] = 'velocities'
-        parameters['transmutated_atoms'] = None
         parameters['weights'] = 'equal'
         job = REGISTRY['job']['gacf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_gdisf.py

@@ -9,6 +9,7 @@ class TestGDISF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
@@ -17,7 +18,6 @@ class TestGDISF(UnitTest):
         parameters['q_shells'] = (0, 10, 1)
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None
         parameters['weights'] = 'b_incoherent'
         job = REGISTRY['job']['gdisf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_msd.py

@@ -9,13 +9,13 @@ class TestMSD(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['projection'] = None
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None
         parameters['weights'] = 'equal'
         job = REGISTRY['job']['msd']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_mvi.py

@@ -11,7 +11,7 @@ class TestMVI(UnitTest):
         parameters['display'] = False
         parameters['frames'] = (0, 10, 1)
         parameters['instrument'] = '../../../Data/McStas/Instruments/Simple_ToF_Flat_Sample.out'
-        parameters['options'] = {'ncount': 10000, 'dir': '/tmp/mcstas_output/29.09.2015-16:29:41'}
+        parameters['options'] = {'ncount': 10000, 'dir': '/tmp/mcstas_output/06.10.2015-17:23:53'}
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['parameters'] = {'beam_wavelength_Angs': 2.0, 'container_thickness_m': 5e-05, 'environment_radius_m': 0.025, 'sample_detector_distance_m': 4.0, 'container': '/users/pellegrini/workspace/MDANSE/Data/McStas/Samples/Al.laz', 'environment_thickness_m': 0.002, 'detector_height_m': 3.0, 'beam_resolution_meV': 0.1, 'sample_height_m': 0.05, 'sample_thickness_m': 0.001, 'environment': '/users/pellegrini/workspace/MDANSE/Data/McStas/Samples/Al.laz', 'sample_width_m': 0.02, 'sample_rotation_deg': 45.0}
         parameters['sample_coh'] = '../../../Data/NetCDF/dcsf_prot.nc'

Tests/FunctionalTests/Jobs/Test_pacf.py

@@ -9,6 +9,7 @@ class TestPACF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['grouping_level'] = 'atom'
         parameters['normalize'] = False
@@ -16,7 +17,6 @@ class TestPACF(UnitTest):
         parameters['projection'] = None
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None
         parameters['weights'] = 'equal'
         job = REGISTRY['job']['pacf']()
         self.assertNotRaises(job.run, parameters, status=False)

Tests/FunctionalTests/Jobs/Test_pdf.py

@@ -9,12 +9,12 @@ class TestPDF(UnitTest):
     def test(self):
         parameters = {}
         parameters['atom_selection'] = 'all'
+        parameters['atom_transmutation'] = None
         parameters['frames'] = (0, 10, 1)
         parameters['output_files'] = ('/tmp/output', ['netcdf'])
         parameters['r_values'] = (0, 10, 1)
         parameters['running_mode'] = ('monoprocessor', 1)
         parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['transmutated_atoms'] = None