Merge pull request #363 from simphony/update-metadata

Updates against recent metadata. Fixes a few problems with yapf/setup.py

dev_requirements.txt

@@ -10,3 +10,4 @@ coverage
 flake8<3
 numpy >= 1.4.1
 hypothesis
+yapf

scripts/tests/test_meta_class.py

@@ -324,7 +324,7 @@ def test_Origin(self):
 
     def test_Box(self):
         box = meta_class.Box()
-        arr = box.vector == numpy.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
+        arr = box.vector == numpy.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
         self.assertTrue(arr.all())
 
     def test_Berendsen(self):
@@ -355,5 +355,5 @@ def test_NoseHooverBoundary(self):
     def test_not_sharing_mutable(self):
         box1 = meta_class.Box()
         box2 = meta_class.Box()
-        box1.vector[0][0] = 1.
+        box1.vector[0][0] = 3.
         self.assertNotEqual(box1.vector[0][0], box2.vector[0][0])

setup.cfg

@@ -3,4 +3,5 @@
 exclude = doc/*
 
 [build_meta]
-repotag=89797b0d85096c0119cab8ee6dfdf1ed66e6c930
+repotag=555be66fc307899a5a9bcd8fe91760f58c487115
+

setup.py

@@ -63,6 +63,13 @@ def run(self):
                     print("Failed to run git stash.")
                     raise
 
+                try:
+                    print("Fetching")
+                    check_call(["git", "fetch"])
+                except CalledProcessError:
+                    print("Failed to fetch")
+                    raise
+
                 try:
                     print("Checking out {}".format(self.repotag))
                     check_call(["git", "checkout", self.repotag])

simphony/core/keywords.py

@@ -233,12 +233,6 @@
         key='EXTERNAL_FORCING',
         shape=[1],
         dtype=bool),
-    'FACE': Keyword(
-        name='Face',
-        definition='A face of a three dimensional object defined by the nodes',  # noqa
-        key='FACE',
-        shape=[1],
-        dtype=numpy.float64),
     'FINAL': Keyword(
         name='Final',
         definition='final value of a parameter',  # noqa
@@ -787,7 +781,7 @@
         dtype=None),
     'BOX': Keyword(
         name='Box',
-        definition='A simple hexahedron (with six faces) simulation box defined by the three vectors and three directions. The condition should be specified for each direction (two faces at a time).',  # noqa
+        definition='A simple hexahedron simulation box defining six boundary faces that are defined by three box vectors. The same boundary condition should be specified for each direction (two faces at a time).',  # noqa
         key='BOX',
         shape=[1],
         dtype=None),

simphony/cuds/meta/base_centered_monoclinic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A base centered monoclinic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/base_centered_orthorhombic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A base centered orthorhombic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/body_centered_cubic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A body centred cubic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/body_centered_orthorhombic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A body centered orthorhombic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/body_centered_tetragonal_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A body centered tetragonal lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/box.py

@@ -6,7 +6,7 @@
 
 
 class Box(Boundary):
-    '''A simple hexahedron (with six faces) simulation box defined by the three vectors and three directions. The condition should be specified for each direction (two faces at a time).  # noqa
+    '''A simple hexahedron simulation box defining six boundary faces that are defined by three box vectors. The same boundary condition should be specified for each direction (two faces at a time).  # noqa
     '''
 
     cuba_key = CUBA.BOX
@@ -16,12 +16,12 @@ def __init__(self, description="", name="", condition=None, vector=None):
         self._data = DataContainer()
 
         if vector is None:
-            self.vector = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
+            self.vector = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
         self.condition = condition
         self.name = name
         self.description = description
         # This is a system-managed, read-only attribute
-        self._definition = 'A simple hexahedron (with six faces) simulation box defined by the three vectors and three directions. The condition should be specified for each direction (two faces at a time).'  # noqa
+        self._definition = 'A simple hexahedron simulation box defining six boundary faces that are defined by three box vectors. The same boundary condition should be specified for each direction (two faces at a time).'  # noqa
 
     @property
     def vector(self):

simphony/cuds/meta/bravais_lattice.py

@@ -31,6 +31,8 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A Bravais lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def origin(self):
@@ -88,6 +90,10 @@ def lattice_parameter(self, value):
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -109,4 +115,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.LATTICE, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+        return (CUBA.LATTICE, CUBA.DATA_SET, CUBA.CUDS_COMPONENT,
+                CUBA.CUDS_ITEM)

simphony/cuds/meta/computational_method.py

@@ -1,10 +1,10 @@
 import uuid
 from simphony.core.data_container import DataContainer
 from simphony.core.cuba import CUBA
-from .cuds_component import CUDSComponent
+from .solver_parameter import SolverParameter
 
 
-class ComputationalMethod(CUDSComponent):
+class ComputationalMethod(SolverParameter):
     '''A computational method according to the RoMM  # noqa
     '''
 
@@ -49,4 +49,4 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+        return (CUBA.SOLVER_PARAMETER, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/cubic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A cubic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -57,4 +63,4 @@ def supported_parameters(cls):
     @classmethod
     def parents(cls):
         return (CUBA.TETRAGONAL_LATTICE, CUBA.BRAVAIS_LATTICE, CUBA.LATTICE,
-                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+                CUBA.DATA_SET, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/dem.py

@@ -49,4 +49,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.COMPUTATIONAL_METHOD, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+        return (CUBA.COMPUTATIONAL_METHOD, CUBA.SOLVER_PARAMETER,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/face_centered_cubic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A face centred cubic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/face_centered_orthorhombic_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A face centered orthorhombic lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/fem.py

@@ -49,4 +49,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.COMPUTATIONAL_METHOD, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+        return (CUBA.COMPUTATIONAL_METHOD, CUBA.SOLVER_PARAMETER,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/fvm.py

@@ -49,4 +49,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.COMPUTATIONAL_METHOD, CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)
+        return (CUBA.COMPUTATIONAL_METHOD, CUBA.SOLVER_PARAMETER,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)

simphony/cuds/meta/hexagonal_lattice.py

@@ -30,11 +30,17 @@ def __init__(self,
         self.description = description
         # This is a system-managed, read-only attribute
         self._definition = 'A hexagonal lattice'  # noqa
+        # This is a system-managed, read-only attribute
+        self._models = []
 
     @property
     def definition(self):
         return self._definition
 
+    @property
+    def models(self):
+        return self._models
+
     @property
     def data(self):
         return DataContainer(self._data)
@@ -56,5 +62,5 @@ def supported_parameters(cls):
 
     @classmethod
     def parents(cls):
-        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.CUDS_COMPONENT,
-                CUBA.CUDS_ITEM)
+        return (CUBA.BRAVAIS_LATTICE, CUBA.LATTICE, CUBA.DATA_SET,
+                CUBA.CUDS_COMPONENT, CUBA.CUDS_ITEM)