fix issue #45: convert several classes to abstract

LayerModel, Material, and DarwinModelAlloy are now abstract classes

xrayutilities/gridder.py

@@ -25,11 +25,6 @@
 from . import config, cxrayutilities, utilities
 from .exception import InputError
 
-try:  # works in Python >3.4
-    ABC = abc.ABC
-except:  # Python 2.7
-    ABC = abc.ABCMeta('ABC', (object, ), {'__slots__': ()})
-
 
 def delta(min_value, max_value, n):
     """
@@ -75,7 +70,7 @@ def ones(*args):
     return numpy.ones(args, dtype=numpy.double)
 
 
-class Gridder(ABC):
+class Gridder(utilities.ABC):
     """
     Basis class for gridders in xrayutilities. A gridder is a function mapping
     irregular spaced data onto a regular grid by binning the data into equally

xrayutilities/materials/material.py

@@ -23,7 +23,7 @@
 materials their crystalline state is defined few materials are also included as
 amorphous which can be useful for calculation of their optical properties.
 """
-
+import abc
 import copy
 import numbers
 import operator
@@ -120,7 +120,7 @@ def Cijkl2Cij(cijkl):
     return cij
 
 
-class Material(object):
+class Material(utilities.ABC):
     """
     base class for all Materials. common properties of amorphous and
     crystalline materials are described by this class from which Amorphous and
@@ -176,10 +176,20 @@ def _getdensity(self):
     lam = property(_getlam)
     nu = property(_getnu)
 
+    @abc.abstractmethod
     def delta(self, en='config'):
+        """
+        abstract method which every implementation of a Material has to
+        override
+        """
         pass
 
+    @abc.abstractmethod
     def ibeta(self, en='config'):
+        """
+        abstract method which every implementation of a Material has to
+        override
+        """
         pass
 
     def chi0(self, en='config'):

xrayutilities/simpack/darwin_theory.py

@@ -14,7 +14,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>.
 #
 # Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
-
+import abc
 import collections
 import copy
 import warnings
@@ -24,7 +24,7 @@
 from scipy.misc import derivative
 
 from . import LayerModel
-from .. import materials
+from .. import materials, utilities
 from ..math import heaviside
 
 
@@ -112,7 +112,7 @@ def __init__(self, qz, qx=0, qy=0, **kwargs):
         super(LayerModel, self).__init__(exp, **kwargs)
 
         self.npoints = len(qz)
-        self.qz = qz
+        self.qz = numpy.asarray(qz)
         self.qinp = (qx, qy)
         if self.qinp != (0, 0):
             raise NotImplementedError('asymmetric CTR simulation is not yet '
@@ -242,7 +242,7 @@ def _recur_sim(self, nrep, ml, r, rbar, t, pol):
         return r, rbar, t
 
 
-class DarwinModelAlloy(DarwinModel):
+class DarwinModelAlloy(DarwinModel, utilities.ABC):
     """
     extension of the DarwinModel for an binary alloy system were one parameter
     is used to determine the chemical composition
@@ -251,11 +251,11 @@ class DarwinModelAlloy(DarwinModel):
     get_dperp_apar() method and define the substrate lattice parameter (asub).
     See the DarwinModelSiGe001 class for an implementation example.
     """
-    @classmethod
-    def get_dperp_apar(cls, x, apar, r=1):
+    @abc.abstractmethod
+    def get_dperp_apar(self, x, apar, r=1):
         """
         calculate inplane lattice parameter and the out of plane lattice plane
-        spacing (of the atomic planes!) from composition and relaxation
+        spacing (of the atomic planes!) from composition and relaxation.
 
         Parameters
         ----------
@@ -269,7 +269,7 @@ def get_dperp_apar(cls, x, apar, r=1):
         -------
          dperp, apar
         """
-        pass
+        raise NotImplementedError("abstract method needs to be overwritten")
 
     def make_monolayers(self, s):
         """

xrayutilities/simpack/models.py

@@ -15,6 +15,8 @@
 #
 # Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
 
+import abc
+
 import numpy
 import scipy.constants as constants
 import scipy.interpolate as interpolate
@@ -124,7 +126,7 @@ def scale_simulation(self, y):
         return y * self.I0 + self.background
 
 
-class LayerModel(Model):
+class LayerModel(Model, utilities.ABC):
     """
     generic model class from which further thin film models can be derived from
     """
@@ -150,6 +152,14 @@ def __init__(self, *args, **kwargs):
             self.lstack = LayerStack('Stack for %s' % self.__class__.__name__,
                                      *args)
 
+    @abc.abstractmethod
+    def simulate(self):
+        """
+        abstract method that every implementation of a LayerModel has to
+        override 
+        """
+        pass
+
     def _create_return(self, x, E, ai=None, af=None, Ir=None,
                        rettype='intensity'):
         """

xrayutilities/utilities_noconf.py

@@ -20,6 +20,7 @@
 this part of utilities does not need the config class
 """
 
+import abc
 import numbers
 import os.path
 
@@ -28,6 +29,11 @@
 
 from .exception import InputError
 
+try:  # works in Python >3.4
+    ABC = abc.ABC
+except:  # Python 2.7
+    ABC = abc.ABCMeta('ABC', (object, ), {'__slots__': ()})
+
 # python 2to3 compatibility
 try:
     basestring