Merge branch 'fix-linked-atom-attributes'

* avoid creating linked array values in separate Atom objects.
* preserve type when setting linked structure attribute to scalar.
* use napoleon format for `_linkAtomAttribute` docstring.

Resolve #25.

Author: pavoljuhas

src/diffpy/structure/tests/teststructure.py

@@ -474,6 +474,14 @@ def test_xyz(self):
         stru.xyz += 0.1
         self.assertTrue(numpy.array_equal([0.1, 0.1, 0.1], stru[0].xyz))
         self.assertTrue(numpy.array_equal([1.1, 1.1, 1.1], stru[1].xyz))
+        stru.xyz = 0
+        stru[1].xyz[:] = 1
+        self.assertTrue(numpy.array_equal([0, 0, 0], stru[0].xyz))
+        self.assertTrue(numpy.array_equal([1, 1, 1], stru[1].xyz))
+        # verify noop when changing empty slice
+        xyz0 = numpy.copy(stru.xyz)
+        stru[1:1].xyz += 1
+        self.assertTrue(numpy.array_equal(xyz0, stru.xyz))
         return
 
 
@@ -535,6 +543,8 @@ def test_occupancy(self):
         self.assertTrue(numpy.array_equal(numpy.ones(4), cdse.occupancy))
         self.stru.occupancy *= 0.5
         self.assertEqual(1.0, sum([a.occupancy for a in self.stru]))
+        cdse.occupancy = 1
+        self.assertTrue(all(isinstance(a.occupancy, int) for a in cdse))
         return
 
 
@@ -589,6 +599,9 @@ def test_U(self):
         stru.U = 0
         self.assertTrue(numpy.all(stru.anisotropy))
         self.assertFalse(numpy.any(stru.U != 0.0))
+        stru[1].U[:] = 1
+        self.assertTrue(numpy.all(stru[0].U == 0.0))
+        self.assertTrue(numpy.all(stru[1].U == 1.0))
         return
 
 

src/diffpy/structure/utils.py

@@ -56,25 +56,45 @@ def atomBareSymbol(smbl):
 
 def _linkAtomAttribute(attrname, doc, toarray=numpy.array):
     '''Create property wrapper that maps the specified atom attribute.
+
     The returned property object provides convenient access to atom
     attributes from the owner Structure class.
 
-    attrname -- string name of the Atom class attribute to be mapped
-    doc      -- docstring of the property wrapper
-    toarray  -- factory function that converts list of attributes to
-                numpy.array.  Use numpy.char.array for string attributes.
+    Parameters
+    ----------
+    attrname : str
+        The string name of the Atom class attribute to be mapped.
+    doc : str
+        The docstring for the property wrapper.
+    toarray : callable, optional
+        Factory function that converts list of attributes to `numpy.ndarray`.
+        Use `numpy.char.array` for string attributes.
 
     Return a property object.
     '''
+    from itertools import repeat
+    from operator import setitem
+    _all = slice(None)
     def fget(self):
         va = toarray([getattr(a, attrname) for a in self])
         return va
     def fset(self, value):
-        if len(self) == 0:  return
-        # dummy array va helps to broadcast the value to proper iterable
-        va = numpy.asarray(len(self) * [getattr(self[0], attrname)])
-        for a, v in zip(self, numpy.broadcast_arrays(va, value)[1]):
-            setattr(a, attrname, v)
+        n = len(self)
+        if n == 0:
+            return
+        v0 = getattr(self[0], attrname)
+        # replace scalar values, but change array attributes in place
+        if numpy.isscalar(v0):
+            setvalue = lambda a, v: setattr(a, attrname, v)
+        else:
+            setvalue = lambda a, v: setitem(getattr(a, attrname), _all, v)
+        # avoid broadcasting if the new value is a scalar
+        if numpy.isscalar(value):
+            genvalues = repeat(value)
+        else:
+            genvalues = numpy.broadcast_to(value, (n,) + numpy.shape(v0))
+        for a, v in zip(self, genvalues):
+            setvalue(a, v)
         return
     rv = property(fget, fset, doc=doc)
     return rv