Merge pull request #65 from MDAnalysis/more-tests-fixes

more tests/fixes

Author: orbeckst

CHANGELOG

@@ -26,6 +26,8 @@ The rules for this file:
   * fix incorrect reading of ncstart and nrstart in CCP4 (#57)
   * fix that arithemtical operations broke inheritance (#56)
   * fix so that subclasses of ndarray are retained on input (#56)
+  * fix Grid.save(filename) so that it respects the user's filename (#64)
+  * fix grid equality test g == h (relied on old numpy behavior)
 
   Changes (do not affect user)
 

gridData/core.py

@@ -106,14 +106,16 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
         # file formats are guess from extension == lower case key
         self._exporters = {
             'DX': self._export_dx,
-            'PICKLE': self._export_python,
+            'PKL': self._export_python,
+            'PICKLE': self._export_python,  # compatibility
             'PYTHON': self._export_python,  # compatibility
         }
         self._loaders = {
             'CCP4': self._load_cpp4,
             'DX': self._load_dx,
             'PLT': self._load_plt,
-            'PICKLE': self._load_python,
+            'PKL': self._export_python,
+            'PICKLE': self._load_python,  # compatibility
             'PYTHON': self._load_python,  # compatibility
         }
 
@@ -454,9 +456,6 @@ def _export_python(self, filename, **kwargs):
         The object is dumped as a dictionary with grid and edges: This
         is sufficient to recreate the grid object with __init__().
         """
-        root, ext = os.path.splitext(filename)
-        filename = root + ".pickle"
-
         data = dict(grid=self.grid, edges=self.edges, metadata=self.metadata)
         with open(filename, 'wb') as f:
             cPickle.dump(data, f, cPickle.HIGHEST_PROTOCOL)
@@ -603,8 +602,10 @@ def interpolatedF(*coordinates):
     def __eq__(self, other):
         if not isinstance(other, Grid):
             return False
-        return numpy.all(other.grid == self.grid) and numpy.all(
-            other.origin == self.origin) and other.edges == self.edges
+        return numpy.all(other.grid == self.grid) and \
+            numpy.all(other.origin == self.origin) and \
+            numpy.all(numpy.all(other_edge == self_edge) for other_edge, self_edge in
+                      zip(other.edges, self.edges))
 
     def __ne__(self, other):
         return not self.__eq__(other)

gridData/tests/test_grid.py

@@ -144,6 +144,17 @@ def test_resample_factor(self, data):
         assert_array_almost_equal(g.grid[::5, ::5, ::5],
                                   data['grid'].grid[::2, ::2, ::2])
 
+    def test_pickle(self, data, tmpdir):
+        g = data['grid']
+        fn = str(tmpdir.mkdir('grid').join('grid.pkl'))
+        g.save(fn)
+
+        h = Grid()
+        h.load(fn, file_format="pickle")
+
+        assert h == g
+
+
 
 def test_inheritance(data):
     class DerivedGrid(Grid):