Fixed high dimensional GroupBase indexing.

package/AUTHORS

@@ -243,7 +243,7 @@ Chronological list of authors
   - Kurt McKee
   - Fabian Zills
   - Laksh Krishna Sharma
-
+  - Matthew Davies
 
 
 External code

package/CHANGELOG

@@ -22,6 +22,7 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * Sanitise and catch higher dimensional indexing in GroupBase (Issue #4647)
  * Do not raise an Error reading H5MD files with datasets like
    `observables/<particle>/<property>` (part of Issue #4598, PR #4615)
  * Fix failure in double-serialization of TextIOPicklable file reader.

package/MDAnalysis/core/groups.py

@@ -597,6 +597,16 @@ def __getitem__(self, item):
                 # hack to make lists into numpy arrays
                 # important for boolean slicing
                 item = np.array(item)
+
+            # correctly flatten oddly shaped, but 1d arrays
+            # raises issues if flattening already suitable arrays
+            if isinstance(item, np.ndarray) and item.ndim > 1:
+                item = np.squeeze(item)
+                # disallow high dimensional indexing.
+                # this doesnt stop the underlying issue
+                if item.ndim > 1:
+                    raise IndexError('Group index must be 1d')
+
             # We specify _derived_class instead of self.__class__ to allow
             # subclasses, such as UpdatingAtomGroup, to control the class
             # resulting from slicing.

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -1592,6 +1592,25 @@ def test_index_advancedslice(self, universe):
                                                            "an AtomGroup")
         assert_equal(ag[1], ag[-1], "advanced slicing does not preserve order")
 
+    @pytest.mark.parametrize('shape', [(-1, 1), (1, -1)])
+    def test_1d_index_invariance(self, universe, shape):
+        u = universe
+        ag1 = u.atoms[np.arange(5)]
+        ag2 = u.atoms[np.arange(5).reshape(shape)]
+
+        # without correct sanitising, n_atoms is 1 when reshaped 'incorrectly'
+        assert ag2.n_atoms == 5, ("indexing with a 1d array was not "
+                                  "invarient of row vs column order")
+        assert_equal(ag1, ag2), ("indexing with a 1d array was not "
+                                 "invarient of row vs column order")
+
+    def test_2d_indexing_caught(self, universe):
+        u = universe
+        index_2d = [[1, 2, 3],
+                    [4, 5, 6]]
+        with pytest.raises(IndexError):
+            u.atoms[index_2d]
+
     @pytest.mark.parametrize('sel', (np.array([True, False, True]),
                                      [True, False, True]))
     def test_boolean_indexing_2(self, universe, sel):