Frankenatom fix

package/CHANGELOG

@@ -17,12 +17,12 @@ The rules for this file:
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
-         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst
+         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies
 
  * 2.8.0
 
 Fixes
- * Catch higher dimensional indexing in GroupBase (Issue #4647)
+ * Catch higher dimensional indexing in GroupBase & ComponentBase (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

@@ -570,7 +570,10 @@ def __init__(self, *args):
             raise TypeError(errmsg) from None
 
         # indices for the objects I hold
-        self._ix = np.asarray(ix, dtype=np.intp)
+        ix = np.asarray(ix, dtype=np.intp)
+        if ix.ndim > 1:
+            raise IndexError('Group index must be 1d')
+        self._ix = ix
         self._u = u
         self._cache = dict()
 
@@ -598,11 +601,6 @@ def __getitem__(self, item):
                 # important for boolean slicing
                 item = np.array(item)
 
-            if isinstance(item, np.ndarray) and item.ndim > 1:
-                # disallow high dimensional indexing.
-                # this doesnt stop the underlying issue
-                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.
@@ -4252,6 +4250,9 @@ class ComponentBase(_MutableBase):
 
     def __init__(self, ix, u):
         # index of component
+        if not isinstance(ix, numbers.Integral):
+            raise IndexError('Component can only be indexed by a single integer')
+
         self._ix = ix
         self._u = u
 

testsuite/MDAnalysisTests/core/test_atom.py

@@ -121,6 +121,11 @@ def test_atom_pickle(self, universe, ix):
         atm_in = pickle.loads(pickle.dumps(atm_out))
         assert atm_in == atm_out
 
+    def test_improper_initialisation(self, universe):
+        with pytest.raises(IndexError):
+            indices = [0, 1]
+            mda.core.groups.Atom(indices, universe)
+
 
 class TestAtomNoForceNoVel(object):
     @staticmethod

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -1237,6 +1237,12 @@ def test_bad_make(self):
         with pytest.raises(TypeError):
             mda.core.groups.AtomGroup(['these', 'are', 'not', 'atoms'])
 
+    def test_invalid_index_initialisation(self, universe):
+        indices = [[1, 2, 3],
+                   [4, 5, 6]]
+        with pytest.raises(IndexError):
+            mda.core.groups.AtomGroup(indices, universe)
+
     def test_n_atoms(self, ag):
         assert ag.n_atoms == 3341