DOC: fix doctests in universe.py for newer NumPy and optional rdkit

package/CHANGELOG

@@ -21,6 +21,8 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * Fix doctests in universe.py for newer NumPy and optional rdkit
+    (Issue #3925, PR #5297)
  * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
  * Fixed bug in add_transformations allowing non-callable transformations
    (Issue #2558, PR #2558)

package/MDAnalysis/core/universe.py

@@ -1123,7 +1123,7 @@ def add_TopologyAttr(self, topologyattr, values=None):
         >>> u = mda.Universe(PSF, DCD)
         >>> u.add_TopologyAttr('tempfactors')
         >>> u.atoms.tempfactors
-        array([0., 0., 0., ..., 0., 0., 0.])
+        array([0., 0., 0., ..., 0., 0., 0.], shape=(3341,))
 
         .. versionchanged:: 0.17.0
            Can now also add TopologyAttrs with a string of the name of the
@@ -1775,18 +1775,18 @@ def from_smiles(
         --------
         To create a Universe with 10 conformers of ethanol:
 
-        >>> from rdkit.Chem import AllChem
-        >>> u = mda.Universe.from_smiles('CCO', numConfs=10)
-        >>> u
+        >>> from rdkit.Chem import AllChem # doctest: +SKIP
+        >>> u = mda.Universe.from_smiles('CCO', numConfs=10) # doctest: +SKIP
+        >>> u # doctest: +SKIP
         <Universe with 9 atoms>
-        >>> u.trajectory
+        >>> u.trajectory # doctest: +SKIP
         <RDKitReader with 10 frames of 9 atoms>
 
         To use a different conformer generation algorithm, like ETKDGv3:
 
-        >>> u = mda.Universe.from_smiles('CCO', rdkit_kwargs=dict(
+        >>> u = mda.Universe.from_smiles('CCO', rdkit_kwargs=dict( # doctest: +SKIP
         ...      params=AllChem.ETKDGv3()))
-        >>> u.trajectory
+        >>> u.trajectory # doctest: +SKIP
         <RDKitReader with 1 frames of 9 atoms>