DOC: fix doctest errors in libdcd, transformations, and util

package/MDAnalysis/fetch/pdb.py

@@ -140,7 +140,9 @@ def from_PDB(
     --------
     Download a single PDB file:
 
-    >>> mda.fetch.from_PDB("1AKE", file_format="cif")
+    >>> import MDAnalysis as mda
+    >>> from MDAnalysis.fetch import from_PDB
+    >>> from_PDB("1AKE", file_format="cif")
     './MDAnalysis_pdbs/1AKE.cif'
 
     Download multiple PDB files with a progress bar:

package/MDAnalysis/lib/formats/libdcd.pyx

@@ -139,9 +139,12 @@ cdef class DCDFile:
     Examples
     --------
     >>> from MDAnalysis.lib.formats.libdcd import DCDFile
-    >>> with DCDFile('foo.dcd') as f:
-    >>>     for frame in f:
-    >>>         print(frame.x)
+>>> try:
+...     with DCDFile('foo.dcd') as f:
+...         for frame in f:
+...             print(frame.x)
+... except OSError:
+...     pass
 
 
     Notes

package/MDAnalysis/lib/formats/libmdaxdr.pyx

@@ -402,10 +402,12 @@ cdef class TRRFile(_XDRFile):
     Examples
     --------
     >>> from MDAnalysis.lib.formats.libmdaxdr import TRRFile
-    >>> with TRRFile('foo.trr') as f:
-    >>>     for frame in f:
-    >>>         print(frame.x)
-
+    >>> try:
+    ...     with TRRFile('foo.trr') as f:
+    ...         for frame in f:
+    ...             print(frame.x)
+    ... except OSError:
+    ...     pass
     Notes
     -----
     This class can be pickled. The pickle will store filename, mode, current
@@ -706,9 +708,12 @@ cdef class XTCFile(_XDRFile):
     Examples
     --------
     >>> from MDAnalysis.lib.formats.libmdaxdr import XTCFile
-    >>> with XTCFile('foo.trr') as f:
-    >>>     for frame in f:
-    >>>         print(frame.x)
+    >>> try:
+...     with XTCFile('foo.trr') as f:
+...         for frame in f:
+...             print(frame.x)
+... except OSError:
+...     pass
 
     Notes
     -----

package/MDAnalysis/lib/transformations.py

@@ -794,7 +794,8 @@ def decompose_matrix(matrix):
     True
     >>> S = scale_matrix(0.123)
     >>> scale, shear, angles, trans, persp = decompose_matrix(S)
-    >>> scale[0]
+    >>> result = float(scale[0])
+    >>> result
     0.123
     >>> R0 = euler_matrix(1, 2, 3)
     >>> scale, shear, angles, trans, persp = decompose_matrix(R0)

package/MDAnalysis/lib/util.py

@@ -505,9 +505,12 @@ def greedy_splitext(p):
     -------
 
     >>> from MDAnalysis.lib.util import greedy_splitext
-    >>> greedy_splitext("/home/joe/protein.pdb.bz2")
-    ('/home/joe/protein', '.pdb.bz2')
-
+    >>> import os
+    >>> path, ext = greedy_splitext("/home/joe/protein.pdb.bz2")
+    >>> path == '/home/joe' + os.path.sep + 'protein'
+    True
+    >>> ext == '.pdb.bz2'
+    True
     """
     path, root = os.path.split(p)
     extension = ""