ENH: support GROMACS pathlib

* the creation of a `Universe` object involving
GROMACS formats should now accept `pathlib`
objects as requested in MDAnalysisgh-2497; resolving that
issue entirely is a separate matter, this branch
focuses only on the GROMACS format and only if
you proceed via the public `Universe` creation
API

* probably could make it work in Cython directly,
though I'm not convinced we need to do that for
this part of the fix at least, and we probably
should still support strings as well of course

package/MDAnalysis/coordinates/XDR.py

@@ -145,7 +145,7 @@ def __init__(self, filename, convert_units=True, sub=None,
         super(XDRBaseReader, self).__init__(filename,
                                             convert_units=convert_units,
                                             **kwargs)
-        self._xdr = self._file(self.filename)
+        self._xdr = self._file(str(self.filename))
 
         self._sub = sub
         if self._sub is not None:

testsuite/MDAnalysisTests/coordinates/test_xdr.py

@@ -29,6 +29,7 @@
 from os.path import split
 import shutil
 import subprocess
+from pathlib import Path
 
 from numpy.testing import (assert_equal,
                            assert_almost_equal,
@@ -904,3 +905,14 @@ class TestTRRReader_offsets(_GromacsReader_offsets):
         9155712, 10300176
     ])
     _reader = mda.coordinates.TRR.TRRReader
+
+
+def test_pathlib():
+    # regression test for XDR path of
+    # gh-2497
+    top = Path(GRO)
+    traj = Path(XTC)
+    u = mda.Universe(top, traj)
+    # we really only care that pathlib
+    # object handling worked
+    assert u.atoms.n_atoms == 47681