ENH: support pathlib in ReaderBase

package/MDAnalysis/coordinates/base.py

@@ -143,6 +143,7 @@
 from ..auxiliary.core import get_auxreader_for
 from ..auxiliary import _AUXREADERS
 from ..lib.util import asiterable, Namespace, store_init_arguments
+from ..lib.util import NamedStream
 
 
 class FrameIteratorBase(object):
@@ -1458,7 +1459,10 @@ class ReaderBase(ProtoReader):
     def __init__(self, filename, convert_units=True, **kwargs):
         super(ReaderBase, self).__init__()
 
-        self.filename = filename
+        if isinstance(filename, NamedStream):
+            self.filename = filename
+        else:
+            self.filename = str(filename)
         self.convert_units = convert_units
 
         ts_kwargs = {}

testsuite/MDAnalysisTests/coordinates/test_dcd.py

@@ -20,6 +20,7 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
+from pathlib import Path
 import numpy as np
 
 import MDAnalysis as mda
@@ -424,3 +425,14 @@ def test_ts_time(universe):
                  for ts in u.trajectory]
     times = [ts.time for ts in u.trajectory]
     assert_almost_equal(times, ref_times, decimal=5)
+
+
+def test_pathlib():
+    # regression test for DCD path of
+    # gh-2497
+    top = Path(PSF)
+    traj = Path(DCD)
+    u = mda.Universe(top, traj)
+    # we really only care that pathlib
+    # object handling worked
+    assert u.atoms.n_atoms == 3341

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