Pathlib object handling for Universe, SingleFrameReaderBase and Toplogy parsers (Issue #3937)

package/CHANGELOG

@@ -14,7 +14,7 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev
+??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, hmacdope
 
  * 2.9.0
 
@@ -25,6 +25,7 @@ Fixes
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
+ * Handling of Pathlib.Path in SingleFrameReaderBase, Topology and Universe (Issue #3937)
  * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
  * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
  * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)

package/MDAnalysis/coordinates/base.py

@@ -1662,7 +1662,11 @@ class SingleFrameReaderBase(ProtoReader):
     def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
         super(SingleFrameReaderBase, self).__init__()
 
-        self.filename = filename
+        if isinstance(filename, NamedStream):
+            self.filename = filename
+        else:
+            self.filename = str(filename)
+
         self.convert_units = convert_units
 
         self.n_frames = 1

package/MDAnalysis/core/universe.py

@@ -60,6 +60,7 @@
 import warnings
 import contextlib
 import collections
+import pathlib
 
 import MDAnalysis
 import sys
@@ -102,6 +103,9 @@ def _check_file_like(topology):
         else:
             _name = None
         return NamedStream(topology, _name)
+
+    elif isinstance(topology, pathlib.Path):
+        return str(topology)
     return topology
 
 def _topology_from_file_like(topology_file, topology_format=None,

package/MDAnalysis/topology/base.py

@@ -47,6 +47,7 @@
 from ..lib import util
 
 
+
 class _Topologymeta(type):
     """Internal: Topology Parser registration voodoo
 
@@ -115,7 +116,12 @@ class TopologyReaderBase(IOBase, metaclass=_Topologymeta):
        Added keyword 'universe' to pass to Atom creation.
     """
     def __init__(self, filename):
-        self.filename = filename
+
+        if isinstance(filename, util.NamedStream):
+            self.filename = filename
+        else:
+            self.filename = str(filename)
+
 
     def parse(self, **kwargs):  # pragma: no cover
         raise NotImplementedError("Override this in each subclass")

testsuite/MDAnalysisTests/coordinates/base.py

@@ -25,12 +25,14 @@
 
 import numpy as np
 import pytest
+from pathlib import Path
 from unittest import TestCase
 from numpy.testing import (assert_equal, assert_almost_equal,
                            assert_array_almost_equal, assert_allclose)
 
 import MDAnalysis as mda
 from MDAnalysis.coordinates.timestep import Timestep
+from MDAnalysis.coordinates.memory import MemoryReader
 from MDAnalysis.transformations import translate
 
 
@@ -134,6 +136,12 @@ def test_pickle_singleframe_reader(self):
         assert_equal(reader.ts, reader_p.ts,
                      "Modification of ts not preserved after serialization")
 
+    def test_pathlib_input_single(self):
+        path = Path(self.filename)
+        u_str = mda.Universe(self.filename)
+        u_path = mda.Universe(path)
+        assert u_str.atoms.n_atoms == u_path.atoms.n_atoms
+
 
 class BaseReference(object):
     def __init__(self):
@@ -537,6 +545,16 @@ def test_timeseries_atomgroup_asel_mutex(self, reader):
         atoms = mda.Universe(reader.filename, to_guess=()).select_atoms("index 1")
         with pytest.raises(ValueError, match="Cannot provide both"):
             timeseries = reader.timeseries(atomgroup=atoms, asel=atoms, order='fac')
+
+    def test_pathlib_input_base(self, reader):     
+        if isinstance(reader, MemoryReader):
+            if isinstance(reader, MemoryReader):
+                skip_reason = "MemoryReader"
+            pytest.skip(f"Skipping test for Pathlib input with reason: {skip_reason}")
+        path = Path(reader.filename)
+        u_str = mda.Universe(reader.filename)
+        u_path = mda.Universe(path)
+        assert u_str.atoms.n_atoms == u_path.atoms.n_atoms
 
 
 class MultiframeReaderTest(BaseReaderTest):

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -46,7 +46,6 @@
     assert_equal,
 )
 import pytest
-from io import StringIO
 
 
 class TestGROReaderOld(RefAdK):

testsuite/MDAnalysisTests/topology/base.py

@@ -91,6 +91,14 @@ def test_creates_universe(self, filename):
         u = mda.Universe(filename)
         assert isinstance(u, mda.Universe)
 
+    def test_pathlib_input(self, filename):
+        """Check that pathlib.Path objects are accepted"""
+        import pathlib
+        path = pathlib.Path(filename)
+        u_str = mda.Universe(filename)
+        u_path = mda.Universe(path)
+        assert u_str.atoms.n_atoms == u_path.atoms.n_atoms
+
     def test_guessed_attributes(self, filename):
         """check that the universe created with certain parser have the same
         guessed attributes as  when it was guessed inside the parser"""