From 3a11c9c750817b10500bc7376df7369536a9b090 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 9 Feb 2020 17:03:06 +0000
Subject: [PATCH] made parmed checking not require parmed import

---
 package/MDAnalysis/core/_get_readers.py       | 21 +++++++++++++----
 .../coordinates/test_parmed.py                | 23 ++++++++++++++-----
 .../MDAnalysisTests/topology/test_parmed.py   |  5 ++--
 3 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/package/MDAnalysis/core/_get_readers.py b/package/MDAnalysis/core/_get_readers.py
index 0d21735f485..79e65a4c26d 100644
--- a/package/MDAnalysis/core/_get_readers.py
+++ b/package/MDAnalysis/core/_get_readers.py
@@ -32,6 +32,15 @@
 from ..lib import util
 
 
+def _is_parmed_object(thing):
+    module = inspect.getmodule(thing.__class__)
+
+    if module is None:
+        return False
+    else:
+        return module.__name__.startswith('parmed')
+
+
 def get_reader_for(filename, format=None):
     """Return the appropriate trajectory reader class for `filename`.
 
@@ -66,7 +75,7 @@ def get_reader_for(filename, format=None):
       :class:`~MDAnalysis.coordinates.memory.MemoryReader` is returned.
     - If `filename` is an MMTF object,
       :class:`~MDAnalysis.coordinates.MMTF.MMTFReader` is returned.
-    - If `filename` is a ParmEd Structure, 
+    - If `filename` is a ParmEd Structure,
       :class:`~MDAnalysis.coordinates.ParmEd.ParmEdReader` is returned.
     - If `filename` is an iterable of filenames,
       :class:`~MDAnalysis.coordinates.chain.ChainReader` is returned.
@@ -93,6 +102,8 @@ def get_reader_for(filename, format=None):
         elif isinstance(filename, mmtf.MMTFDecoder):
             # mmtf slurps mmtf object
             format = 'MMTF'
+        elif _is_parmed_object(filename):
+            format = 'PARMED'
         else:
             # else let the guessing begin!
             format = util.guess_format(filename)
@@ -178,7 +189,7 @@ def get_writer_for(filename, format=None, multiframe=None):
                 None)
         else:
             format = util.check_compressed_format(root, ext)
-    
+
     if format == '':
         raise ValueError((
             'File format could not be guessed from {}, '
@@ -236,6 +247,8 @@ def get_parser_for(filename, format=None):
     if format is None:
         if isinstance(filename, mmtf.MMTFDecoder):
             format = 'mmtf'
+        elif _is_parmed_object(filename):
+            format = 'PARMED'
         else:
             format = util.guess_format(filename)
     format = format.upper()
@@ -273,7 +286,7 @@ def get_converter_for(format):
     TypeError
         If no appropriate parser could be found.
 
-    
+
     .. versionadded:: 0.21.0
     """
     try:
@@ -281,4 +294,4 @@ def get_converter_for(format):
     except KeyError:
         errmsg = 'No converter found for {} format'
         raise_from(TypeError(errmsg.format(format)), None)
-    return writer
\ No newline at end of file
+    return writer
diff --git a/testsuite/MDAnalysisTests/coordinates/test_parmed.py b/testsuite/MDAnalysisTests/coordinates/test_parmed.py
index 31a2d3871bc..319f43e7a87 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_parmed.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_parmed.py
@@ -46,10 +46,23 @@
 
 pmd = pytest.importorskip('parmed')
 
+from MDAnalysis.core._get_readers import _is_parmed_object
+
+
+@pytest.mark.parametrize('thing,reference', [
+    ('foo', False),
+    ([1,2,3], False),
+    (pmd.load_file(GRO), True),
+])
+def test_is_parmed_object(thing, reference):
+    assert _is_parmed_object(thing) == reference
+
+
+
 class TestParmEdReaderGRO:
     ref_filename = GRO
 
-    universe = mda.Universe(pmd.load_file(GRO), format='parmed')
+    universe = mda.Universe(pmd.load_file(GRO))
     ref = mda.Universe(GRO)
     prec = 3
 
@@ -68,10 +81,8 @@ def test_coordinates(self):
 
 
 class BaseTestParmEdReader(_SingleFrameReader):
-
     def setUp(self):
-        self.universe = mda.Universe(pmd.load_file(self.ref_filename),
-                                     format='parmed')
+        self.universe = mda.Universe(pmd.load_file(self.ref_filename))
         self.ref = mda.Universe(self.ref_filename)
         self.prec = 3
 
@@ -135,7 +146,7 @@ def output(self, universe):
 
     @pytest.fixture(scope='class')
     def roundtrip(self, ref):
-        u = mda.Universe(ref, format='parmed')
+        u = mda.Universe(ref)
         return u.atoms.convert_to('PARMED')
 
     def test_equivalent_connectivity_counts(self, universe, output):
@@ -232,7 +243,7 @@ class BaseTestParmEdConverterFromParmed(BaseTestParmEdConverter):
 
     @pytest.fixture(scope='class')
     def universe(self, ref):
-        return mda.Universe(ref, format='parmed')
+        return mda.Universe(ref)
 
     def test_equivalent_connectivity_counts(self, ref, output):
         for attr in ('atoms', 'bonds', 'angles', 'dihedrals', 'impropers',
diff --git a/testsuite/MDAnalysisTests/topology/test_parmed.py b/testsuite/MDAnalysisTests/topology/test_parmed.py
index 2886b4c108b..07c93436387 100644
--- a/testsuite/MDAnalysisTests/topology/test_parmed.py
+++ b/testsuite/MDAnalysisTests/topology/test_parmed.py
@@ -61,10 +61,10 @@ def filename(self):
 
     @pytest.fixture
     def universe(self, filename):
-        return mda.Universe(filename, format='parmed')
+        return mda.Universe(filename)
 
     def test_creates_universe(self, filename):
-        u = mda.Universe(filename, format='parmed')
+        u = mda.Universe(filename)
         assert isinstance(u, mda.Universe)
 
     def test_bonds_total_counts(self, top, filename):
@@ -241,4 +241,3 @@ def test_dihedral_types(self, universe):
         )):
             assert dih.type[i].type.phi_k == phi_k
             assert dih.type[i].type.per == per
-                                            
\ No newline at end of file