Adds filename attribute to MemoryReader & associated tests

package/CHANGELOG

@@ -21,6 +21,7 @@ The rules for this file:
   * 0.16.0
 
 Enhancements
+  * Added 'filename' attribute to 'MemoryReader'
   * Improved __str__ and __repr__ of 'GroupBase' class in
     MDAnalysis.core.groups (addresses Issue #1223)
   * Added dynamic selections (addresses Issues #175 and #1074).

package/MDAnalysis/coordinates/memory.py

@@ -222,7 +222,7 @@ class MemoryReader(base.ProtoReader):
     _Timestep = Timestep
 
     def __init__(self, coordinate_array, order='fac',
-                 dimensions = None, dt=1, **kwargs):
+                 dimensions=None, dt=1, filename=None, **kwargs):
         """
 
         Parameters
@@ -242,10 +242,14 @@ def __init__(self, coordinate_array, order='fac',
         dt: float, optional
             The time difference between frames (ps).  If :attr:`time`
             is set, then `dt` will be ignored.
+        filename: string, optional
+            The name of the file from which this instance is created. Set to None
+            when created from an array
         """
 
         super(MemoryReader, self).__init__()
 
+        self.filename = filename
         self.stored_order = order
         self.set_array(np.asarray(coordinate_array), order)
         self.n_frames = \

package/MDAnalysis/core/universe.py

@@ -486,11 +486,12 @@ def transfer_to_memory(self, start=None, stop=None, step=None,
             self.trajectory = MemoryReader(
                 coordinates,
                 dimensions=self.trajectory.ts.dimensions,
-                dt=self.trajectory.ts.dt)
+                dt=self.trajectory.ts.dt,
+                filename=self.filename)
 
     # python 2 doesn't allow an efficient splitting of kwargs in function
     # argument signatures.
-    # In python3-only we'd be able to explicitely define this function with
+    # In python3-only we'd be able to explicitly define this function with
     # something like (sel, *othersels, updating=False, **selgroups)
     def select_atoms(self, *args, **kwargs):
         """Select atoms.

testsuite/CHANGELOG

@@ -17,6 +17,7 @@ and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
          tyler.je.reddy, utkbansal, vedantrathore, kash1102
 
   * 0.16
+    - Added two unit tests for MDAnalysis.coordinates.memory.MemoryReader
     - Make knownfailure work even without parentheses.
     - added two unit tests for MDAnalysis.analysis.polymer
     - added test for LeafletFinder handling a selection string

testsuite/MDAnalysisTests/coordinates/test_memory.py

@@ -58,12 +58,24 @@ def iter_ts(self, i):
         return ts
 
 
-
 class TestMemoryReader(BaseReaderTest):
     def __init__(self):
         reference = MemoryReference()
         super(TestMemoryReader, self).__init__(reference)
 
+    def test_filename_transefer_to_memory(self):
+        # MemoryReader should have a filename attribute set to the trajaectory filename
+        universe = mda.Universe(PSF, DCD)
+        universe.transfer_to_memory()
+        assert_equal(universe.trajectory.filename, PSF)
+
+    def test_filename_array(self):
+        # filename attribute of MemoryReader should be None when generated from an array
+        universe = mda.Universe(PSF, DCD)
+        coordinates = universe.trajectory.timeseries(universe.atoms)
+        universe2 = mda.Universe(PSF, coordinates, format=MemoryReader, order='afc')
+        assert_equal(universe2.trajectory.filename, None)
+
     def test_default_memory_layout(self):
         universe1 = mda.Universe(PSF, DCD, in_memory=True)
         universe2 = mda.Universe(PSF, DCD, in_memory=True, order='fac')