Ensure Timestep in ChainReader is updated for multiple trajectory files

package/CHANGELOG

@@ -13,13 +13,14 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud
+??/??/?? IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud, jaclark5
 
  * 2.4.0
 
 Fixes
   * Fixes distances.between not always returning AtomGroup (Issue #3794)
   * Upgrade to chemfiles 0.10.3 (Issue #3798)
+  * Ensure Timestep passed to transform is the same as AtomGroup Trajectory Timestep (Issue #3657)
 
 Enhancements
   * Added benchmarks for bonds topology attribute (Issue #3785, PR #3806)

package/MDAnalysis/transformations/wrap.py

@@ -99,6 +99,8 @@ def __init__(self, ag, compound='atoms',
         self.compound = compound
 
     def _transform(self, ts):
+        if id(ts) != id(self.ag.universe.trajectory.ts):
+            self.ag.universe.trajectory.ts = ts
         self.ag.wrap(compound=self.compound)
         return ts
 

testsuite/MDAnalysisTests/transformations/test_translate.py

@@ -26,7 +26,7 @@
 from numpy.testing import assert_array_almost_equal
 
 import MDAnalysis as mda
-from MDAnalysis.transformations import translate, center_in_box
+from MDAnalysis.transformations import translate, center_in_box, wrap
 from MDAnalysisTests import make_Universe
 
 
@@ -49,6 +49,19 @@ def test_translate_coords(translate_universes):
     trans = translate(vector)(trans_u.trajectory.ts)
     assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
 
+def test_wrap_id(translate_universes):
+    # If the translation is given a different timestep from what is has, the timestep will 
+    # be updated to the new one given. This should only matter in a ChainReader
+    ref_u, trans_u = translate_universes
+    trans_u.dimensions = [363., 364., 365., 90., 90., 90.]
+    ref_u.dimensions = [363., 364., 365., 90., 90., 90.]
+
+    ag = trans_u.residues[24].atoms
+    trans = wrap(ag)
+    id_trans = id(trans_u.trajectory.ts)
+    trans = trans._transform(ref_u.trajectory.ts)
+    assert id_trans != id(trans_u.trajectory.ts) and id(trans_u.trajectory.ts) == id(ref_u.trajectory.ts)
+
 
 @pytest.mark.parametrize('vector', (
     [0, 1],