backported fix for DCD and XTC/TRR pickling

- fix issue #2878
- add tests to the base tests (but xfail for any format that does not
  implement pickling yet)

package/CHANGELOG

@@ -13,7 +13,7 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/20 orbeckst, VOD555, lilyminium
+??/??/20 orbeckst, VOD555, lilyminium, yuxuanzhuang
 
   * 1.0.1
 
@@ -24,6 +24,7 @@ Fixes
     density=True; the keyword was available since 0.19.0 but with incorrect
     semantics and not documented and did not produce correct results (Issue
     #2811, PR #2812)
+  * pickle correct frames of DCD, TRR, and XTC (#2878)
 
 
 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,

package/MDAnalysis/lib/formats/libdcd.pyx

@@ -265,7 +265,8 @@ cdef class DCDFile:
             return
 
         current_frame = state[1]
-        self.seek(current_frame)
+        self.seek(current_frame - 1)
+        self.current_frame = current_frame
 
 
     def tell(self):

package/MDAnalysis/lib/formats/libmdaxdr.pyx

@@ -306,7 +306,8 @@ cdef class _XDRFile:
 
         # where was I
         current_frame = state[1]
-        self.seek(current_frame)
+        self.seek(current_frame - 1)
+        self.current_frame = current_frame
 
     def seek(self, frame):
         """Seek to Frame.

testsuite/MDAnalysisTests/coordinates/base.py

@@ -25,6 +25,7 @@
 import numpy as np
 import pytest
 from six.moves import zip, range
+from six.moves import cPickle as pickle
 from unittest import TestCase
 from numpy.testing import (assert_equal, assert_almost_equal,
                            assert_array_almost_equal, assert_allclose)
@@ -419,12 +420,22 @@ def test_transformations_copy(self,ref,transformed):
             ideal_coords = ref.iter_ts(i).positions + v1 + v2
             assert_array_almost_equal(ts.positions, ideal_coords, decimal = ref.prec)
 
-
     def test_add_another_transformations_raises_ValueError(self, transformed):
         # After defining the transformations, the workflow cannot be changed
         with pytest.raises(ValueError):
             transformed.add_transformations(translate([2,2,2]))
 
+    def test_pickle_reader(self, reader):
+        try:
+            reader_p = pickle.loads(pickle.dumps(reader))
+        except (TypeError, ValueError):
+            pytest.xfail("Pickling not yet implemented for format {}".format(
+                reader.format))
+        assert_equal(len(reader), len(reader_p))
+        assert_equal(reader.ts, reader_p.ts,
+                     "Timestep is changed after pickling")
+
+
 class MultiframeReaderTest(BaseReaderTest):
     def test_last_frame(self, ref, reader):
         ts = reader[-1]
@@ -490,6 +501,33 @@ def test_iter_as_aux_lowf(self, ref, reader):
                                          ref.iter_ts(ref.aux_lowf_frames_with_steps[i]),
                                          decimal=ref.prec)
 
+    #  To make sure we not only save the current timestep information,
+    #  but also maintain its relative position.
+    def test_pickle_next_ts_reader(self, reader):
+        try:
+            reader_p = pickle.loads(pickle.dumps(reader))
+        except (TypeError, ValueError):
+            pytest.xfail("Pickling not yet implemented for format {}".format(
+                reader.format))
+        assert_equal(next(reader), next(reader_p),
+                     "Next timestep is changed after pickling")
+
+    #  To make sure pickle works for last frame.
+    def test_pickle_last_ts_reader(self, reader):
+        #  move current ts to last frame.
+        reader[-1]
+        try:
+            reader_p = pickle.loads(pickle.dumps(reader))
+        except (TypeError, ValueError):
+            pytest.xfail("Pickling not yet implemented for format {}".format(
+                reader.format))
+        assert_equal(len(reader), len(reader_p),
+                     "Last timestep is changed after pickling")
+        assert_equal(reader.ts, reader_p.ts,
+                     "Last timestep is changed after pickling")
+
+
+
 
 class BaseWriterTest(object):
     @staticmethod