No need to redirect to the original frame explicitly during deserialization

package/CHANGELOG

@@ -23,6 +23,8 @@ Fixes
   * add a 0.5 for correct midpoints in hole analysis (Issue #3715)
   * Fix reading error when PDB CONECT records are corrupt. (Issue #988)
   * Fix writing unusable PDB CONECT records with index>100000. (Issue #988)
+  * Fixes failure in double-serialization of TextIOPicklable file reader.
+    (Issue #3723, PR #3722)
 
 Enhancements
   * Add a new `formalcharge` attribute for storing formal charges (PR #3755)
@@ -36,6 +38,8 @@ Enhancements
     (CZI Performance track, PR #3683)
   * Refactor make_downshift_arrays with vector operation in numpy(PR #3724)
   * Optimize topology serialization/construction by lazy-building _RA and _SR.
+  * Improve performance in Universe serialization by no explicit redirection to
+    the timestep. (Issue #3721, PR #3722)
 
 Changes
   * To add additional optional packages for different file formats when
@@ -45,6 +49,8 @@ Changes
     as per NEP29 (PR #3737)
   * Narrowed variable scope to reduce use of OpenMP `private` clause (PR #3706, PR
     #3728)
+  * TextIOPicklable serializes the raw class instance instead of class name.
+    (PR #3722)
 
 Deprecations
   * The extras_requires target "AMBER" for `pip install ./package[AMBER]`

package/MDAnalysis/coordinates/base.py

@@ -1316,10 +1316,6 @@ def _apply_transformations(self, ts):
 
         return ts
 
-    def __setstate__(self, state):
-        self.__dict__ = state
-        self[self.ts.frame]
-
 
 class ReaderBase(ProtoReader):
     """Base class for trajectory readers that extends :class:`ProtoReader` with a

package/MDAnalysis/lib/picklable_file_io.py

@@ -117,7 +117,7 @@ def __getstate__(self):
 
     def __setstate__(self, args):
         name = args[0]
-        super().__init__(name, mode='r')
+        self.__init__(name, mode='r')
         self.seek(args[1])
 
 
@@ -151,29 +151,26 @@ def __init__(self, raw):
         super().__init__(raw)
         self.raw_class = raw.__class__
 
+
     def __getstate__(self):
         return self.raw_class, self.name, self.tell()
 
+
     def __setstate__(self, args):
+        # raw in BufferIOPicklable is immutable.
+        # need to reconstruct from class
         raw_class = args[0]
         name = args[1]
         raw = raw_class(name)
-        super().__init__(raw)
+        self.__init__(raw)
         self.seek(args[2])
 
-
 class TextIOPicklable(io.TextIOWrapper):
     """Character and line based picklable file-like object.
 
     This class provides a file-like :class:`io.TextIOWrapper` object that can
     be pickled. Note that this only works in read mode.
 
-    Note
-    ----
-    After pickling, the current position is reset. `universe.trajectory[i]` has
-    to be used to return to its original frame.
-
-
     Parameters
     ----------
     raw : FileIO object
@@ -192,26 +189,30 @@ class TextIOPicklable(io.TextIOWrapper):
 
 
     .. versionadded:: 2.0.0
+    .. versionchanged:: 2.3.0
+       The raw class instance instead of the class name
+       that is wrapped inside will be serialized.
+       After deserialization, the current position is no longer reset
+       so `universe.trajectory[i]` is not needed to seek to the
+       original position.
     """
     def __init__(self, raw):
         super().__init__(raw)
-        self.raw_class = raw.__class__
+        self.raw = raw
 
     def __getstate__(self):
         try:
-            name = self.name
-        except AttributeError:
-            # This is kind of ugly--BZ2File does not save its name.
-            name = self.buffer._fp.name
-        return self.raw_class, name
+            curr_loc = self.tell()
+        # some readers (e.g. GMS) disable tell() due to using next()
+        except OSError:
+            curr_loc = None
+        return self.raw, curr_loc
 
     def __setstate__(self, args):
-        raw_class = args[0]
-        name = args[1]
-        # raw_class is used for further expansion this functionality to
-        # Gzip files, which also requires a text wrapper.
-        raw = raw_class(name)
-        super().__init__(raw)
+        raw = args[0]
+        self.__init__(raw)
+        if args[1] is not None:
+            self.seek(args[1])
 
 
 class BZ2Picklable(bz2.BZ2File):
@@ -272,7 +273,7 @@ def __getstate__(self):
         return self._fp.name, self.tell()
 
     def __setstate__(self, args):
-        super().__init__(args[0])
+        self.__init__(args[0])
         self.seek(args[1])
 
 
@@ -334,7 +335,7 @@ def __getstate__(self):
         return self.name, self.tell()
 
     def __setstate__(self, args):
-        super().__init__(args[0])
+        self.__init__(args[0])
         self.seek(args[1])
 
 

testsuite/MDAnalysisTests/coordinates/base.py

@@ -123,9 +123,13 @@ def test_last_slice(self):
     def test_pickle_singleframe_reader(self):
         reader = self.universe.trajectory
         reader_p = pickle.loads(pickle.dumps(reader))
+        reader_p_p = pickle.loads(pickle.dumps(reader_p))
         assert_equal(len(reader), len(reader_p))
         assert_equal(reader.ts, reader_p.ts,
                      "Single-frame timestep is changed after pickling")
+        assert_equal(len(reader), len(reader_p_p))
+        assert_equal(reader.ts, reader_p_p.ts,
+                     "Single-frame timestep is changed after double pickling")
 
 
 class BaseReference(object):
@@ -444,6 +448,10 @@ def test_pickle_reader(self, reader):
         assert_equal(len(reader), len(reader_p))
         assert_equal(reader.ts, reader_p.ts,
                      "Timestep is changed after pickling")
+        reader_p_p = pickle.loads(pickle.dumps(reader_p))
+        assert_equal(len(reader), len(reader_p_p))
+        assert_equal(reader.ts, reader_p_p.ts,
+                     "Timestep is changed after double pickling")
 
 
 class MultiframeReaderTest(BaseReaderTest):
@@ -527,6 +535,9 @@ def test_pickle_next_ts_reader(self, reader):
         reader_p = pickle.loads(pickle.dumps(reader))
         assert_equal(next(reader), next(reader_p),
                      "Next timestep is changed after pickling")
+        reader_p_p = pickle.loads(pickle.dumps(reader_p))
+        assert_equal(next(reader), next(reader_p_p),
+                     "Next timestep is changed after double pickling")
 
     #  To make sure pickle works for last frame.
     def test_pickle_last_ts_reader(self, reader):

testsuite/MDAnalysisTests/utils/test_pickleio.py

@@ -89,10 +89,10 @@ def test_iopickle_text(f_text):
     assert_equal(f_text.readlines(), f_text_pickled.readlines())
 
 
-def test_offset_text_to_0(f_text):
+def test_offset_text_same(f_text):
     f_text.readline()
     f_text_pickled = pickle.loads(pickle.dumps(f_text))
-    assert_equal(f_text_pickled.tell(), 0)
+    assert_equal(f_text_pickled.tell(), f_text.tell())
 
 
 @pytest.fixture(params=[