rely on GSDReader for pickling instead, gsd>2 dependency removed

.travis.yml

@@ -27,7 +27,7 @@ env:
     - MAIN_CMD="pytest ${PYTEST_LIST}"
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
-    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd>=2.1.1 codecov"
+    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
     - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True

package/MDAnalysis/coordinates/GSD.py

@@ -54,7 +54,7 @@
 
 from . import base
 
-class GSDReader(base.ReaderBase):
+class GSDReader(base.ReaderBase, base._ExAsciiPickle):
     """Reader for the GSD format.
 
     """
@@ -76,23 +76,27 @@ def __init__(self, filename, **kwargs):
         super(GSDReader, self).__init__(filename, **kwargs)
         self.filename = filename
         self.open_trajectory()
-        self.n_atoms = self._file[0].particles.N
+        self.n_atoms = self._f[0].particles.N
         self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
         self._read_next_timestep()
 
-    def open_trajectory(self) :
+    def open_trajectory(self):
         """opens the trajectory file using gsd.hoomd module"""
         self._frame = -1
-        self._file = gsd.hoomd.open(self.filename,mode='rb')
+        self._f = gsd.hoomd.open(self.filename,mode='rb')
+
+    def open_trajectory_for_pickle(self):
+        """opens the trajectory file while not reset frame"""
+        self._f = gsd.hoomd.open(self.filename, mode='rb')
 
     def close(self):
         """close reader"""
-        self._file.file.close()
+        self._f.file.close()
 
     @property
     def n_frames(self):
         """number of frames in trajectory"""
-        return len(self._file)
+        return len(self._f)
 
     def _reopen(self):
         """reopen trajectory"""
@@ -101,7 +105,7 @@ def _reopen(self):
 
     def _read_frame(self, frame):
         try :
-            myframe = self._file[frame]
+            myframe = self._f[frame]
         except IndexError:
             raise_from(IOError, None)
 
@@ -131,3 +135,11 @@ def _read_frame(self, frame):
     def _read_next_timestep(self) :
         """read next frame in trajectory"""
         return self._read_frame(self._frame + 1)
+
+#    def __getstate__(self):
+#        """Implement the pickle protocol."""
+#        return dict(name=self.filename)
+#
+#    def __setstate__(self, state):
+#        """Implement the pickle protocol."""
+#        self.__init__(state['name'])

package/MDAnalysis/coordinates/base.py

@@ -2106,6 +2106,27 @@ def __setstate__(self, state):
 
         del self._pickle_fn
 
+class _ExAsciiPickle(object):
+    # For external file reader, e.g. GSD 
+    def __getstate__(self):
+        # Shallow copy of state of self
+        # shallow ie don't recursively copy all objects,
+        # just copy the references that __dict__ holds
+        stuff = self.__dict__.copy()
+        # don't pass the file handle over
+        del stuff['_f']
+        # instead pass enough metadata to reconstruct
+        stuff['_pickle_fn'] = self.filename
+        # TODO: what other state does Reader hold?
+        # TODO: reconstruct file handle position
+        return stuff
+
+    def __setstate__(self, state):
+        self.__dict__.update(state)
+        self.open_trajectory_for_pickle()
+        del self._pickle_fn
+
+
 class ReaderBase(ProtoReader):
     """Base class for trajectory readers that extends :class:`ProtoReader` with a
     :meth:`__del__` method.