Improve libdcd cython

package/MDAnalysis/coordinates/DCD.py

@@ -191,11 +191,10 @@ def _read_next_timestep(self, ts=None):
         if ts is None:
             # use a copy to avoid that ts always points to the same reference
             # removing this breaks lammps reader
-            ts = self.ts.copy() # why is this copy required ??
+            ts = self.ts # why is this copy required ??
         frame = self._file.read()
         self._frame += 1
-        ts = self._frame_to_ts(frame, ts)
-        self.ts = ts
+        self._frame_to_ts(frame, ts)
         return ts
 
     def Writer(self, filename, n_atoms=None, **kwargs):

testsuite/MDAnalysisTests/analysis/test_pca.py

@@ -196,7 +196,7 @@ def test_project_compare_projections(u_fresh):
     project1 = pca.project_single_frame(1)
 
     u_fresh.trajectory[0]
-    coord0 = project0(u_fresh.trajectory.ts).positions
+    coord0 = project0(u_fresh.trajectory.ts).positions.copy()
     u_fresh.trajectory[0]
     coord1 = project1(u_fresh.trajectory.ts).positions
     assert not np.allclose(coord0, coord1, rtol=1e-05)

testsuite/MDAnalysisTests/coordinates/base.py

@@ -444,6 +444,17 @@ 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")
+
+    def test_frame_collect_all_same(self, reader):
+        # check that the timestep resets so that the base pointer is the same 
+        # for all timesteps in a collection witht eh exception of memoryreader
+        if isinstance(reader, mda.coordinates.memory.MemoryReader):
+            pytest.xfail() 
+        collected_ts = []
+        for i, ts in enumerate(reader):
+            collected_ts.append(ts.positions)
+        for array  in collected_ts:
+            assert_allclose(array, collected_ts[0])
 
 
 class MultiframeReaderTest(BaseReaderTest):

testsuite/MDAnalysisTests/coordinates/test_lammps.py

@@ -233,7 +233,7 @@ def test_n_frames(self, u):
         assert_equal(u.trajectory.n_frames, self.n_frames)
 
     def test_dimensions(self, u):
-        mean_dimensions = np.mean([ts.dimensions for ts in u.trajectory],
+        mean_dimensions = np.mean([ts.dimensions.copy() for ts in u.trajectory],
                                   axis=0)
         assert_almost_equal(mean_dimensions, self.mean_dimensions)
 

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -125,11 +125,11 @@ def test_write_coordinates(self, u, tmpdir):
     def test_write_frames(self, u, tmpdir, frames):
         destination = str(tmpdir / 'test.dcd')
         selection = u.trajectory[frames]
-        ref_positions = np.stack([ts.positions for ts in selection])
+        ref_positions = np.stack([ts.positions.copy() for ts in selection])
         u.atoms.write(destination, frames=frames)
 
         u_new = mda.Universe(destination)
-        new_positions = np.stack([ts.positions for ts in u_new.trajectory])
+        new_positions = np.stack([ts.positions.copy() for ts in u_new.trajectory])
 
         assert_array_almost_equal(new_positions, ref_positions)
 
@@ -141,11 +141,11 @@ def test_write_frames(self, u, tmpdir, frames):
     def test_write_frame_iterator(self, u, tmpdir, frames):
         destination = str(tmpdir / 'test.dcd')
         selection = u.trajectory[frames]
-        ref_positions = np.stack([ts.positions for ts in selection])
+        ref_positions = np.stack([ts.positions.copy() for ts in selection])
         u.atoms.write(destination, frames=selection)
 
         u_new = mda.Universe(destination)
-        new_positions = np.stack([ts.positions for ts in u_new.trajectory])
+        new_positions = np.stack([ts.positions.copy() for ts in u_new.trajectory])
 
         assert_array_almost_equal(new_positions, ref_positions)
 
@@ -165,8 +165,8 @@ def test_write_frames_all(self, u, tmpdir, compression):
         destination = str(tmpdir / 'test.dcd' + compression)
         u.atoms.write(destination, frames='all')
         u_new = mda.Universe(destination)
-        ref_positions = np.stack([ts.positions for ts in u.trajectory])
-        new_positions = np.stack([ts.positions for ts in u_new.trajectory])
+        ref_positions = np.stack([ts.positions.copy() for ts in u.trajectory])
+        new_positions = np.stack([ts.positions.copy() for ts in u_new.trajectory])
         assert_array_almost_equal(new_positions, ref_positions)
 
     @pytest.mark.parametrize('frames', ('invalid', 8, True, False, 3.2))