Fixed NewReader to work with auxs

Author: richardjgowers

package/MDAnalysis/coordinates/base.py

@@ -1642,6 +1642,7 @@ def __init__(self, filename, convert_units=None, **kwargs):
             convert_units = flags['convert_lengths']
         self.convert_units = convert_units
 
+        self._auxs = {}
         ts_kwargs = {}
         for att in ('dt', 'time_offset'):
             try:
@@ -1657,30 +1658,29 @@ def _update_last_fh_position(self, pos):
         """Update the last known position of the file handle"""
         self._last_fh_pos = pos
 
-    def rewind(self):
-        self._reopen()
-        self.next()
-
     def _full_iter(self):
         self._reopen()
         with util.openany(self.filename, 'r') as self._file:
             while True:
                 try:
-                    yield self._read_next_timestep()
+                    ts = self._read_next_timestep()
+                    for auxname in self.aux_list:
+                        ts = self._auxs[auxname].update_ts(ts)
+                    yield ts
                 except (EOFError, IOError):
                     self.rewind()
                     raise StopIteration
 
-    def _sliced_iter(self, frames):
+    def _sliced_iter(self, start, stop, step):
         with util.openany(self.filename, 'r') as self._file:
-            for f in frames:
-                yield self._read_frame(f)
+            for f in range(start, stop, step):
+                yield self._read_frame_with_aux(f)
         self.rewind()
         raise StopIteration
 
     def _goto_frame(self, i):
         with util.openany(self.filename, 'r') as self._file:
-            ts = self._read_frame(i)
+            ts = self._read_frame_with_aux(i)
         return ts
 
     def __iter__(self):
@@ -1700,7 +1700,10 @@ def apply_limits(frame):
         elif isinstance(item, (list, np.ndarray)):
             return self._sliced_iter(item)
         elif isinstance(item, slice):  # TODO Fix me!
-            return self._sliced_iter(item)
+            start, stop, step = self.check_slice_indices(
+                item.start, item.stop, item.step)
+
+            return self._sliced_iter(start, stop, step)
 
     def __next__(self):
         with util.openany(self.filename, 'r') as self._file:
@@ -1712,6 +1715,8 @@ def __next__(self):
                 raise StopIteration
             else:
                 self._last_fh_pos = self._file.tell()
+                for auxname in self.aux_list:
+                    ts = self._auxs[auxname].update_ts(ts)
                 return ts
 
     next = __next__