Fix bug in PCA trajectory iteration -- avoid explicit usage of self.start

package/CHANGELOG

@@ -19,6 +19,7 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * Fix bug in PCA -- wasn't possible to use `frames=...` syntax before.
  * Fix deploy action to use the correct version of the pypi upload action.
 
 Enhancements

package/MDAnalysis/analysis/pca.py

@@ -230,6 +230,12 @@ class PCA(AnalysisBase):
        ``mean`` input now accepts coordinate arrays instead of atomgroup.
        :attr:`p_components`, :attr:`variance` and :attr:`cumulated_variance`
        are now stored in a :class:`MDAnalysis.analysis.base.Results` instance.
+    .. versionchanged:: 2.8.0
+       ``self.run()`` can now appropriately use ``frames`` parameter (bug
+       described by #4425 and fixed by #4423). Previously, behaviour was to
+       manually iterate through ``self._trajectory``, which starting #3415 that
+       introduced ``frames`` is wrong, and should use ``self._sliced_trajectory``.
+       It is now fixed.
     """
 
     def __init__(self, universe, select='all', align=False, mean=None,
@@ -247,7 +253,7 @@ def __init__(self, universe, select='all', align=False, mean=None,
 
     def _prepare(self):
         # access start index
-        self._u.trajectory[self.start]
+        self._sliced_trajectory[0]
         # reference will be start index
         self._reference = self._u.select_atoms(self._select)
         self._atoms = self._u.select_atoms(self._select)
@@ -275,7 +281,7 @@ def _prepare(self):
         self._ref_atom_positions -= self._ref_cog
 
         if self._calc_mean:
-            for ts in ProgressBar(self._u.trajectory[self.start:self.stop:self.step],
+            for ts in ProgressBar(self._sliced_trajectory,
                                   verbose=self._verbose, desc="Mean Calculation"):
                 if self.align:
                     mobile_cog = self._atoms.center_of_geometry()

testsuite/MDAnalysisTests/analysis/test_pca.py

@@ -133,6 +133,12 @@ def test_no_frames(u):
         PCA(u, select=SELECTION).run(stop=1)
 
 
+def test_can_run_frames(u):
+    atoms = u.select_atoms(SELECTION)
+    u.transfer_to_memory()
+    PCA(u, select=SELECTION).run(frames=[0, 1])
+
+
 def test_transform(pca, u):
     ag = u.select_atoms(SELECTION)
     pca_space = pca.transform(ag, n_components=1)