AlignTraj Writer kwargs fix

package/CHANGELOG

@@ -37,6 +37,8 @@ Fixes
  * Fix doctest errors of lib/picklable_file_io.py (Issue #3925, PR #4371)
  * Fix deploy action to use the correct version of the pypi upload action.
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
+ * Fix `MDAnalysis.analysis.align.AlignTraj` not accepting writer kwargs
+   (Issue #4564, PR #4565)
 
 Enhancements
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`

package/MDAnalysis/analysis/align.py

@@ -756,6 +756,7 @@ def __init__(self, mobile, reference, select='all', filename=None,
           for the remainder of the Python session. If ``mobile.trajectory`` is
           already a :class:`MemoryReader` then it is *always* treated as if
           ``in_memory`` had been set to ``True``.
+        - Writer ``**kwargs`` will be passed to the constructed `mda.Writer`.
 
         .. versionchanged:: 1.0.0
            Default ``filename`` has now been changed to the current directory.
@@ -819,7 +820,7 @@ def __init__(self, mobile, reference, select='all', filename=None,
         # with self.filename == None (in_memory), the NullWriter is chosen
         # (which just ignores input) and so only the in_memory trajectory is
         # retained
-        self._writer = mda.Writer(self.filename, natoms)
+        self._writer = mda.Writer(self.filename, natoms, **kwargs)
 
         self._weights = get_weights(self.ref_atoms, weights)
 

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -353,6 +353,16 @@ def test_AlignTraj_in_memory(self, universe, reference, tmpdir):
         self._assert_rmsd(reference, universe, 0, 6.929083044751061)
         self._assert_rmsd(reference, universe, -1, 0.0)
 
+    def test_AlignTraj_writer_kwargs(self, universe, reference, tmpdir):
+        # Issue 4564
+        with tmpdir.as_cwd():
+            aligner = align.AlignTraj(universe, reference,
+                                      select='protein and name CA',
+                                      filename='aligned_traj.xtc',
+                                      precision=2,
+                                      in_memory=False).run()
+            assert_equal(aligner._writer.precision, 2)
+
     def _assert_rmsd(self, reference, fitted, frame, desired, weights=None):
         fitted.trajectory[frame]
         rmsd = rms.rmsd(reference.atoms.positions, fitted.atoms.positions,