From 3821e259ff7d93f5471d15196b7c0bfd33349f21 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 00:59:17 +0200
Subject: [PATCH 01/19] Update align.py

added backends and aggregators for AverageStructure
---
 package/MDAnalysis/analysis/align.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 2bc80042b69..2e44dd3bef9 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -216,7 +216,7 @@
 from MDAnalysis.lib.log import ProgressBar
 from ..due import due, Doi
 
-from .base import AnalysisBase
+from .base import AnalysisBase, ResultsGroup
 
 logger = logging.getLogger('MDAnalysis.analysis.align')
 
@@ -896,6 +896,12 @@ class AverageStructure(AnalysisBase):
 
     """
 
+    _analysis_algorithm_is_parallelizable = True
+    
+    @classmethod
+    def get_supported_backends(cls):
+        return ("serial", "multiprocessing", "dask")
+     
     def __init__(self, mobile, reference=None, select='all', filename=None,
                 weights=None,
                  tol_mass=0.1, match_atoms=True, strict=False, force=True, in_memory=False,
@@ -1089,6 +1095,15 @@ def _conclude(self):
         if not self._verbose:
             logging.disable(logging.NOTSET)
 
+    def _get_aggregator(self):
+        return ResultsGroup(
+            lookup={
+                "universe": ResultsGroup.ndarray_vstack,
+                "positions": ResultsGroup.ndarray_vstack,
+                "rmsd": ResultsGroup.ndarray_vstack,
+            }
+        )
+     
     @property
     def universe(self):
         wmsg = ("The `universe` attribute was deprecated in MDAnalysis 2.0.0 "
@@ -1669,4 +1684,4 @@ def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):
                 logger.error(errmsg)
                 raise SelectionError(errmsg)
 
-    return ag1, ag2
\ No newline at end of file
+    return ag1, ag2

From 9dcc271f9ecda12858d977695748ff04ed31a0fc Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 01:02:33 +0200
Subject: [PATCH 02/19] Update conftest.py

added AverageStructure to conftest
---
 testsuite/MDAnalysisTests/analysis/conftest.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/testsuite/MDAnalysisTests/analysis/conftest.py b/testsuite/MDAnalysisTests/analysis/conftest.py
index fc3c8a480c7..b044024856c 100644
--- a/testsuite/MDAnalysisTests/analysis/conftest.py
+++ b/testsuite/MDAnalysisTests/analysis/conftest.py
@@ -14,6 +14,7 @@
 from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import (
     HydrogenBondAnalysis,
 )
+from MDAnalysis.analysis.align import AverageStructure
 from MDAnalysis.lib.util import is_installed
 
 
@@ -141,3 +142,10 @@ def client_DSSP(request):
 @pytest.fixture(scope='module', params=params_for_cls(HydrogenBondAnalysis))
 def client_HydrogenBondAnalysis(request):
     return request.param
+
+
+# MDAnalysis.analysis.align
+
+@pytest.fixture(scope="module", params=params_for_cls(AverageStructure))
+def client_AverageStructure(request):
+    return request.param

From a08889487c6318de2a244b4ee52d975013e10c1f Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 01:52:19 +0200
Subject: [PATCH 03/19] Update test_align.py

added client_AverageStructure
---
 .../MDAnalysisTests/analysis/test_align.py    | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 63dfd25db80..025658a706a 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -427,9 +427,9 @@ def universe(self):
     def reference(self):
         return mda.Universe(PSF, CRD)
 
-    def test_average_structure_deprecated_attrs(self, universe, reference):
+    def test_average_structure_deprecated_attrs(self, universe, reference, client_AverageStructure):
         # Issue #3278 - remove in MDAnalysis 3.0.0
-        avg = align.AverageStructure(universe, reference).run(stop=2)
+        avg = align.AverageStructure(universe, reference).run(stop=2, **client_AverageStructure)
 
         wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):
@@ -444,36 +444,36 @@ def test_average_structure_deprecated_attrs(self, universe, reference):
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert avg.rmsd == avg.results.rmsd
 
-    def test_average_structure(self, universe, reference):
+    def test_average_structure(self, universe, reference, client_AverageStructure):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference)
-        avg = align.AverageStructure(universe, reference).run()
+        avg = align.AverageStructure(universe, reference).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_mass_weighted(self, universe, reference):
+    def test_average_structure_mass_weighted(self, universe, reference, client_AverageStructure):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
-        avg = align.AverageStructure(universe, reference, weights='mass').run()
+        avg = align.AverageStructure(universe, reference, weights='mass').run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_select(self, universe, reference):
+    def test_average_structure_select(self, universe, reference, client_AverageStructure):
         select = 'protein and name CA and resid 3-5'
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
-        avg = align.AverageStructure(universe, reference, select=select).run()
+        avg = align.AverageStructure(universe, reference, select=select).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_no_ref(self, universe):
+    def test_average_structure_no_ref(self, universe, client_AverageStructure):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, universe)
-        avg = align.AverageStructure(universe).run()
+        avg = align.AverageStructure(universe).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                         rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_no_msf(self, universe):
-        avg = align.AverageStructure(universe).run()
+    def test_average_structure_no_msf(self, universe, client_AverageStructure):
+        avg = align.AverageStructure(universe).run(**client_AverageStructure)
         assert not hasattr(avg, 'msf')
 
     def test_mismatch_atoms(self, universe):
@@ -481,7 +481,7 @@ def test_mismatch_atoms(self, universe):
         with pytest.raises(SelectionError):
             align.AverageStructure(universe, u)
 
-    def test_average_structure_ref_frame(self, universe):
+    def test_average_structure_ref_frame(self, universe, client_AverageStructure):
         ref_frame = 3
         u = mda.Merge(universe.atoms)
 
@@ -492,13 +492,13 @@ def test_average_structure_ref_frame(self, universe):
         # back to start
         universe.trajectory[0]
         ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
-        avg = align.AverageStructure(universe, ref_frame=ref_frame).run()
+        avg = align.AverageStructure(universe, ref_frame=ref_frame).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                         rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_in_memory(self, universe):
-        avg = align.AverageStructure(universe, in_memory=True).run()
+    def test_average_structure_in_memory(self, universe, client_AverageStructure):
+        avg = align.AverageStructure(universe, in_memory=True).run(**client_AverageStructure)
         reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
         assert_allclose(avg.results.universe.atoms.positions,
                         reference_coordinates, rtol=0, atol=1.5e-4)

From eea17846acabdc9324a8c6133a53ed3d25baaee9 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 19:48:19 +0200
Subject: [PATCH 04/19] Update align.py

added for AlignTraj backends and aggregator
---
 package/MDAnalysis/analysis/align.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 2e44dd3bef9..25dca86974d 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -678,6 +678,12 @@ class AlignTraj(AnalysisBase):
 
     """
 
+    _analysis_algorithm_is_parallelizable = True
+    
+    @classmethod
+    def get_supported_backends(cls):
+        return ("serial", "dask")
+     
     def __init__(self, mobile, reference, select='all', filename=None,
                  prefix='rmsfit_', weights=None,
                  tol_mass=0.1, match_atoms=True, strict=False, force=True, in_memory=False,
@@ -866,6 +872,12 @@ def rmsd(self):
         warnings.warn(wmsg, DeprecationWarning)
         return self.results.rmsd
 
+    def _get_aggregator(self):
+        return ResultsGroup(
+            lookup={
+                "rmsd": ResultsGroup.ndarray_hstack,
+            }
+        )
 
 class AverageStructure(AnalysisBase):
     """RMS-align trajectory to a reference structure using a selection,

From f1206b0002a74595703c030e2b7220b6dec6b9e3 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 19:50:52 +0200
Subject: [PATCH 05/19] Update conftest.py

added client_AlignTraj
---
 testsuite/MDAnalysisTests/analysis/conftest.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/analysis/conftest.py b/testsuite/MDAnalysisTests/analysis/conftest.py
index b044024856c..dc6297abca8 100644
--- a/testsuite/MDAnalysisTests/analysis/conftest.py
+++ b/testsuite/MDAnalysisTests/analysis/conftest.py
@@ -14,7 +14,7 @@
 from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import (
     HydrogenBondAnalysis,
 )
-from MDAnalysis.analysis.align import AverageStructure
+from MDAnalysis.analysis.align import AverageStructure, AlignTraj
 from MDAnalysis.lib.util import is_installed
 
 
@@ -149,3 +149,8 @@ def client_HydrogenBondAnalysis(request):
 @pytest.fixture(scope="module", params=params_for_cls(AverageStructure))
 def client_AverageStructure(request):
     return request.param
+
+
+@pytest.fixture(scope="module", params=params_for_cls(AlignTraj))
+def client_AlignTraj(request):
+    return request.param

From 6c91e91c4a8c28b7c8926a6df262f73cef0cba15 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:09:13 +0200
Subject: [PATCH 06/19] Update test_align.py

added client_AlignTraj to tests
---
 .../MDAnalysisTests/analysis/test_align.py    | 46 +++++++++----------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 025658a706a..6791aeb8f02 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -244,10 +244,10 @@ def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
             finally:
                 x._writer.close()
 
-    def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir):
+    def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        align.AlignTraj(universe, reference, filename=outfile).run()
+        align.AlignTraj(universe, reference, filename=outfile).run(**client_AlignTraj)
         fitted = mda.Universe(PSF, outfile)
 
         # ensure default file exists
@@ -262,25 +262,25 @@ def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir):
             with pytest.raises(IOError):
                 align.AlignTraj(fitted, reference, force=False)
 
-    def test_AlignTraj_step_works(self, universe, reference, tmpdir):
+    def test_AlignTraj_step_works(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
         # this shouldn't throw an exception
-        align.AlignTraj(universe, reference, filename=outfile).run(step=10)
+        align.AlignTraj(universe, reference, filename=outfile).run(step=10, **client_AlignTraj)
 
-    def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir):
+    def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run(stop=2)
+        x = align.AlignTraj(universe, reference, filename=outfile).run(stop=2, **client_AlignTraj)
 
         wmsg = "The `rmsd` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(x.rmsd, x.results.rmsd)
 
-    def test_AlignTraj(self, universe, reference, tmpdir):
+    def test_AlignTraj(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run()
+        x = align.AlignTraj(universe, reference, filename=outfile).run(**client_AlignTraj)
         fitted = mda.Universe(PSF, outfile)
 
         assert_allclose(x.results.rmsd[0], 6.9290, rtol=0, atol=1.5e-3)
@@ -292,10 +292,10 @@ def test_AlignTraj(self, universe, reference, tmpdir):
         self._assert_rmsd(reference, fitted, 0, 6.929083044751061)
         self._assert_rmsd(reference, fitted, -1, 0.0)
 
-    def test_AlignTraj_weighted(self, universe, reference, tmpdir):
+    def test_AlignTraj_weighted(self, universe, reference, tmpdir, client_AlignTraj):
         outfile = str(tmpdir.join('align_test.dcd'))
         x = align.AlignTraj(universe, reference,
-                            filename=outfile, weights='mass').run()
+                            filename=outfile, weights='mass').run(**client_AlignTraj)
         fitted = mda.Universe(PSF, outfile)
         assert_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5e-3)
         assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5e-3)
@@ -305,7 +305,7 @@ def test_AlignTraj_weighted(self, universe, reference, tmpdir):
         self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
                           weights=universe.atoms.masses)
 
-    def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
+    def test_AlignTraj_custom_weights(self, universe, reference, tmpdir, client_AlignTraj):
         weights = np.zeros(universe.atoms.n_atoms)
         ca = universe.select_atoms('name CA')
         weights[ca.indices] = 1
@@ -313,17 +313,17 @@ def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
         outfile = str(tmpdir.join('align_test.dcd'))
 
         x = align.AlignTraj(universe, reference,
-                            filename=outfile, select='name CA').run()
+                            filename=outfile, select='name CA').run(**client_AlignTraj)
         x_weights = align.AlignTraj(universe, reference,
-                                    filename=outfile, weights=weights).run()
+                                    filename=outfile, weights=weights).run(**client_AlignTraj)
 
         assert_allclose(x.results.rmsd, x_weights.results.rmsd, rtol=0, atol=1.5e-7)
 
-    def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
+    def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir, client_AlignTraj):
         outfile = str(tmpdir.join('align_test.dcd'))
         x = align.AlignTraj(universe, reference,
                             filename=outfile,
-                            weights=reference.atoms.masses).run()
+                            weights=reference.atoms.masses).run(**client_AlignTraj)
         fitted = mda.Universe(PSF, outfile)
         assert_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5e-3)
         assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5e-3)
@@ -333,18 +333,18 @@ def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
         self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
                           weights=universe.atoms.masses)
 
-    def test_AlignTraj_partial_fit(self, universe, reference, tmpdir):
+    def test_AlignTraj_partial_fit(self, universe, reference, tmpdir, client_AlignTraj):
         outfile = str(tmpdir.join('align_test.dcd'))
         # fitting on a partial selection should still write the whole topology
         align.AlignTraj(universe, reference, select='resid 1-20',
-                        filename=outfile, weights='mass').run()
+                        filename=outfile, weights='mass').run(**client_AlignTraj)
         mda.Universe(PSF, outfile)
 
-    def test_AlignTraj_in_memory(self, universe, reference, tmpdir):
+    def test_AlignTraj_in_memory(self, universe, reference, tmpdir, client_AlignTraj):
         outfile = str(tmpdir.join('align_test.dcd'))
         reference.trajectory[-1]
         x = align.AlignTraj(universe, reference, filename=outfile,
-                            in_memory=True).run()
+                            in_memory=True).run(**client_AlignTraj)
         assert x.filename is None
         assert_allclose(x.results.rmsd[0], 6.9290, rtol=0, atol=1.5e-3)
         assert_allclose(x.results.rmsd[-1], 5.2797e-07, rtol=0, atol=1.5e-3)
@@ -353,7 +353,7 @@ 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):
+    def test_AlignTraj_writer_kwargs(self, universe, reference, tmpdir, client_AlignTraj):
         # Issue 4564
         writer_kwargs = dict(precision=2)
         with tmpdir.as_cwd():
@@ -361,7 +361,7 @@ def test_AlignTraj_writer_kwargs(self, universe, reference, tmpdir):
                                       select='protein and name CA',
                                       filename='aligned_traj.xtc',
                                       writer_kwargs=writer_kwargs,
-                                      in_memory=False).run()
+                                      in_memory=False).run(**client_AlignTraj)
             assert_equal(aligner._writer.precision, 2)
 
     def _assert_rmsd(self, reference, fitted, frame, desired, weights=None):
@@ -407,9 +407,9 @@ def test_alignto_partial_universe(self, universe, reference):
                                   rtol=0, atol=1.5e-3)
 
 
-def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
+def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs, client_AlignTraj):
     u = mda.Universe(*ref_files, in_memory=True)
-    prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run()
+    prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run(**client_AlignTraj)
     ag = u.select_atoms(select)
     reference_coordinates = u.trajectory.timeseries(asel=ag).mean(axis=1)
     rmsd = sum(prealigner.results.rmsd/len(u.trajectory))

From 17334142551ba3aa2d57aab8b5674dc3d143e7a2 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:29:23 +0200
Subject: [PATCH 07/19] Update align.py

PEP fixes
---
 package/MDAnalysis/analysis/align.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 25dca86974d..ff629661631 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -679,11 +679,11 @@ class AlignTraj(AnalysisBase):
     """
 
     _analysis_algorithm_is_parallelizable = True
-    
+
     @classmethod
     def get_supported_backends(cls):
         return ("serial", "dask")
-     
+
     def __init__(self, mobile, reference, select='all', filename=None,
                  prefix='rmsfit_', weights=None,
                  tol_mass=0.1, match_atoms=True, strict=False, force=True, in_memory=False,
@@ -909,11 +909,11 @@ class AverageStructure(AnalysisBase):
     """
 
     _analysis_algorithm_is_parallelizable = True
-    
+
     @classmethod
     def get_supported_backends(cls):
         return ("serial", "multiprocessing", "dask")
-     
+
     def __init__(self, mobile, reference=None, select='all', filename=None,
                 weights=None,
                  tol_mass=0.1, match_atoms=True, strict=False, force=True, in_memory=False,
@@ -1115,7 +1115,7 @@ def _get_aggregator(self):
                 "rmsd": ResultsGroup.ndarray_vstack,
             }
         )
-     
+
     @property
     def universe(self):
         wmsg = ("The `universe` attribute was deprecated in MDAnalysis 2.0.0 "

From d982d699b7028f1a7ed4d63dbbbed302d0342db2 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:33:17 +0200
Subject: [PATCH 08/19] Update test_align.py

fixing PEP
---
 testsuite/MDAnalysisTests/analysis/test_align.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 6791aeb8f02..2c004bdfa61 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -244,10 +244,14 @@ def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
             finally:
                 x._writer.close()
 
-    def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_outfile_default_exists(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        align.AlignTraj(universe, reference, filename=outfile).run(**client_AlignTraj)
+        align.AlignTraj(universe, reference, filename=outfile).run(
+          **client_AlignTraj
+        )
         fitted = mda.Universe(PSF, outfile)
 
         # ensure default file exists
@@ -262,11 +266,15 @@ def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir, cli
             with pytest.raises(IOError):
                 align.AlignTraj(fitted, reference, force=False)
 
-    def test_AlignTraj_step_works(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_step_works(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
         # this shouldn't throw an exception
-        align.AlignTraj(universe, reference, filename=outfile).run(step=10, **client_AlignTraj)
+        align.AlignTraj(universe, reference, filename=outfile).run(
+          step=10, **client_AlignTraj
+        )
 
     def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]

From fd6b4a424ea384337244d62b2284e696417f3a59 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:36:36 +0200
Subject: [PATCH 09/19] Update test_align.py

fixing pep
---
 .../MDAnalysisTests/analysis/test_align.py    | 40 ++++++++++++++-----
 1 file changed, 30 insertions(+), 10 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 2c004bdfa61..ebea035be0f 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -276,19 +276,27 @@ def test_AlignTraj_step_works(
           step=10, **client_AlignTraj
         )
 
-    def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_deprecated_attribute(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run(stop=2, **client_AlignTraj)
+        x = align.AlignTraj(universe, reference, filename=outfile).run(
+          stop=2, **client_AlignTraj
+        )
 
         wmsg = "The `rmsd` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(x.rmsd, x.results.rmsd)
 
-    def test_AlignTraj(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         reference.trajectory[-1]
         outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run(**client_AlignTraj)
+        x = align.AlignTraj(universe, reference, filename=outfile).run(
+          **client_AlignTraj
+        )
         fitted = mda.Universe(PSF, outfile)
 
         assert_allclose(x.results.rmsd[0], 6.9290, rtol=0, atol=1.5e-3)
@@ -300,10 +308,14 @@ def test_AlignTraj(self, universe, reference, tmpdir, client_AlignTraj):
         self._assert_rmsd(reference, fitted, 0, 6.929083044751061)
         self._assert_rmsd(reference, fitted, -1, 0.0)
 
-    def test_AlignTraj_weighted(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_weighted(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         outfile = str(tmpdir.join('align_test.dcd'))
         x = align.AlignTraj(universe, reference,
-                            filename=outfile, weights='mass').run(**client_AlignTraj)
+                            filename=outfile, weights='mass').run(
+          **client_AlignTraj
+        )
         fitted = mda.Universe(PSF, outfile)
         assert_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5e-3)
         assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5e-3)
@@ -313,7 +325,9 @@ def test_AlignTraj_weighted(self, universe, reference, tmpdir, client_AlignTraj)
         self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
                           weights=universe.atoms.masses)
 
-    def test_AlignTraj_custom_weights(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_custom_weights(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         weights = np.zeros(universe.atoms.n_atoms)
         ca = universe.select_atoms('name CA')
         weights[ca.indices] = 1
@@ -321,13 +335,19 @@ def test_AlignTraj_custom_weights(self, universe, reference, tmpdir, client_Alig
         outfile = str(tmpdir.join('align_test.dcd'))
 
         x = align.AlignTraj(universe, reference,
-                            filename=outfile, select='name CA').run(**client_AlignTraj)
+                            filename=outfile, select='name CA').run(
+          **client_AlignTraj
+        )
         x_weights = align.AlignTraj(universe, reference,
-                                    filename=outfile, weights=weights).run(**client_AlignTraj)
+                                    filename=outfile, weights=weights).run(
+          **client_AlignTraj
+        )
 
         assert_allclose(x.results.rmsd, x_weights.results.rmsd, rtol=0, atol=1.5e-7)
 
-    def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_custom_mass_weights(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         outfile = str(tmpdir.join('align_test.dcd'))
         x = align.AlignTraj(universe, reference,
                             filename=outfile,

From 0022b715c7d3eae5f11df45514f32f83bd5153bb Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:38:57 +0200
Subject: [PATCH 10/19] Update test_align.py

fixing pep
---
 .../MDAnalysisTests/analysis/test_align.py    | 20 ++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index ebea035be0f..c4f8d3b3716 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -351,7 +351,9 @@ def test_AlignTraj_custom_mass_weights(
         outfile = str(tmpdir.join('align_test.dcd'))
         x = align.AlignTraj(universe, reference,
                             filename=outfile,
-                            weights=reference.atoms.masses).run(**client_AlignTraj)
+                            weights=reference.atoms.masses).run(
+          **client_AlignTraj
+        )
         fitted = mda.Universe(PSF, outfile)
         assert_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5e-3)
         assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5e-3)
@@ -361,14 +363,20 @@ def test_AlignTraj_custom_mass_weights(
         self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
                           weights=universe.atoms.masses)
 
-    def test_AlignTraj_partial_fit(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_partial_fit(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         outfile = str(tmpdir.join('align_test.dcd'))
         # fitting on a partial selection should still write the whole topology
         align.AlignTraj(universe, reference, select='resid 1-20',
-                        filename=outfile, weights='mass').run(**client_AlignTraj)
+                        filename=outfile, weights='mass').run(
+          **client_AlignTraj
+        )
         mda.Universe(PSF, outfile)
 
-    def test_AlignTraj_in_memory(self, universe, reference, tmpdir, client_AlignTraj):
+    def test_AlignTraj_in_memory(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         outfile = str(tmpdir.join('align_test.dcd'))
         reference.trajectory[-1]
         x = align.AlignTraj(universe, reference, filename=outfile,
@@ -381,7 +389,9 @@ def test_AlignTraj_in_memory(self, universe, reference, tmpdir, client_AlignTraj
         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, client_AlignTraj):
+    def test_AlignTraj_writer_kwargs(
+      self, universe, reference, tmpdir, client_AlignTraj
+    ):
         # Issue 4564
         writer_kwargs = dict(precision=2)
         with tmpdir.as_cwd():

From 2457c7407770547f38433d183baa83e166ce4a75 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 20:41:08 +0200
Subject: [PATCH 11/19] Update test_align.py

fixing pep
---
 testsuite/MDAnalysisTests/analysis/test_align.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index c4f8d3b3716..97abcc6a297 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -445,9 +445,12 @@ def test_alignto_partial_universe(self, universe, reference):
                                   rtol=0, atol=1.5e-3)
 
 
-def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs, client_AlignTraj):
+def _get_aligned_average_positions(
+  ref_files, ref, select="all", **kwargs, client_AlignTraj
+):
     u = mda.Universe(*ref_files, in_memory=True)
-    prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run(**client_AlignTraj)
+    prealigner = align.AlignTraj(u, ref, select=select,
+                                 **kwargs).run(**client_AlignTraj)
     ag = u.select_atoms(select)
     reference_coordinates = u.trajectory.timeseries(asel=ag).mean(axis=1)
     rmsd = sum(prealigner.results.rmsd/len(u.trajectory))
@@ -465,9 +468,13 @@ def universe(self):
     def reference(self):
         return mda.Universe(PSF, CRD)
 
-    def test_average_structure_deprecated_attrs(self, universe, reference, client_AverageStructure):
+    def test_average_structure_deprecated_attrs(
+      self, universe, reference, client_AverageStructure
+    ):
         # Issue #3278 - remove in MDAnalysis 3.0.0
-        avg = align.AverageStructure(universe, reference).run(stop=2, **client_AverageStructure)
+        avg = align.AverageStructure(universe, reference).run(stop=2,
+                                                              **client_AverageStructure
+                                                             )
 
         wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):

From 0796f4800ce712c54d68fdf6147f6cceea67b4bb Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 21:02:23 +0200
Subject: [PATCH 12/19] Update test_align.py

fixing pep
---
 .../MDAnalysisTests/analysis/test_align.py    | 35 +++++++++++++------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 97abcc6a297..c9f6c24daec 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -472,9 +472,9 @@ def test_average_structure_deprecated_attrs(
       self, universe, reference, client_AverageStructure
     ):
         # Issue #3278 - remove in MDAnalysis 3.0.0
-        avg = align.AverageStructure(universe, reference).run(stop=2,
-                                                              **client_AverageStructure
-                                                             )
+        avg = align.AverageStructure(universe, reference).run(
+          stop=2,**client_AverageStructure
+        )
 
         wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):
@@ -489,23 +489,32 @@ def test_average_structure_deprecated_attrs(
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert avg.rmsd == avg.results.rmsd
 
-    def test_average_structure(self, universe, reference, client_AverageStructure):
+    def test_average_structure(
+      self, universe, reference, client_AverageStructure
+    ):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference)
-        avg = align.AverageStructure(universe, reference).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, reference).run(
+          **client_AverageStructure
+        )
         assert_allclose(avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_mass_weighted(self, universe, reference, client_AverageStructure):
+    def test_average_structure_mass_weighted(
+      self, universe, reference, client_AverageStructure
+    ):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
         avg = align.AverageStructure(universe, reference, weights='mass').run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_select(self, universe, reference, client_AverageStructure):
+    def test_average_structure_select(
+      self, universe, reference, client_AverageStructure
+    ):
         select = 'protein and name CA and resid 3-5'
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
-        avg = align.AverageStructure(universe, reference, select=select).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, reference,
+                                     select=select).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
@@ -537,13 +546,17 @@ def test_average_structure_ref_frame(self, universe, client_AverageStructure):
         # back to start
         universe.trajectory[0]
         ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
-        avg = align.AverageStructure(universe, ref_frame=ref_frame).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, 
+                                     ref_frame=ref_frame).run(**client_AverageStructure)
         assert_allclose(avg.results.universe.atoms.positions, ref,
                         rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_in_memory(self, universe, client_AverageStructure):
-        avg = align.AverageStructure(universe, in_memory=True).run(**client_AverageStructure)
+    def test_average_structure_in_memory(
+      self, universe, client_AverageStructure
+    ):
+        avg = align.AverageStructure(universe, 
+                                     in_memory=True).run(**client_AverageStructure)
         reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
         assert_allclose(avg.results.universe.atoms.positions,
                         reference_coordinates, rtol=0, atol=1.5e-4)

From 7023aa1b11c39a53af4e8a781c1b20a9156f4201 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 21:04:59 +0200
Subject: [PATCH 13/19] Update test_align.py

fixing pep
---
 .../MDAnalysisTests/analysis/test_align.py    | 25 ++++++++++++-------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index c9f6c24daec..eda10f20e52 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -473,7 +473,7 @@ def test_average_structure_deprecated_attrs(
     ):
         # Issue #3278 - remove in MDAnalysis 3.0.0
         avg = align.AverageStructure(universe, reference).run(
-          stop=2,**client_AverageStructure
+          stop=2, **client_AverageStructure
         )
 
         wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0"
@@ -503,7 +503,9 @@ def test_average_structure_mass_weighted(
       self, universe, reference, client_AverageStructure
     ):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
-        avg = align.AverageStructure(universe, reference, weights='mass').run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, reference, weights='mass').run(
+          **client_AverageStructure
+        )
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
@@ -513,8 +515,9 @@ def test_average_structure_select(
     ):
         select = 'protein and name CA and resid 3-5'
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
-        avg = align.AverageStructure(universe, reference,
-                                     select=select).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, reference, select=select).run(
+          **client_AverageStructure
+        )
         assert_allclose(avg.results.universe.atoms.positions, ref,
                             rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
@@ -535,7 +538,9 @@ def test_mismatch_atoms(self, universe):
         with pytest.raises(SelectionError):
             align.AverageStructure(universe, u)
 
-    def test_average_structure_ref_frame(self, universe, client_AverageStructure):
+    def test_average_structure_ref_frame(
+      self, universe, client_AverageStructure
+    ):
         ref_frame = 3
         u = mda.Merge(universe.atoms)
 
@@ -546,8 +551,9 @@ def test_average_structure_ref_frame(self, universe, client_AverageStructure):
         # back to start
         universe.trajectory[0]
         ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
-        avg = align.AverageStructure(universe, 
-                                     ref_frame=ref_frame).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, ref_frame=ref_frame).run(
+          **client_AverageStructure
+        )
         assert_allclose(avg.results.universe.atoms.positions, ref,
                         rtol=0, atol=1.5e-4)
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
@@ -555,8 +561,9 @@ def test_average_structure_ref_frame(self, universe, client_AverageStructure):
     def test_average_structure_in_memory(
       self, universe, client_AverageStructure
     ):
-        avg = align.AverageStructure(universe, 
-                                     in_memory=True).run(**client_AverageStructure)
+        avg = align.AverageStructure(universe, in_memory=True).run(
+          **client_AverageStructure
+        )
         reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
         assert_allclose(avg.results.universe.atoms.positions,
                         reference_coordinates, rtol=0, atol=1.5e-4)

From 6d05d72201f0de649e6e49640135331ccac7ebed Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 21:49:37 +0200
Subject: [PATCH 14/19] Update test_align.py

adjusted position of inputs
---
 testsuite/MDAnalysisTests/analysis/test_align.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index eda10f20e52..80d6f2a1e8b 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -446,7 +446,7 @@ def test_alignto_partial_universe(self, universe, reference):
 
 
 def _get_aligned_average_positions(
-  ref_files, ref, select="all", **kwargs, client_AlignTraj
+  ref_files, ref, client_AlignTraj, select="all", **kwargs
 ):
     u = mda.Universe(*ref_files, in_memory=True)
     prealigner = align.AlignTraj(u, ref, select=select,

From 40316f72aaa42880258f2e827bf2a947e50d935c Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 21:56:18 +0200
Subject: [PATCH 15/19] Update test_align.py

fix positional arguments
---
 testsuite/MDAnalysisTests/analysis/test_align.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 80d6f2a1e8b..4b77da41ab1 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -445,12 +445,9 @@ def test_alignto_partial_universe(self, universe, reference):
                                   rtol=0, atol=1.5e-3)
 
 
-def _get_aligned_average_positions(
-  ref_files, ref, client_AlignTraj, select="all", **kwargs
-):
+def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
     u = mda.Universe(*ref_files, in_memory=True)
-    prealigner = align.AlignTraj(u, ref, select=select,
-                                 **kwargs).run(**client_AlignTraj)
+    prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run()
     ag = u.select_atoms(select)
     reference_coordinates = u.trajectory.timeseries(asel=ag).mean(axis=1)
     rmsd = sum(prealigner.results.rmsd/len(u.trajectory))

From b745ad09f1709ec25684c83882c0186d59ef126b Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 22:40:35 +0200
Subject: [PATCH 16/19] Update align.py

added multiprocessing to test
---
 package/MDAnalysis/analysis/align.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index ff629661631..308b37e4288 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -682,7 +682,7 @@ class AlignTraj(AnalysisBase):
 
     @classmethod
     def get_supported_backends(cls):
-        return ("serial", "dask")
+        return ("serial", "multiprocessing", "dask")
 
     def __init__(self, mobile, reference, select='all', filename=None,
                  prefix='rmsfit_', weights=None,

From bcbffeafc01be27e3fca1b4eb368affc963bb943 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 18 Oct 2024 23:03:35 +0200
Subject: [PATCH 17/19] Update align.py

removed multiprocessing from AlignTraj
---
 package/MDAnalysis/analysis/align.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 308b37e4288..ff629661631 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -682,7 +682,7 @@ class AlignTraj(AnalysisBase):
 
     @classmethod
     def get_supported_backends(cls):
-        return ("serial", "multiprocessing", "dask")
+        return ("serial", "dask")
 
     def __init__(self, mobile, reference, select='all', filename=None,
                  prefix='rmsfit_', weights=None,

From fdb4f35a95b0631de536b9177953c7cf23484463 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sat, 11 Jan 2025 20:54:48 +0100
Subject: [PATCH 18/19] Update test_align.py

test again
---
 .../MDAnalysisTests/analysis/test_align.py    | 164 ++----------------
 1 file changed, 17 insertions(+), 147 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 2fcc8df3a53..ad78f7bcf77 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -303,18 +303,11 @@ def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
                 x._writer.close()
 
     def test_AlignTraj_outfile_default_exists(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
-        reference.trajectory[-1]
-        outfile = str(tmpdir.join('align_test.dcd'))
-        align.AlignTraj(universe, reference, filename=outfile).run(
-          **client_AlignTraj
-        )
-        self, universe, reference, tmpdir
+        self, universe, reference, tmpdir, client_AlignTraj
     ):
         reference.trajectory[-1]
         outfile = str(tmpdir.join("align_test.dcd"))
-        align.AlignTraj(universe, reference, filename=outfile).run()
+        align.AlignTraj(universe, reference, filename=outfile).run(**client_AlignTraj)
         fitted = mda.Universe(PSF, outfile)
 
         # ensure default file exists
@@ -331,24 +324,14 @@ def test_AlignTraj_outfile_default_exists(
             with pytest.raises(IOError):
                 align.AlignTraj(fitted, reference, force=False)
 
-    def test_AlignTraj_step_works(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
+    def test_AlignTraj_step_works(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
         outfile = str(tmpdir.join("align_test.dcd"))
         # this shouldn't throw an exception
-        align.AlignTraj(universe, reference, filename=outfile).run(
-          step=10, **client_AlignTraj
-        )
+        align.AlignTraj(universe, reference, filename=outfile).run(step=10)
 
-    def test_AlignTraj_deprecated_attribute(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
+    def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
-        outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run(
-          stop=2, **client_AlignTraj
-        )
         outfile = str(tmpdir.join("align_test.dcd"))
         x = align.AlignTraj(universe, reference, filename=outfile).run(stop=2)
 
@@ -356,14 +339,8 @@ def test_AlignTraj_deprecated_attribute(
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(x.rmsd, x.results.rmsd)
 
-    def test_AlignTraj(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
+    def test_AlignTraj(self, universe, reference, tmpdir, client_AlignTraj):
         reference.trajectory[-1]
-        outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference, filename=outfile).run(
-          **client_AlignTraj
-        )
         outfile = str(tmpdir.join("align_test.dcd"))
         x = align.AlignTraj(universe, reference, filename=outfile).run()
         fitted = mda.Universe(PSF, outfile)
@@ -377,15 +354,7 @@ def test_AlignTraj(
         self._assert_rmsd(reference, fitted, 0, 6.929083044751061)
         self._assert_rmsd(reference, fitted, -1, 0.0)
 
-    def test_AlignTraj_weighted(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
-        outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference,
-                            filename=outfile, weights='mass').run(
-          **client_AlignTraj
-        )
-    def test_AlignTraj_weighted(self, universe, reference, tmpdir):
+    def test_AlignTraj_weighted(self, universe, reference, tmpdir, client_AlignTraj):
         outfile = str(tmpdir.join("align_test.dcd"))
         x = align.AlignTraj(
             universe, reference, filename=outfile, weights="mass"
@@ -405,23 +374,13 @@ def test_AlignTraj_weighted(self, universe, reference, tmpdir):
             weights=universe.atoms.masses,
         )
 
-    def test_AlignTraj_custom_weights(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
+    def test_AlignTraj_custom_weights(self, universe, reference, tmpdir, client_AlignTraj):
         weights = np.zeros(universe.atoms.n_atoms)
         ca = universe.select_atoms("name CA")
         weights[ca.indices] = 1
 
         outfile = str(tmpdir.join("align_test.dcd"))
 
-        x = align.AlignTraj(universe, reference,
-                            filename=outfile, select='name CA').run(
-          **client_AlignTraj
-        )
-        x_weights = align.AlignTraj(universe, reference,
-                                    filename=outfile, weights=weights).run(
-          **client_AlignTraj
-        )
         x = align.AlignTraj(
             universe, reference, filename=outfile, select="name CA"
         ).run()
@@ -433,16 +392,6 @@ def test_AlignTraj_custom_weights(
             x.results.rmsd, x_weights.results.rmsd, rtol=0, atol=1.5e-7
         )
 
-    def test_AlignTraj_custom_mass_weights(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
-        outfile = str(tmpdir.join('align_test.dcd'))
-        x = align.AlignTraj(universe, reference,
-                            filename=outfile,
-                            weights=reference.atoms.masses).run(
-          **client_AlignTraj
-        )
-        
     def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
         outfile = str(tmpdir.join("align_test.dcd"))
         x = align.AlignTraj(
@@ -466,25 +415,6 @@ def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
             weights=universe.atoms.masses,
         )
 
-    def test_AlignTraj_partial_fit(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
-        outfile = str(tmpdir.join('align_test.dcd'))
-        # fitting on a partial selection should still write the whole topology
-        align.AlignTraj(universe, reference, select='resid 1-20',
-                        filename=outfile, weights='mass').run(
-          **client_AlignTraj
-        )
-        mda.Universe(PSF, outfile)
-
-    def test_AlignTraj_in_memory(
-      self, universe, reference, tmpdir, client_AlignTraj
-    ):
-        outfile = str(tmpdir.join('align_test.dcd'))
-        reference.trajectory[-1]
-        x = align.AlignTraj(universe, reference, filename=outfile,
-                            in_memory=True).run(**client_AlignTraj)
-
     def test_AlignTraj_partial_fit(self, universe, reference, tmpdir):
         outfile = str(tmpdir.join("align_test.dcd"))
         # fitting on a partial selection should still write the whole topology
@@ -511,17 +441,10 @@ 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, client_AlignTraj
-    ):
+    def test_AlignTraj_writer_kwargs(self, universe, reference, tmpdir):
         # Issue 4564
         writer_kwargs = dict(precision=2)
         with tmpdir.as_cwd():
-            aligner = align.AlignTraj(universe, reference,
-                                      select='protein and name CA',
-                                      filename='aligned_traj.xtc',
-                                      writer_kwargs=writer_kwargs,
-                                      in_memory=False).run(**client_AlignTraj)
             aligner = align.AlignTraj(
                 universe,
                 reference,
@@ -584,7 +507,7 @@ def test_alignto_partial_universe(self, universe, reference):
         )
 
 
-def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
+def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs, ):
     u = mda.Universe(*ref_files, in_memory=True)
     prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run()
     ag = u.select_atoms(select)
@@ -605,13 +528,9 @@ def universe(self):
     def reference(self):
         return mda.Universe(PSF, CRD)
 
-    def test_average_structure_deprecated_attrs(
-      self, universe, reference, client_AverageStructure
-    ):
+    def test_average_structure_deprecated_attrs(self, universe, reference):
         # Issue #3278 - remove in MDAnalysis 3.0.0
-        avg = align.AverageStructure(universe, reference).run(
-          stop=2, **client_AverageStructure
-        )
+        avg = align.AverageStructure(universe, reference).run(stop=2,)
 
         wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0"
         with pytest.warns(DeprecationWarning, match=wmsg):
@@ -628,38 +547,8 @@ def test_average_structure_deprecated_attrs(
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert avg.rmsd == avg.results.rmsd
 
-    def test_average_structure(
-      self, universe, reference, client_AverageStructure
-    ):
+    def test_average_structure(self, universe, reference):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, reference)
-        avg = align.AverageStructure(universe, reference).run(
-          **client_AverageStructure
-        )
-        assert_allclose(avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4)
-        assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
-
-    def test_average_structure_mass_weighted(
-      self, universe, reference, client_AverageStructure
-    ):
-        ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
-        avg = align.AverageStructure(universe, reference, weights='mass').run(
-          **client_AverageStructure
-        )
-        assert_allclose(avg.results.universe.atoms.positions, ref,
-                            rtol=0, atol=1.5e-4)
-        assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
-
-    def test_average_structure_select(
-      self, universe, reference, client_AverageStructure
-    ):
-        select = 'protein and name CA and resid 3-5'
-        ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
-        avg = align.AverageStructure(universe, reference, select=select).run(
-          **client_AverageStructure
-        )
-        assert_allclose(avg.results.universe.atoms.positions, ref,
-                            rtol=0, atol=1.5e-4)
-=======
         avg = align.AverageStructure(universe, reference).run()
         assert_allclose(
             avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4
@@ -687,16 +576,8 @@ def test_average_structure_select(self, universe, reference):
         )
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_no_ref(self, universe, client_AverageStructure):
+    def test_average_structure_no_ref(self, universe):
         ref, rmsd = _get_aligned_average_positions(self.ref_files, universe)
-        avg = align.AverageStructure(universe).run(**client_AverageStructure)
-        assert_allclose(avg.results.universe.atoms.positions, ref,
-                        rtol=0, atol=1.5e-4)
-        assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
-
-    def test_average_structure_no_msf(self, universe, client_AverageStructure):
-        avg = align.AverageStructure(universe).run(**client_AverageStructure)
-        assert not hasattr(avg, 'msf')
         avg = align.AverageStructure(universe).run()
         assert_allclose(
             avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4
@@ -712,9 +593,7 @@ def test_mismatch_atoms(self, universe):
         with pytest.raises(SelectionError):
             align.AverageStructure(universe, u)
 
-    def test_average_structure_ref_frame(
-      self, universe, client_AverageStructure
-    ):
+    def test_average_structure_ref_frame(self, universe):
         ref_frame = 3
         u = mda.Merge(universe.atoms)
 
@@ -725,23 +604,14 @@ def test_average_structure_ref_frame(
         # back to start
         universe.trajectory[0]
         ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
-        avg = align.AverageStructure(universe, ref_frame=ref_frame).run(
-          **client_AverageStructure
-        )
-        assert_allclose(avg.results.universe.atoms.positions, ref,
-                        rtol=0, atol=1.5e-4)
         avg = align.AverageStructure(universe, ref_frame=ref_frame).run()
         assert_allclose(
             avg.results.universe.atoms.positions, ref, rtol=0, atol=1.5e-4
         )
         assert_allclose(avg.results.rmsd, rmsd, rtol=0, atol=1.5e-7)
 
-    def test_average_structure_in_memory(
-      self, universe, client_AverageStructure
-    ):
-        avg = align.AverageStructure(universe, in_memory=True).run(
-          **client_AverageStructure
-        )
+    def test_average_structure_in_memory(self, universe):
+        avg = align.AverageStructure(universe, in_memory=True).run()
         reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
         assert_allclose(
             avg.results.universe.atoms.positions,

From c37add2dc80e3791183113b8e4bc092ffdca2c45 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sat, 11 Jan 2025 22:40:12 +0100
Subject: [PATCH 19/19] Update align.py

check possible fix
---
 package/MDAnalysis/analysis/align.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 76303818675..ab73ed4d1dc 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -860,7 +860,8 @@ def _single_frame(self):
         self._writer.write(mobile_atoms)
 
     def _conclude(self):
-        self._writer.close()
+        if self._writer:
+            self._writer.close()
         if not self._verbose:
             logging.disable(logging.NOTSET)