Update test_align.py

fixing pep
MDAnalysis · Oct 18, 2024 · 0796f48 · 0796f48
1 parent 2457c74
commit 0796f48
Showing 1 changed file with 24 additions and 11 deletions.
diff --git 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)