Implementing Numpy Performance Improvements for Array Copying (#4987)

* faster array copying

---------

Co-authored-by: Lexi Xu <[email protected]>

Author: lexi-x

package/AUTHORS

@@ -249,6 +249,7 @@ Chronological list of authors
  2025
   - Joshua Raphael Uy 
   - Namir Oues
+  - Lexi Xu
 
 External code
 -------------

testsuite/MDAnalysisTests/lib/test_distances.py

@@ -1973,7 +1973,7 @@ def test_input_unchanged_transform_RtoS_and_StoR(
         res = distances.transform_RtoS(crd, box, backend=backend)
         assert_equal(crd, ref)
         crd = res
-        ref = crd.copy()
+        np.copyto(ref, crd)
         res = distances.transform_StoR(crd, box, backend=backend)
         assert_equal(crd, ref)
 

testsuite/MDAnalysisTests/transformations/test_positionaveraging.py

@@ -45,7 +45,7 @@ def test_posavging_fwd(posaveraging_universes):
     )
     avgd = np.empty(size)
     for ts in posaveraging_universes.trajectory:
-        avgd[..., ts.frame] = ts.positions.copy()
+        np.copyto(avgd[..., ts.frame], ts.positions)
 
     assert_array_almost_equal(ref_matrix_fwd, avgd[1, :, -1], decimal=5)
 
@@ -63,7 +63,7 @@ def test_posavging_bwd(posaveraging_universes):
     )
     back_avgd = np.empty(size)
     for ts in posaveraging_universes.trajectory[::-1]:
-        back_avgd[..., 9 - ts.frame] = ts.positions.copy()
+        np.copyto(back_avgd[..., 9 - ts.frame], ts.positions)
     assert_array_almost_equal(ref_matrix_bwd, back_avgd[1, :, -1], decimal=5)
 
 
@@ -78,7 +78,7 @@ def test_posavging_reset(posaveraging_universes):
     )
     avgd = np.empty(size)
     for ts in posaveraging_universes.trajectory:
-        avgd[..., ts.frame] = ts.positions.copy()
+        np.copyto(avgd[..., ts.frame], ts.positions)
     after_reset = ts.positions.copy()
     assert_array_almost_equal(avgd[..., 0], after_reset, decimal=5)
 
@@ -99,7 +99,7 @@ def test_posavging_specific(posaveraging_universes):
     specr_avgd = np.empty(size)
     idx = 0
     for ts in posaveraging_universes.trajectory[fr_list]:
-        specr_avgd[..., idx] = ts.positions.copy()
+        np.copyto(specr_avgd[..., idx], ts.positions)
         idx += 1
     assert_array_almost_equal(
         ref_matrix_specr, specr_avgd[1, :, -1], decimal=5
@@ -122,7 +122,7 @@ def test_posavging_specific_noreset(posaveraging_universes_noreset):
     specr_avgd = np.empty(size)
     idx = 0
     for ts in posaveraging_universes_noreset.trajectory[fr_list]:
-        specr_avgd[..., idx] = ts.positions.copy()
+        np.copyto(specr_avgd[..., idx], ts.positions)
         idx += 1
     assert_array_almost_equal(
         ref_matrix_specr, specr_avgd[1, :, -1], decimal=5