Merge branch 'develop' into develop

Author: orbeckst

package/AUTHORS

@@ -249,7 +249,8 @@ Chronological list of authors
  2025
   - Joshua Raphael Uy 
   - Namir Oues
-  - BHM-Bob G  
+  - Lexi Xu
+  - BHM-Bob G    
 
 External code
 -------------

package/CHANGELOG

@@ -14,7 +14,7 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, BHM-Bob G
+??/??/?? IAlibay, orbeckst, BHM-Bob
 
 
  * 2.10.0

package/MDAnalysis/lib/distances.py

@@ -48,9 +48,12 @@
 
    "OpenMP"   :mod:`c_distances_openmp` parallel implementation in C/Cython
                                         with OpenMP
-   "distopia"  `_distopia`               SIMD-accelerated implementation
+
+   "distopia"  `_distopia`              SIMD-accelerated implementation
+                                        with the `distopia`_ library
    ========== ========================= ======================================
 
+
 Use of the distopia library
 ---------------------------
 
@@ -65,25 +68,27 @@
 .. table:: Functions available using the `distopia`_ backend.
    :align: center
 
-   +-----------------------------------------------+
-   | Functions                                     |
-   +===============================================+
-   | MDAnalysis.lib.distances.calc_bonds           |
-   +-----------------------------------------------+
-   | MDAnalysis.lib.distances.calc_angles          |
-   +-----------------------------------------------+
-   | MDAnalysis.lib.distances.calc_dihedrals       |
-   +-----------------------------------------------+
-   | MDAnalysis.lib.distances.distance_array       | 
-   +-----------------------------------------------+
-   | MDAnalysis.lib.distances.self_distance_array  |
-   +-----------------------------------------------+
+   +-------------------------------------------------------+
+   | Functions                                             |
+   +=======================================================+
+   | :func:`MDAnalysis.lib.distances.calc_bonds`           |
+   +-------------------------------------------------------+
+   | :func:`MDAnalysis.lib.distances.calc_angles`          |
+   +-------------------------------------------------------+
+   | :func:`MDAnalysis.lib.distances.calc_dihedrals`       |
+   +-------------------------------------------------------+
+   | :func:`MDAnalysis.lib.distances.distance_array`       |
+   +-------------------------------------------------------+
+   | :func:`MDAnalysis.lib.distances.self_distance_array`  |
+   +-------------------------------------------------------+
 
 If `distopia`_ is installed, the functions in this table will accept the key
-'distopia' for the `backend` keyword argument. If the distopia backend is
-selected the `distopia` library will be used to calculate the distances. Note
-that for functions listed in this table **distopia is not the default backend
-and must be selected.**
+'distopia' for the `backend` keyword argument. The variable
+:data:`HAS_DISTOPIA` is set to ``True`` if distopia is available.
+
+If the distopia backend is selected the `distopia` library will be used to
+calculate the distances. Note that for functions listed in this table
+**distopia is not the default backend and must be explicitly selected.**
 
 
 .. Note::
@@ -109,6 +114,14 @@
 .. versionchanged:: 2.9.0
    Distopia support greatly expanded (with distopia ≥ 0.4.0).
 
+Constants
+---------
+.. data:: HAS_DISTOPIA
+
+   This variable is ``True`` if the :mod:`distopia` package has been
+   installed and is available as a `backend`. Otherwise it is
+   ``False``.
+
 Functions
 ---------
 .. autofunction:: distance_array
@@ -124,6 +137,7 @@
 .. autofunction:: augment_coordinates(coordinates, box, r)
 .. autofunction:: undo_augment(results, translation, nreal)
 .. autofunction:: minimize_vectors(vectors, box)
+
 """
 import numpy as np
 import numpy.typing as npt

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