Merge branch 'develop' into pdbparser_chainid_segid

Author: yuyuan871111

README.rst

@@ -8,7 +8,7 @@
 
 |docs| |devdocs| |discussions|
 
-|anaconda| |asv|
+|pypi| |anaconda| |asv|
 
 MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. 
 
@@ -179,6 +179,10 @@ For citations of included algorithms and sub-modules please see the references_.
    :alt: Coverage Status
    :target: https://codecov.io/gh/MDAnalysis/mdanalysis
 
+.. |pypi| image:: https://img.shields.io/pypi/v/MDAnalysis
+   :alt: PyPI Version
+   :target: https://pypi.org/project/MDAnalysis/
+
 .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg
    :alt: Anaconda
    :target: https://anaconda.org/conda-forge/mdanalysis

package/AUTHORS

@@ -249,9 +249,9 @@ Chronological list of authors
  2025
   - Joshua Raphael Uy 
   - Namir Oues
+  - Lexi Xu
   - Yu-Yuan (Stuart) Yang
 
-
 External code
 -------------
 

package/CHANGELOG

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