distopia 0.4.0 compatibility changes

.github/actions/setup-deps/action.yaml

@@ -59,7 +59,7 @@ inputs:
   dask:
     default: 'dask'
   distopia:
-    default: 'distopia>=0.2.0,<0.3.0'
+    default: 'distopia>=0.3.1'
   h5py:
     default: 'h5py>=2.10'
   hole2:

package/CHANGELOG

@@ -18,7 +18,7 @@ The rules for this file:
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher, 
          yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
-         talagayev, aya9aladdin
+         talagayev, aya9aladdin, hmacdope
 
  * 2.8.0
 
@@ -59,6 +59,8 @@ Fixes
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
 
 Enhancements
+ * Improve distopia backend support in line with new functionality available 
+   in distopia >= 0.3.1 (PR #4734)
  * Removed type and mass guessing from all topology parsers (PR #3753)
  * Added guess_TopologyAttrs() API to the Universe to handle attribute
    guessing (PR #3753)

package/MDAnalysis/lib/_distopia.py

@@ -28,57 +28,123 @@
 as a selectable backend.
 """
 import warnings
+from packaging.version import Version
+
+MIN_DISTOPIA_VERSION = Version("0.3.1")
 
 # check for distopia
 try:
     import distopia
 except ImportError:
     HAS_DISTOPIA = False
+    distopia_version = Version("0.0.0")
 else:
     HAS_DISTOPIA = True
 
-    # check for compatibility: currently needs to be >=0.2.0,<0.3.0 (issue
-    # #4740) No distopia.__version__ available so we have to do some probing.
-    needed_funcs = ['calc_bonds_no_box_float', 'calc_bonds_ortho_float']
-    has_distopia_020 = all([hasattr(distopia, func) for func in needed_funcs])
-    if not has_distopia_020:
-        warnings.warn("Install 'distopia>=0.2.0,<0.3.0' to be used with this "
-                      "release of MDAnalysis. Your installed version of "
-                      "distopia >=0.3.0 will NOT be used.",
-                      category=RuntimeWarning)
-        del distopia
+    # check for compatibility: currently needs to be >=0.3.1,
+    # some versions of `distopia` don't have a version attribute
+    try:
+        distopia_version = Version(distopia.__version__)
+    except AttributeError:
+        warnings.warn("distopia version cannot be determined, assuming 0.0.0")
+        distopia_version = Version("0.0.0")
+    if distopia_version < MIN_DISTOPIA_VERSION:
+        warnings.warn(
+            f"distopia version {distopia_version} is too old; "
+            f"need at least {MIN_DISTOPIA_VERSION}, Your installed version of "
+            "distopia will NOT be used.", category=RuntimeWarning
+        )
         HAS_DISTOPIA = False
 
 
-from .c_distances import (
-    calc_bond_distance_triclinic as _calc_bond_distance_triclinic_serial,
-)
 import numpy as np
 
 
 def calc_bond_distance_ortho(
     coords1, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
 ) -> None:
-    distopia.calc_bonds_ortho_float(
+    distopia.calc_bonds_ortho(
         coords1, coords2, box[:3], results=results
     )
-    # upcast is currently required, change for 3.0, see #3927
+
 
 
 def calc_bond_distance(
     coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
 ) -> None:
-    distopia.calc_bonds_no_box_float(
+    distopia.calc_bonds_no_box(
         coords1, coords2, results=results
     )
-    # upcast is currently required, change for 3.0, see #3927
 
 
 def calc_bond_distance_triclinic(
     coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
 ) -> None:
-    # redirect to serial backend
-    warnings.warn(
-        "distopia does not support triclinic boxes, using serial backend instead."
-    )
-    _calc_bond_distance_triclinic_serial(coords1, coords2, box, results)
+    distopia.calc_bonds_triclinic(coords1, coords2, box, results=results)
+
+
+def calc_angle(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_angles_no_box(coords1, coords2, coords3, results=results)
+
+
+def calc_angle_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_angles_ortho(coords1, coords2, coords3, box[:3], results=results)
+
+
+def calc_angle_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+
+    distopia.calc_angles_triclinic(coords1, coords2, coords3, box, results=results)
+
+
+def calc_dihedral(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_no_box(coords1, coords2, coords3, coords4, results=results)
+
+def calc_dihedral_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_ortho(coords1, coords2, coords3, coords4, box[:3], results=results)
+
+def calc_dihedral_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_triclinic(coords1, coords2, coords3, coords4, box, results=results)
+
+def calc_distance_array(
+    coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_no_box(coords1, coords2, results=results)
+
+
+def calc_distance_array_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_ortho(coords1, coords2, box[:3], results=results)
+
+def calc_distance_array_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_triclinic(coords1, coords2, box, results=results)
+
+def calc_self_distance_array(
+    coords: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_no_box(coords, results=results)
+
+def calc_self_distance_array_ortho(
+    coords: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_ortho(coords, box[:3], results=results)
+
+def calc_self_distance_array_triclinic(
+    coords: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_triclinic(coords, box, results=results)
+