distopia 0.4.0 compatibility changes (#4734)

* start of docs

* improve distopia stup

* add backend conditionals

* fix wrong backend

* shims

* working except for dihedrals

* move to 0.3.0

* bump ci

* bump ci

* Update package/MDAnalysis/lib/distances.py

Co-authored-by: Oliver Beckstein <[email protected]>

* fix versioning

* add version checking

* remove erroneous triclinic note

* remove unnesecary import

* add explanatory notes

* change tests in line with discussion

* changelog

* Apply suggestions from code review

Co-authored-by: Oliver Beckstein <[email protected]>

* add more tests

* improve docs

* improve docs again

* hmmm

* add type for calc_bond_distance_ortho()

* just stuff answers back in if we used a buffer

* add cram for distance array also

* fix changelogs

* black

* imporve mock test

* fix typo

* add debug printing

* add explanatory comment on use of serial backend comparison

* add testing

* black

* fix typo

* fix test

* fix dih

* black

* fix dihedrals

* fix reference values

* change function names for 0.4.0

* black

* fix typo

* fix wrong versions

---------

Co-authored-by: Oliver Beckstein <[email protected]>

.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>=0.4.0'
   h5py:
     default: 'h5py>=2.10'
   hole2:

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
-         marinegor
+         marinegor, hmacdope
 
  * 2.9.0
 
@@ -27,12 +27,14 @@ Fixes
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
+ * Improve distopia backend support in line with new functionality available 
+   in distopia >= 0.3.1 (PR #4734)
  * Addition of 'water' token for water selection (Issue #4839)
  * Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729)
  * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
  * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
  * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
- * Added `precision` for XYZWriter (Issue #4775, PR #4771)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771) 
 
 
 Changes

package/MDAnalysis/lib/_distopia.py

@@ -28,48 +28,51 @@
 as a selectable backend.
 """
 import warnings
+from packaging.version import Version
+
+MIN_DISTOPIA_VERSION = Version("0.4.0")
 
 # 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:
+    # check for compatibility: currently needs to be >=0.4.0,
+    # some versions of `distopia` don't have a version attribute
+    try:
+        distopia_version = Version(distopia.__version__)
+    except AttributeError:
+        distopia_version = Version("0.0.0")
+    if distopia_version < MIN_DISTOPIA_VERSION:
         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.",
+            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,
         )
-        del distopia
         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
+    coords1: np.ndarray,
+    coords2: np.ndarray,
+    box: np.ndarray,
+    results: np.ndarray,
 ) -> None:
-    distopia.calc_bonds_ortho_float(coords1, coords2, box[:3], results=results)
-    # upcast is currently required, change for 3.0, see #3927
+    distopia.distances_ortho(coords1, coords2, box[:3], results=results)
 
 
 def calc_bond_distance(
     coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
 ) -> None:
-    distopia.calc_bonds_no_box_float(coords1, coords2, results=results)
-    # upcast is currently required, change for 3.0, see #3927
+    distopia.distances_no_box(coords1, coords2, results=results)
 
 
 def calc_bond_distance_triclinic(
@@ -78,8 +81,112 @@ def calc_bond_distance_triclinic(
     box: np.ndarray,
     results: np.ndarray,
 ) -> None:
-    # redirect to serial backend
-    warnings.warn(
-        "distopia does not support triclinic boxes, using serial backend instead."
+    distopia.distances_triclinic(coords1, coords2, box, results=results)
+
+
+def calc_angle(
+    coords1: np.ndarray,
+    coords2: np.ndarray,
+    coords3: np.ndarray,
+    results: np.ndarray,
+) -> None:
+    distopia.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.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.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.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.dihedrals_ortho(
+        coords1, coords2, coords3, coords4, box[:3], results=results
     )
-    _calc_bond_distance_triclinic_serial(coords1, coords2, box, 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.dihedrals_triclinic(
+        coords1, coords2, coords3, coords4, box, results=results
+    )
+
+
+def calc_distance_array(
+    coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.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.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.distance_array_triclinic(coords1, coords2, box, results=results)
+
+
+def calc_self_distance_array(coords: np.ndarray, results: np.ndarray) -> None:
+    distopia.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.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.self_distance_array_triclinic(coords, box, results=results)