Merge remote-tracking branch 'upstream/develop' into develop

.github/workflows/gh-ci.yaml

@@ -85,6 +85,8 @@ jobs:
       with:
         micromamba: true
         full-deps: ${{ matrix.full-deps }}
+        # disable GSD because it occasionally introduce hanging in testing #4209
+        gsd: ''
         # in most cases will just default to empty, i.e. pick up max version from other deps
         numpy: ${{ matrix.numpy }}
         extra-pip-deps: ${{ matrix.extra-pip-deps }}
@@ -113,7 +115,7 @@ jobs:
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
         fi
         echo $PYTEST_FLAGS
-        pytest -n auto --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n logical --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS
 
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
@@ -161,6 +163,7 @@ jobs:
       with:
         micromamba: true
         full-deps: true
+        gsd: ''
         extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils"
         extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0"
 
@@ -281,4 +284,4 @@ jobs:
 
     - name: run tests
       working-directory: ./dist
-      run: python -m pytest --timeout=200 -n auto --pyargs MDAnalysisTests
+      run: python -m pytest --timeout=200 -n logical --pyargs MDAnalysisTests

azure-pipelines.yml

@@ -105,7 +105,6 @@ jobs:
       biopython
       "chemfiles>=0.10,<0.10.4"
       duecredit
-      "gsd>3.0.0"
       joblib
       GridDataFormats
       mmtf-python
@@ -114,6 +113,8 @@ jobs:
       pytng>=0.2.3
       rdkit>=2020.03.1
       tidynamics>=1.0.0
+    # remove from azure to avoid test hanging #4707
+    # "gsd>3.0.0"
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - script: >-
@@ -128,7 +129,7 @@ jobs:
     displayName: 'Check installed packages'
   - powershell: |
       cd testsuite
-      pytest MDAnalysisTests --disable-pytest-warnings -n auto --timeout=200 -rsx --cov=MDAnalysis
+      pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis
     displayName: 'Run MDAnalysis Test Suite'
   - script: |
       curl -s https://codecov.io/bash | bash

package/CHANGELOG

@@ -58,6 +58,7 @@ Enhancements
    (Issue #4158, PR #4304)
  * Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
  * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
+ * enables parallelization for analysis.bat.BAT (Issue #4663)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`

package/MDAnalysis/analysis/bat.py

@@ -164,7 +164,7 @@ class to calculate dihedral angles for a given set of atoms or residues
 import copy
 
 import MDAnalysis as mda
-from .base import AnalysisBase
+from .base import AnalysisBase, ResultsGroup
 
 from MDAnalysis.lib.distances import calc_bonds, calc_angles, calc_dihedrals
 from MDAnalysis.lib.mdamath import make_whole
@@ -253,10 +253,28 @@ class BAT(AnalysisBase):
     Bond-Angle-Torsions (BAT) internal coordinates will be computed for
     the group of atoms and all frame in the trajectory belonging to `ag`.
 
+    .. versionchanged:: 2.8.0
+       Enabled **parallel execution** with the ``multiprocessing`` and ``dask`` 
+       backends; use the new method :meth:`get_supported_backends` to see all 
+       supported backends.
+
     """
-    @due.dcite(Doi("10.1002/jcc.26036"),
-               description="Bond-Angle-Torsions Coordinate Transformation",
-               path="MDAnalysis.analysis.bat.BAT")
+    _analysis_algorithm_is_parallelizable = True
+
+    @classmethod
+    def get_supported_backends(cls):
+        return (
+            "serial",
+            "multiprocessing",
+            "dask",
+        )
+
+    @due.dcite(
+       Doi("10.1002/jcc.26036"),
+       description="Bond-Angle-Torsions Coordinate Transformation",
+       path="MDAnalysis.analysis.bat.BAT",
+    )
+
     def __init__(self, ag, initial_atom=None, filename=None, **kwargs):
         r"""Parameters
         ----------
@@ -558,3 +576,6 @@ def Cartesian(self, bat_frame):
     def atoms(self):
         """The atomgroup for which BAT are computed (read-only property)"""
         return self._ag
+
+    def _get_aggregator(self):
+        return ResultsGroup(lookup={'bat': ResultsGroup.ndarray_vstack})

testsuite/MDAnalysisTests/analysis/conftest.py

@@ -7,6 +7,7 @@
     OldAPIAnalysis,
 )
 from MDAnalysis.analysis.rms import RMSD, RMSF
+from MDAnalysis.analysis.bat import BAT
 from MDAnalysis.lib.util import is_installed
 from MDAnalysis.analysis.gnm import GNMAnalysis
 
@@ -93,3 +94,8 @@ def client_RMSF(request):
 @pytest.fixture(scope='module', params=params_for_cls(GNMAnalysis))
 def client_GNMAnalysis(request):
     return request.param
+
+
+@pytest.fixture(scope='module', params=params_for_cls(BAT))
+def client_BAT(request):
+  return request.param

testsuite/MDAnalysisTests/analysis/test_bat.py

@@ -41,16 +41,16 @@ def selected_residues(self):
         return ag
 
     @pytest.fixture()
-    def bat(self, selected_residues):
+    def bat(self, selected_residues, client_BAT):
         R = BAT(selected_residues)
-        R.run()
+        R.run(**client_BAT)
         return R.results.bat
 
     @pytest.fixture
-    def bat_npz(self, tmpdir, selected_residues):
+    def bat_npz(self, tmpdir, selected_residues, client_BAT):
         filename = str(tmpdir / 'test_bat_IO.npy')
         R = BAT(selected_residues)
-        R.run()
+        R.run(**client_BAT)
         R.save(filename)
         return filename
 
@@ -73,8 +73,8 @@ def test_bat_coordinates(self, bat):
             atol=1.5e-5,
             err_msg="error: BAT coordinates should match test values")
 
-    def test_bat_coordinates_single_frame(self, selected_residues):
-        bat = BAT(selected_residues).run(start=1, stop=2).results.bat
+    def test_bat_coordinates_single_frame(self, selected_residues, client_BAT):
+        bat = BAT(selected_residues).run(start=1, stop=2, **client_BAT).results.bat
         test_bat = [np.load(BATArray)[1]]
         assert_allclose(
             bat,