Merge branch 'develop' into fix-filelocktest-5382

Author: orbeckst

.github/CONTRIBUTING.md

@@ -2,17 +2,17 @@
 
 Thanks for contributing to MDAnalysis!
 
-All members of the MDAnalysis community adhere to our [Code of Conduct](https://www.mdanalysis.org/pages/conduct/). By contributing code and interacting with us on GitHub, the forums, or by any other means you consent to follow the Code of Conduct.
+All members of the MDAnalysis community adhere to our [Code of Conduct](https://github.com/MDAnalysis/mdanalysis/?tab=coc-ov-file). By contributing code and interacting with us on GitHub, the forums, or by any other means you consent to follow the Code of Conduct.
 
 #### Reporting issues
 
 If you've found a defect with MDAnalysis we'd love to know so we can fix it.  Please follow the Issue template so we can quickly diagnose the problem, in particular the piece of code that causes the problem.
 
-If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion forum](https://groups.google.com/forum/#!forum/mdnalysis-discussion).
+If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by in [discord #users or GitHub discussions](https://www.mdanalysis.org/community/#ask-questions--get-help).
 
 #### Contributing code
 
-If you're contributing code, please check out [How to contribute](https://www.mdanalysis.org/UserGuide/contributing.html) in the User Guide and look at the [Style guide](https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide).
+We welcome your code contributions! Please check out the [Contributing](https://www.mdanalysis.org/contribute/) section on our web page for how you can contribute to the whole MDAnalysis project and in particular the [User Guide's section on Contributing](https://userguide.mdanalysis.org/stable/contributing_code.html) for the MDAnalysis package in particular. Please also familiarize yourself with the current version of our [AI Policy](https://github.com/MDAnalysis/mdanalysis/blob/develop/AI_POLICY.md)
 
-MDAnalysis devs are most easily reached through the [development list](https://groups.google.com/forum/#!forum/mdnalysis-devel).
+MDAnalysis devs are most easily reached in the [discord #developers channel](https://www.mdanalysis.org/community/#ask-questions--get-help).
 

.github/workflows/linters.yaml

@@ -36,13 +36,13 @@ jobs:
 
     - uses: psf/black@stable
       with:
-        options: "--check --verbose"
+        options: "--check"
         src: "./package"
         version: "~= 24.0"
-    
+
     - uses: psf/black@stable
       with:
-        options: "--check --verbose"
+        options: "--check"
         src: "./testsuite"
         version: "~= 24.0"
 

package/CHANGELOG

@@ -17,12 +17,14 @@ The rules for this file:
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
-         ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01
+         ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
+         raulloiscuns
 
  * 2.11.0
 
 Fixes
  * Fix FileLock tests for XTC and TRR: lock file is no longer removed (#5382)
+ * InterRDF now correctly returns bins in parallel (PR #5344)
  * `Merge()` no longer raises a TypeError on Universes that have a `cmaps`
    attribute; cmaps are now combined like the other connection attributes
    (bonds, angles, dihedrals, impropers) (Issue #3672).

package/MDAnalysis/analysis/rdf.py

@@ -369,7 +369,7 @@ def _get_aggregator(self):
             lookup={
                 "count": ResultsGroup.ndarray_sum,
                 "volume_cum": ResultsGroup.ndarray_sum,
-                "bins": ResultsGroup.ndarray_sum,
+                "bins": ResultsGroup.ndarray_mean,
                 "edges": ResultsGroup.ndarray_mean,
             }
         )

testsuite/MDAnalysisTests/analysis/test_rdf.py

@@ -28,8 +28,11 @@
 
 from MDAnalysisTests.datafiles import two_water_gro
 
+import numpy as np
 from numpy.testing import assert_allclose
 
+NFRAMES = 5
+
 
 @pytest.fixture()
 def u():
@@ -44,6 +47,10 @@ def sels(u):
     # (NOTE: requires in-memory coordinates to make them permanent)
     for at, (x, y) in zip(u.atoms, zip([1] * 3 + [2] * 3, [2, 1, 3] * 2)):
         at.position = x, y, 0.0
+    # Create a fake trajectory with the same frame for testing parallel backends
+    trajectory_data = np.tile(u.atoms.positions, (NFRAMES, 1, 1))
+    dimensions_data = np.tile(u.dimensions, (NFRAMES, 1))
+    u.load_new(trajectory_data, format="MEMORY", dimensions=dimensions_data)
     s1 = u.select_atoms("name OW")
     s2 = u.select_atoms("name HW1 HW2")
     return s1, s2
@@ -72,29 +79,31 @@ def test_count_sum(sels, client_InterRDF):
     # should see 8 comparisons in count
     s1, s2 = sels
     rdf = InterRDF(s1, s2).run(**client_InterRDF)
-    assert rdf.results.count.sum() == 8
+    assert rdf.results.count.sum() == 8 * NFRAMES
 
 
 def test_count(sels, client_InterRDF):
     # should see two distances with 4 counts each
     s1, s2 = sels
     rdf = InterRDF(s1, s2).run(**client_InterRDF)
-    assert len(rdf.results.count[rdf.results.count == 4]) == 2
+    assert len(rdf.results.count[rdf.results.count == 4 * NFRAMES]) == 2
 
 
-def test_double_run(sels, client_InterRDF):
+def test_double_run(sels):
     # running rdf twice should give the same result
+    # Note: this only make sense for serial backend as results aggregator can not handle
+    # rdf flag if rdf.results object is not restarted when parallel backend is used
     s1, s2 = sels
-    rdf = InterRDF(s1, s2).run(**client_InterRDF)
-    rdf.run(**client_InterRDF)
-    assert len(rdf.results.count[rdf.results.count == 4]) == 2
+    rdf = InterRDF(s1, s2).run()
+    rdf.run()
+    assert len(rdf.results.count[rdf.results.count == 4 * NFRAMES]) == 2
 
 
 def test_exclusion(sels, client_InterRDF):
     # should see two distances with 4 counts each
     s1, s2 = sels
     rdf = InterRDF(s1, s2, exclusion_block=(1, 2)).run(**client_InterRDF)
-    assert rdf.results.count.sum() == 4
+    assert rdf.results.count.sum() == 4 * NFRAMES
 
 
 @pytest.mark.parametrize(
@@ -105,7 +114,7 @@ def test_ignore_same_residues(sels, attr, count, client_InterRDF):
     s1, s2 = sels
     rdf = InterRDF(s2, s2, exclude_same=attr).run(**client_InterRDF)
     assert rdf.rdf[0] == 0
-    assert rdf.results.count.sum() == count
+    assert rdf.results.count.sum() == count * NFRAMES
 
 
 def test_ignore_same_residues_fails(sels, client_InterRDF):
@@ -158,7 +167,7 @@ def test_unknown_norm(sels):
 
 
 @pytest.mark.parametrize("backend", distopia_conditional_backend())
-def test_norm(sels, backend):
+def test_backend(sels, backend):
     s1, s2 = sels
     rdf = InterRDF(s1, s2, norm="none", backend=backend).run()
     assert_allclose(max(rdf.results.rdf), 4)