Fix AnalysisBase.run misreading numpy boolean frame masks

package/AUTHORS

@@ -281,6 +281,7 @@ Chronological list of authors
   - Amarendra Mohan
   - Shubham Mittal  
   - Charity Grey
+  - barlowa124
   - Sai Udayagiri
   - Apoorva Verma
   - Aryaman Chaudhri

package/CHANGELOG

@@ -18,7 +18,7 @@ The rules for this file:
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
          ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
-         raulloiscuns, Aryaman-Chaudhri, sici17
+         raulloiscuns, Aryaman-Chaudhri, sici17, barlowa124
 
  * 2.11.0
 
@@ -33,6 +33,9 @@ Fixes
    apply their fit via `AtomGroup.rotate()`. Note: this changes existing
    behavior, as velocities/forces were previously left untouched by
    rotation. (Issue #5421, PR #5452)
+ * `AnalysisBase.run()` no longer misinterprets NumPy boolean masks passed
+   via the ``frames`` argument as integer frame indices, which silently
+   selected the wrong frames (Issue #5472, PR #5480).
  * 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`

package/MDAnalysis/analysis/base.py

@@ -616,7 +616,7 @@ def _setup_computation_groups(
         else:
             used_frames = frames
 
-        if all(isinstance(obj, bool) for obj in used_frames):
+        if all(isinstance(obj, (bool, np.bool_)) for obj in used_frames):
             arange = np.arange(len(used_frames))
             used_frames = arange[used_frames]
 

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -337,6 +337,26 @@ def test_start_stop_step(u, run_kwargs, frames):
             },
             (0, 1, 3, 5, 6, 8),
         ),
+        (
+            {
+                "frames": np.array(
+                    [
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                    ],
+                    dtype=bool,
+                )
+            },
+            (0, 1, 3, 5, 6, 8),
+        ),
     ],
 )
 def test_frame_slice(u_xtc, run_kwargs, frames):
@@ -370,6 +390,26 @@ def test_frame_slice(u_xtc, run_kwargs, frames):
             },
             (0, 1, 3, 5, 6, 8),
         ),
+        (
+            {
+                "frames": np.array(
+                    [
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                    ],
+                    dtype=bool,
+                )
+            },
+            (0, 1, 3, 5, 6, 8),
+        ),
     ],
 )
 def test_frame_slice_parallel(run_kwargs, frames, client_FrameAnalysis):