Merge branch 'develop' into fix/replace-numpy-asserts

Author: Dreamstick9

.github/workflows/deploy.yaml

@@ -38,7 +38,6 @@ jobs:
       matrix:
         buildplat:
           - [ubuntu-22.04, manylinux_x86_64, x86_64]
-          - [macos-13, macosx_*, x86_64]
           - [windows-2022, win_amd64, AMD64]
           - [macos-14, macosx_*, arm64]
         python: ["cp311", "cp312", "cp313", "cp314"]

.github/workflows/gh-ci-cron.yaml

@@ -140,7 +140,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-13]
+        os: [ubuntu-22.04, macos-14]
 
     steps:
     - uses: actions/checkout@v4

package/CHANGELOG

@@ -15,11 +15,15 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
-         spyke7, talagayev, tanii1125
+         spyke7, talagayev, tanii1125, BradyAJohnston
 
  * 2.11.0
 
 Fixes
+ * HydrogenBondAnalysis: Fixed `count_by_time()` when using `run(FrameIterator)` that
+   results in `self.start` and `self.end` being None (Issue #5200, PR #5202)
+ * NoJump shows a more informative message and fails  when applied
+   outside of the first frame (Issue #4915, PR #5201)
  * DSSP now explicitly checks for a minimum of 6 residues and raises a clear
    error message, unlike the previous behavior where it would fail with an
    incomprehensible broadcasting error at execution time (Issue #5046, PR #5163)

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -911,17 +911,13 @@ def count_by_time(self):
              Can be used along with :attr:`HydrogenBondAnalysis.times` to plot
              the number of hydrogen bonds over time.
         """
+        hbond_frames = self.results.hbonds[:, 0].astype(int)
+        frame_unique, frame_counts = np.unique(hbond_frames, return_counts=True)
+        frame_min, frame_max = self.frames.min(), self.frames.max()
 
-        indices, tmp_counts = np.unique(self.results.hbonds[:, 0], axis=0,
-                                        return_counts=True)
-
-        indices -= self.start
-        indices /= self.step
-
-        counts = np.zeros_like(self.frames)
-        counts[indices.astype(np.intp)] = tmp_counts
-
-        return counts
+        counts = np.zeros(frame_max - frame_min + 1, dtype=int)
+        counts[frame_unique - frame_min] = frame_counts
+        return counts[self.frames - frame_min]
 
     def count_by_type(self):
         """Counts the total number of each unique type of hydrogen bond.

package/MDAnalysis/analysis/msd.py

@@ -70,7 +70,34 @@
    
    In MDAnalysis you can use the 
    :class:`~MDAnalysis.transformations.nojump.NoJump`
-   transformation. 
+   transformation to unwrap coordinates on-the-fly.
+    
+   A minimal example:
+
+   .. code-block:: python
+      
+      import MDAnalysis as mda
+      from MDAnalysis.transformations import NoJump
+      
+      u = mda.Universe(TOP, TRAJ)
+      
+      # Apply NoJump transformation to unwrap coordinates
+      u.trajectory.add_transformations(NoJump(u))
+       
+      # Now the trajectory is unwrapped and MSD can be computed normally:
+      from MDAnalysis.analysis.msd import EinsteinMSD
+      MSD = EinsteinMSD(u, select="all", msd_type="xyz")
+      MSD.run()
+
+   This example assumes that the trajectory contains periodic box
+   dimensions. If no periodic boundary information is present, box
+   dimensions must be defined before applying ``NoJump``, which can
+   be accomplished by applying the
+   :class:`~MDAnalysis.transformations.boxdimensions.set_dimensions`
+   transformation *before* the 
+   :class:`~MDAnalysis.transformations.nojump.NoJump` transformation.
+   
+   This replaces the need to preprocess trajectories externally.
    
    In GROMACS, for example, this can be done using `gmx trjconv`_ with the
    ``-pbc nojump`` flag.

package/MDAnalysis/transformations/nojump.py

@@ -118,6 +118,13 @@ def _transform(self, ts):
         except np.linalg.LinAlgError:
             msg = f"Periodic box dimensions are not invertible at step {ts.frame}"
             raise NoDataError(msg)
+
+        if self.prev is None and ts.frame != 0:
+            raise ValueError(
+                "NoJump transformation must be applied starting from frame 0. "
+                f"Currently at frame {ts.frame}. Please reset trajectory to frame 0 before adding this transformation."
+            )
+
         if ts.frame == 0:
             # We don't need to apply the transformation here. However, we need to
             # ensure we have the 0th frame coordinates in reduced form. We also need to

testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py

@@ -760,3 +760,23 @@ def test_hbond_analysis(self, universe, client_HydrogenBondAnalysis):
         assert h.hydrogens_sel == ""
         assert h.acceptors_sel == ""
         assert h.results.hbonds.size == 0
+
+
+class TestHydrogenBondAnalysisFrameIterator:
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def universe():
+        return MDAnalysis.Universe(waterPSF, waterDCD)
+
+    def test_frame_iterator(self, universe):
+        frames = np.array([0, 1, 2, 5, 6, 7, 8])
+        hbonds = HydrogenBondAnalysis(
+            universe=universe,
+            hydrogens_sel="name H1 H2",
+            acceptors_sel="name OH2",
+            update_selections=False,
+        )
+        hbonds.run(frames=frames)
+        assert np.array_equal(
+            hbonds.count_by_time(), np.array([2, 1, 4, 3, 3, 2, 2])
+        )

testsuite/MDAnalysisTests/transformations/test_nojump.py

@@ -379,3 +379,18 @@ def test_notinvertible(nojump_universe):
         ]
         u.trajectory.add_transformations(*workflow)
         transformed_coordinates = u.trajectory.timeseries()[0]
+
+
+@pytest.mark.parametrize("frame_index", [-1, 5])
+def test_nojump_fails_when_not_at_frame_0(frame_index):
+    """
+    Test that NoJump raises a clear error when applied to a trajectory
+    that is not at frame 0.
+    """
+    u = mda.Universe(data.PSF_TRICLINIC, data.DCD_TRICLINIC)
+    u.trajectory[frame_index]
+
+    with pytest.raises(
+        ValueError, match="must be applied starting from frame 0"
+    ):
+        u.trajectory.add_transformations(NoJump())