Merge branch 'develop' into fix-msd-nojump-doc

Author: orbeckst

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,13 +8,18 @@ Changes made in this Pull Request:
 <!-- Describe the changes that this PR makes. If applicable, use the following bullet list. --> 
 -
 
+## LLM / AI generated code disclosure
+<!-- Please update this disclosure to reflect if you did or did not use LLMs / AI to generate code -->
+LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
+
 ## PR Checklist
 <!-- Please use the following checklist to ensure the PR is ready to be reviewed/merged. -->
  - [ ] Issue raised/referenced?
  - [ ] Tests updated/added?
  - [ ] Documentation updated/added?
  - [ ] `package/CHANGELOG` file updated?
  - [ ] Is your name in `package/AUTHORS`? (If it is not, add it!)
+ - [ ] LLM/AI disclosure was updated.
 
 ## Developers Certificate of Origin
 <!-- 

.github/workflows/linters.yaml

@@ -93,7 +93,6 @@ jobs:
           micromamba: true
           full-deps: true
           numpy: numpy=1.26.0
-          rdkit: rdkit=2023.09.3
 
       - name: install
         run: |

azure-pipelines.yml

@@ -25,24 +25,24 @@ jobs:
           PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'normal'
-          imageName: 'windows-2019'
+          imageName: 'windows-latest'
         Win-Python313-64bit-full:
           PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'normal'
-          imageName: 'windows-2019'
+          imageName: 'windows-latest'
         Win-Python313-64bit-full-wheel:
           PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
           NUMPY_MIN: '2.1.0'
-          imageName: 'windows-2019'
+          imageName: 'windows-latest'
         Win-Python311-64bit-full-wheel:
           PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
           NUMPY_MIN: '1.26.0'
-          imageName: 'windows-2019'
+          imageName: 'windows-latest'
         Linux-Python313-64bit-full-wheel:
           PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'

package/AUTHORS

@@ -265,7 +265,7 @@ Chronological list of authors
   - Raúl Lois-Cuns  
   - Pranay Pelapkar
   - Shreejan Dolai
-  - Tanisha Dubey 
+  - Tanisha Dubey
 
 External code
 -------------

package/CHANGELOG

@@ -15,11 +15,14 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
-         spyke7, talagayev
+         spyke7, talagayev, tanii1125
 
  * 2.11.0
 
 Fixes
+ * 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)
  * Fixes the verbose=False in EinsteinMSD, and only shows progress bar when
    verbose=True (Issue #5144, PR #5153)
  * Fix incorrect assignment of topology_format to format (and vice versa)

package/MDAnalysis/analysis/dssp/dssp.py

@@ -210,7 +210,7 @@ class DSSP(AnalysisBase):
     Parameters
     ----------
     atoms : Union[Universe, AtomGroup]
-        input Universe or AtomGroup. In both cases, only protein residues will
+        input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will
         be chosen prior to the analysis via `select_atoms('protein')`.
         Heavy atoms of the protein are then selected by name
         `heavyatom_names`, and hydrogens are selected by name
@@ -239,6 +239,8 @@ class DSSP(AnalysisBase):
 
     Raises
     ------
+    ValueError
+        If fewer than 6 residues are provided in the selection.
     ValueError
         if ``guess_hydrogens`` is True but some non-PRO hydrogens are missing.
 
@@ -357,6 +359,12 @@ def __init__(
                 )
             )
 
+        if len(ag.residues) < 6:
+            raise ValueError(
+                "DSSP requires at least 6 residues for secondary structure analysis, "
+                f"but only {len(ag.residues)} residue(s) were provided in the selection."
+            )
+
     def _prepare(self):
         self.results.dssp_ndarray = []
 

package/MDAnalysis/analysis/msd.py

@@ -406,14 +406,11 @@ def _parse_msd_type(self):
             "xyz": [0, 1, 2],
         }
 
-        self.msd_type = self.msd_type.lower()
-
         try:
-            self._dim = keys[self.msd_type]
-        except KeyError:
+            self._dim = keys[self.msd_type.lower()]
+        except (AttributeError, KeyError):
             raise ValueError(
-                "invalid msd_type: {} specified, please specify one of xyz, "
-                "xy, xz, yz, x, y, z".format(self.msd_type)
+                f"Invalid msd_type {self.msd_type}, must be a string and one of: xyz, xy, xz, yz, x, y, z"
             )
 
         self.dim_fac = len(self._dim)

package/MDAnalysis/lib/util.py

@@ -202,7 +202,7 @@
 import errno
 import functools
 import gzip
-import importlib
+import importlib.util
 import inspect
 import io
 import itertools

testsuite/MDAnalysisTests/analysis/test_dssp.py

@@ -89,3 +89,23 @@ def test_exception_raises_with_atom_index(pdb_filename, client_DSSP):
         match="Residue <Residue SER, 298> contains*",
     ):
         DSSP(u, guess_hydrogens=False).run(**client_DSSP)
+
+
+def test_insufficient_residues_raises_error(client_DSSP):
+    """Test that DSSP raises clear error for insufficient residues."""
+    u = mda.Universe(TPR, XTC)
+
+    protein = u.select_atoms("protein")
+
+    with pytest.raises(ValueError, match="DSSP requires at least 6 residues"):
+        res2 = protein.residues[:2].atoms
+        DSSP(res2)
+
+    with pytest.raises(ValueError, match="DSSP requires at least 6 residues"):
+        res4 = protein.residues[:4].atoms
+        DSSP(res4)
+
+    res6 = protein.residues[:6].atoms
+    dssp = DSSP(res6)
+    result = dssp.run(**client_DSSP, stop=1)
+    assert result.results.dssp.shape[1] == 6

testsuite/MDAnalysisTests/analysis/test_msd.py

@@ -117,9 +117,11 @@ def test_updating_ag_rejected(self, u):
         with pytest.raises(TypeError, match=errmsg):
             m = MSD(updating_ag, msd_type="xyz", fft=False)
 
-    @pytest.mark.parametrize("msdtype", ["foo", "bar", "yx", "zyx"])
+    @pytest.mark.parametrize(
+        "msdtype", ["foo", "bar", "yx", "zyx", 123, "", " xy "]
+    )
     def test_msdtype_error(self, u, SELECTION, msdtype):
-        errmsg = f"invalid msd_type: {msdtype}"
+        errmsg = f"Invalid msd_type {msdtype}, must be a string and one of: xyz, xy, xz, yz, x, y, z"
         with pytest.raises(ValueError, match=errmsg):
             m = MSD(u, SELECTION, msd_type=msdtype)