Fix failing unit tests for DihedralAnalysis._get_dihedrals by:

- Instantiating a DihedralAnalysis object before calling `_get_dihedrals`
- Correcting test expectations to match actual behavior:
  - united_atom level now asserts returned `.atoms` values
  - residue level tests now validate atom-group construction
  - residue tests with < 4 residues now expect empty list

Author: harryswift01

tests/test_CodeEntropy/test_dihedral_tools.py

@@ -11,57 +11,78 @@ class TestDihedralAnalysis(BaseTestCase):
 
     def setUp(self):
         super().setUp()
+        self.analysis = DihedralAnalysis()
 
     def test_get_dihedrals_united_atom(self):
         """
-        Test `get_dihedrals` for 'united_atom' level.
-        Ensures it returns the dihedrals directly from the data container.
+        Test `_get_dihedrals` for 'united_atom' level.
+
+        The function should:
+        - read dihedrals from `data_container.dihedrals`
+        - extract `.atoms` from each dihedral
+        - return a list of atom groups
+
+        Expected behavior:
+        If dihedrals = [d1, d2, d3] and each dihedral has an `.atoms`
+        attribute, then the returned list must be:
+            [d1.atoms, d2.atoms, d3.atoms]
         """
         data_container = MagicMock()
-        mock_dihedrals = ["d1", "d2", "d3"]
-        data_container.dihedrals = mock_dihedrals
 
-        result = DihedralAnalysis._get_dihedrals(data_container, level="united_atom")
-        self.assertEqual(result, mock_dihedrals)
+        # Mock dihedral objects with `.atoms`
+        d1 = MagicMock()
+        d1.atoms = "atoms1"
+        d2 = MagicMock()
+        d2.atoms = "atoms2"
+        d3 = MagicMock()
+        d3.atoms = "atoms3"
+
+        data_container.dihedrals = [d1, d2, d3]
+
+        result = self.analysis._get_dihedrals(data_container, level="united_atom")
+
+        self.assertEqual(result, ["atoms1", "atoms2", "atoms3"])
 
     def test_get_dihedrals_residue(self):
         """
-        Test `get_dihedrals` for 'residue' level with 5 residues.
-        Mocks bonded atom selections and verifies that dihedrals are constructed.
+        Test `_get_dihedrals` for 'residue' level with 5 residues.
+
+        The implementation:
+        - iterates over residues 4 → N
+        - for each, selects 4 bonded atom groups
+        - merges them using __add__ to form a single atom_group
+        - appends to result list
+
+        For 5 residues (0–4), two dihedral groups should be created.
+        Expected:
+        - result of length 2
+        - each item equal to the merged mock atom group
         """
         data_container = MagicMock()
-        data_container.residues = [0, 1, 2, 3, 4]  # 5 residues
+        data_container.residues = [0, 1, 2, 3, 4]
 
-        # Mock select_atoms to return atom groups with .dihedral
-        mock_dihedral = MagicMock()
         mock_atom_group = MagicMock()
         mock_atom_group.__add__.return_value = mock_atom_group
-        mock_atom_group.dihedral = mock_dihedral
+
+        # Every MDAnalysis selection returns the same mock atom group
         data_container.select_atoms.return_value = mock_atom_group
 
-        result = DihedralAnalysis._get_dihedrals(data_container, level="residue")
+        result = self.analysis._get_dihedrals(data_container, level="residue")
 
-        # Should create 2 dihedrals for 5 residues (residues 0–3 and 1–4)
         self.assertEqual(len(result), 2)
-        self.assertTrue(all(d == mock_dihedral for d in result))
+        self.assertTrue(all(r is mock_atom_group for r in result))
 
     def test_get_dihedrals_no_residue(self):
         """
-        Test `get_dihedrals` for 'residue' level with 3 residues.
-        Mocks bonded atom selections and verifies that dihedrals are constructed.
-        """
+        Test `_get_dihedrals` for 'residue' level when fewer than
+        4 residues exist (here: 3 residues).
 
+        Expected:
+        - The function returns an empty list.
+        """
         data_container = MagicMock()
-        data_container.residues = [0, 1, 2]  # 3 residues
-
-        # Mock select_atoms to return atom groups with .dihedral
-        mock_dihedral = MagicMock()
-        mock_atom_group = MagicMock()
-        mock_atom_group.__add__.return_value = mock_atom_group
-        mock_atom_group.dihedral = mock_dihedral
-        data_container.select_atoms.return_value = mock_atom_group
+        data_container.residues = [0, 1, 2]  # Only 3 residues → too few
 
-        result = DihedralAnalysis._get_dihedrals(data_container, level="residue")
+        result = self.analysis._get_dihedrals(data_container, level="residue")
 
-        # Should result in no residue dihedrals
         self.assertEqual(result, [])