more testing

Author: skfegan

CodeEntropy/levels/search.py

@@ -44,7 +44,7 @@ def get_RAD_neighbors(self, universe, mol_id):
             if molecule_index_j != mol_id:
                 j_position = universe.atoms.fragments[molecule_index_j].center_of_mass()
                 distances[molecule_index_j] = self.get_distance(
-                    j_position, central_position, universe.dimensions
+                    j_position, central_position, universe.dimensions[:3]
                 )
 
         # Sort distances smallest to largest

tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py

@@ -0,0 +1,33 @@
+from types import SimpleNamespace
+from unittest.mock import MagicMock
+
+from CodeEntropy.levels.nodes.find_neighbors import ComputeNeighborsNode
+
+
+def test_compute_find_neighbors_node_runs_and_writes_shared_data():
+    node = ComputeNeighborsNode()
+
+    node._neighbor_analysis.get_neighbors = MagicMock(return_value=({0: 7.8}))
+
+    node._neighbor_analysis.get_symmetry = MagicMock(return_value=({0: 2}, {0: False}))
+
+    shared = {
+        "reduced_universe": MagicMock(),
+        "levels": {0: ["united_atom"]},
+        "groups": {0: [0]},
+        "start": 0,
+        "end": 10,
+        "step": 1,
+        "args": SimpleNamespace(search_type="RAD"),
+    }
+
+    out = node.run(shared)
+
+    assert "neighbors" in out
+    assert "symmetry_number" in out
+    assert "linear" in out
+    assert shared["neighbors"] == {0: 7.8}
+    assert shared["symmetry_number"] == {0: 2}
+    assert shared["linear"] == {0: False}
+    node._neighbor_analysis.get_neighbors.assert_called_once()
+    node._neighbor_analysis.get_symmetry.assert_called_once()

tests/unit/CodeEntropy/levels/test_neighbors.py

@@ -196,8 +196,12 @@ class HybridizationType:
             def SP():
                 return "SP"
 
-    rdkit_heavy.GetAtoms = MagicMock(return_value=[a1, a2, a3])
-    a1.GetHybridization = MagicMock(return_value="SP2")
+    def _get_atoms():
+        return [a1, a2, a3]
+
+    rdkit_heavy.GetAtoms = MagicMock(side_effect=_get_atoms)
+
+    a1.GetHybridization = MagicMock(return_value="SP3")
     a2.GetHybridization = MagicMock(return_value="SP")
     a3.GetHybridization = MagicMock(return_value="SP3")
 

tests/unit/CodeEntropy/levels/test_search.py

@@ -1,6 +1,12 @@
+from pathlib import Path
+
 import numpy as np
 import pytest
+import yaml
 
+import tests.regression.helpers as Helpers
+from CodeEntropy.config.runtime import CodeEntropyRunner
+from CodeEntropy.levels.mda import UniverseOperations
 from CodeEntropy.levels.search import Search
 
 # some dummy atom positions
@@ -11,6 +17,59 @@
 e = np.array([0, 11, 11])
 dimensions = np.array([10, 10, 10])
 
+DEFAULT_TESTDATA_BASE_URL = "https://www.ccpbiosim.ac.uk/file-store/codeentropy-testing"
+
+
+def test_get_RAD_neighbors(tmp_path: Path):
+    """
+    Args:
+        tmp_path: Pytest provided temporatry directory
+    """
+    args = {}
+    search = Search()
+    system = "methane"
+    repo_root = Path(__file__).resolve().parents[4]
+    config_path = (
+        repo_root / "tests" / "regression" / "configs" / system / "config.yaml"
+    )
+
+    tmp_path.mkdir(parents=True, exist_ok=True)
+
+    raw = yaml.safe_load(config_path.read_text())
+    if not isinstance(raw, dict):
+        raise ValueError(
+            f"Config must parse to a dict. Got {type(raw)} from {config_path}"
+        )
+
+    cooked = Helpers._abspathify_config_paths(raw, base_dir=config_path.parent)
+    required: list[Path] = []
+    run1 = cooked.get("run1")
+    if isinstance(run1, dict):
+        ff = run1.get("force_file")
+        if isinstance(ff, str) and ff:
+            required.append(Path(ff))
+        for p in run1.get("top_traj_file") or []:
+            if isinstance(p, str) and p:
+                required.append(Path(p))
+
+    if required:
+        Helpers.ensure_testdata_for_system(system, required_paths=required)
+
+    runner = CodeEntropyRunner(tmp_path)
+    parser = runner._config_manager.build_parser()
+    args, _ = parser.parse_known_args()
+    args.end = run1.get("end")
+    args.top_traj_file = run1.get("top_traj_file")
+    args.file_format = run1.get("file_format")
+    assert args.end == 1
+
+    universe_operations = UniverseOperations()
+    universe = CodeEntropyRunner._build_universe(args, universe_operations)
+
+    neighbors = search.get_RAD_neighbors(universe=universe, mol_id=0)
+
+    assert neighbors == [151, 3, 75, 219, 229, 488, 460, 118, 230, 326]
+
 
 def test_get_angle():
     search = Search()