adding tests for explicit network plannings

src/konnektor/network_planners/generators/explicit_network_generator.py

@@ -87,7 +87,7 @@ def generate_network_from_indices(
 
         Parameters
         ----------
-        components : list of SmallMoleculeComponent
+        components : list of Components
           the small molecules to place into the network
         mapper: AtomMapper
           the atom mapper to use to construct edges
@@ -119,15 +119,15 @@ def generate_network_from_indices(
 
     def generate_network_from_names(
         self,
-        ligands: list[Component],
+        components: list[Component],
         names: list[tuple[str, str]],
     ) -> LigandNetwork:
         """
         Generate a :class:`.LigandNetwork` by specifying edges as tuples of names.
 
         Parameters
         ----------
-        ligands : list of SmallMoleculeComponent
+        components : list of Components
           the small molecules to place into the network
         mapper: AtomMapper
           the atom mapper to use to construct edges
@@ -148,10 +148,10 @@ def generate_network_from_names(
           if multiple molecules have the same name (this would otherwise be
           problematic)
         """
-        nm2comp = {l.name: l for l in enumerate(ligands)}
+        nm2comp = {l.name: l for l in components}
 
-        if len(nm2comp) < len(ligands):
-            dupes = Counter((l.name for l in ligands))
+        if len(nm2comp) < len(components):
+            dupes = Counter((l.name for l in components))
             dupe_names = [k for k, v in dupes.items() if v > 1]
             raise ValueError(f"Duplicate names: {dupe_names}")
 
@@ -165,7 +165,7 @@ def generate_network_from_names(
                     for nm in itertools.chain.from_iterable(names)
                     if nm not in nm2comp
                 ]
-                available = [ligand.name for ligand in ligands]
+                available = [ligand.name for ligand in components]
                 raise KeyError(
                     f"Invalid name(s) requested {badnames}.  " f"Available: {available}"
                 )

src/konnektor/tests/network_planners/generators/test_explicit_network_planner.py

@@ -26,3 +26,39 @@ def test_explicit_network_planner():
     assert len(ligand_network.nodes) == n_compounds
     assert len(ligand_network.edges) == (n_compounds * (n_compounds - 1)) // 2
     assert get_is_connected(ligand_network)
+
+
+def test_explicit_network_planner_with_indices():
+    n_compounds = 20
+    components, genMapper, genScorer = build_random_dataset(n_compounds=n_compounds)
+    indices = [(1, 2), (2, 3), (3, 4), (2, 5), (2, 6)]
+    unique_indices = set([i for e in indices for i in e])
+    planner = ExplicitNetworkGenerator(genMapper, genScorer, n_processes=1)
+
+    ligand_network = planner.generate_network_from_indices(
+        components=components, indices=indices
+    )
+
+    assert isinstance(ligand_network, LigandNetwork)
+    assert len(ligand_network.nodes) == len(unique_indices)
+    assert len(ligand_network.edges) == len(indices)
+    assert get_is_connected(ligand_network)
+
+
+def test_explicit_network_planner_with_names():
+    n_compounds = 20
+    components, genMapper, genScorer = build_random_dataset(n_compounds=n_compounds)
+    print(components[0].name)
+    names = [("0", "1"), ("1", "2"), ("2", "3"), ("1", "5"), ("1", "6")]
+    unique_names = set([i for e in names for i in e])
+
+    planner = ExplicitNetworkGenerator(genMapper, genScorer, n_processes=1)
+
+    ligand_network = planner.generate_network_from_names(
+        components=components, names=names
+    )
+
+    assert isinstance(ligand_network, LigandNetwork)
+    assert len(ligand_network.nodes) == len(unique_names)
+    assert len(ligand_network.edges) == len(names)
+    assert get_is_connected(ligand_network)