Refactor into modular molecular workloads

tests/test_similarity_search.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from rdkit import Chem, DataStructs
+
+from scimesh.chemistry.dataset import DatasetStats, find_molecule_by_id, iter_valid_molecules
+from scimesh.chemistry.fingerprints import fingerprint
+from scimesh.workloads.similarity_search import SimilarityMatch, search_similar
+
+
+def test_search_matches_full_sorting_and_skips_query_and_invalid(
+    small_dataset: Path,
+) -> None:
+    query = find_molecule_by_id(small_dataset, "QUERY")
+    result = search_similar(small_dataset, query, top_k=2)
+
+    query_smiles = Chem.MolToSmiles(query.molecule, canonical=True)
+    expected = []
+    for record in iter_valid_molecules(small_dataset, DatasetStats()):
+        if record.molecule_id == query.molecule_id:
+            continue
+        if Chem.MolToSmiles(record.molecule, canonical=True) == query_smiles:
+            continue
+        expected.append(
+            SimilarityMatch(
+                DataStructs.TanimotoSimilarity(
+                    fingerprint(query.molecule), fingerprint(record.molecule)
+                ),
+                record.molecule_id,
+                record.smiles,
+            )
+        )
+
+    assert result.matches == sorted(expected, key=SimilarityMatch.sort_key)[:2]
+    assert "QUERY" not in {match.molecule_id for match in result.matches}
+    assert "DUPLICATE" not in {match.molecule_id for match in result.matches}
+    assert result.stats.invalid == 1
+    assert result.stats.valid == 5