Fix coordinator worker integration

tests/test_similarity_graph.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from pathlib import Path
 
+import pytest
 from rdkit import DataStructs
 
 from scimesh.chemistry.dataset import DatasetStats, iter_valid_molecules
@@ -61,3 +62,19 @@ def test_graph_supports_less_than_threshold_direction(small_dataset: Path) -> No
     )
 
     assert all(edge.similarity <= 0.15 for edge in result.edges)
+
+
+def test_graph_rejects_duplicate_identifiers(tmp_path: Path) -> None:
+    dataset = tmp_path / "duplicate_ids.tsv"
+    dataset.write_text(
+        "chembl_id\tcanonical_smiles\nDUP\tCCO\nDUP\tCCC\n", encoding="utf-8"
+    )
+
+    with pytest.raises(ValueError, match="duplicate chembl_id"):
+        build_similarity_graph(dataset, threshold=0.1, block_size=1)
+
+
+def test_graph_writer_creates_missing_output_directory(tmp_path: Path) -> None:
+    output = tmp_path / "nested" / "edges.csv"
+    write_graph_edges(output, [])
+    assert output.read_text(encoding="utf-8").startswith("source_id,target_id")