Merge branch 'main' into 2023-sep3-loosen-alg-test-tolerance

CHANGELOG.md

@@ -25,6 +25,7 @@ and the project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.
 
 ### Fixed
 
+- Fix bug where standardizing MolSetGraphs crashed ([#24](https://github.com/microsoft/syntheseus/pull/24)) ([@austint])
 - Change default node depth to infinity ([#16](https://github.com/microsoft/syntheseus/pull/16)) ([@austint])
 - Adapt tutorials to the renaming from PR #9 ([#17](https://github.com/microsoft/syntheseus/pull/17)) ([@jagarridotorres])
 - Pin `pydantic` version to `1.*` ([#10](https://github.com/microsoft/syntheseus/pull/10)) ([@kmaziarz])

syntheseus/search/graph/standardization.py

@@ -106,7 +106,7 @@ def _unique_node_andor_from_molset(
     # Get all mols and reactions
     all_nodes: set[MolSetNode] = set(graph._graph.nodes())
     mols = set(mol for node in all_nodes for mol in node.mols)
-    rxns = set(edge["reaction"] for edge in graph._graph.edges())
+    rxns = set(graph._graph.edges[n1, n2]["reaction"] for n1, n2 in graph._graph.edges())
 
     # Make initial nodes
     mol_to_node = {mol: OrNode(mol) for mol in mols}

syntheseus/tests/search/graph/test_standardization.py

@@ -1 +1,23 @@
-"""Graph standardization is not tested at this time, but should be tested in the future."""
+"""
+At the moment, only a smoke-test is done for graph standardization,
+but the exact behaviour is not well-tested.
+These tests should be added in the future.
+"""
+
+import pytest
+
+from syntheseus.search.graph.and_or import AndOrGraph
+from syntheseus.search.graph.molset import MolSetGraph
+from syntheseus.search.graph.standardization import get_unique_node_andor_graph
+
+
+def test_smoke_andor(andor_graph_non_minimal: AndOrGraph):
+    with pytest.warns(UserWarning):
+        output = get_unique_node_andor_graph(andor_graph_non_minimal)
+
+    assert len(output) == len(andor_graph_non_minimal)  # no nodes deleted here
+
+
+def test_smoke_molset(molset_tree_non_minimal: MolSetGraph):
+    with pytest.warns(UserWarning):
+        get_unique_node_andor_graph(molset_tree_non_minimal)