Prepare release 0.0.13 (#14)

* update

* test mod compatible

* add graph visualizer

* fix lint

* add copy right for FGUtils

* prepare release

* add partial map expansion

* add testcase for partial expansion ver1

* update new features

* prepare release

* prepare release

* fix dependency

* fix bug

Author: TieuLongPhan

Test/SynGraph/Descriptor/test_graph_signature.py

@@ -10,43 +10,92 @@ def setUp(self):
         data = load_from_pickle("Data/test.pkl.gz")
         self.rc = data[0]["GraphRules"][2]
         self.its = data[0]["ITSGraph"][2]
+        self.graph_signature = GraphSignature(self.its)
 
-    def test_create_topology_signature(self):
-        signature = GraphSignature(self.rc)
-        self.assertEqual(
-            signature.create_topology_signature(
-                topo="Single Cyclic", cycle=[4], rstep=1
-            ),
-            "114",
+    def test_validate_graph(self):
+        """Test the validation of graph structure"""
+        # Test should pass if graph is valid (no exceptions)
+        try:
+            self.graph_signature._validate_graph()
+        except ValueError as e:
+            self.fail(f"Graph validation failed: {str(e)}")
+
+    def test_edge_signature(self):
+        """Test edge signature creation"""
+        edge_signature = self.graph_signature.create_edge_signature(
+            include_neighbors=False, max_hop=1
+        )
+
+        # Check that the edge signature is a non-empty string
+        self.assertIsInstance(edge_signature, str)
+        self.assertGreater(len(edge_signature), 0)
+        self.assertIn("Br0", edge_signature)
+        self.assertIn("{0.0,1.0}", edge_signature)
+        self.assertIn("H0", edge_signature)
+
+    def test_edge_signature_with_neighbors(self):
+        """Test edge signature creation including neighbors"""
+        edge_signature_with_neighbors = self.graph_signature.create_edge_signature(
+            include_neighbors=True, max_hop=1
         )
 
-    def test_create_node_signature(self):
-        signature = GraphSignature(self.rc)
-        self.assertEqual(signature.create_node_signature(), "BrCHN")
+        # Check that the edge signature with neighbors includes node degrees and neighbors
+        self.assertIsInstance(edge_signature_with_neighbors, str)
+        self.assertGreater(len(edge_signature_with_neighbors), 0)
+        self.assertIn("d1", edge_signature_with_neighbors)  # node degree for neighbor
 
-    def test_create_node_signature_condensed(self):
-        signature = GraphSignature(self.its)
-        self.assertEqual(signature.create_node_signature(), "BrC{23}ClHN{3}O{5}S")
+    def test_wl_hash(self):
+        """Test the Weisfeiler-Lehman hash generation"""
+        wl_hash = self.graph_signature.create_wl_hash(iterations=3)
 
-    def test_create_edge_signature(self):
-        signature = GraphSignature(self.rc)
-        self.assertEqual(
-            signature.create_edge_signature(), "Br[-1]H/Br[1]C/C[-1]N/H[1]N"
+        # Check that the WL hash is a valid hexadecimal string
+        self.assertIsInstance(wl_hash, str)
+        self.assertRegex(wl_hash, r"^[a-f0-9]{64}$")  # SHA-256 hash format
+
+    def test_graph_signature(self):
+        """Test the complete graph signature creation"""
+        complete_graph_signature = self.graph_signature.create_graph_signature(
+            include_wl_hash=True, include_neighbors=True, max_hop=1
         )
 
-    def test_create_graph_signature(self):
-        # Ensure the graph signature combines the results correctly
-        signature = GraphSignature(self.rc)
-        node_signature = "BrCHN"
-        edge_signature = "Br[-1]H/Br[1]C/C[-1]N/H[1]N"
-        topo_signature = "114"
-        expected = f"{topo_signature}.{node_signature}.{edge_signature}"
-        self.assertEqual(
-            signature.create_graph_signature(topo="Single Cyclic", cycle=[4], rstep=1),
-            expected,
+        # Check that the graph signature is a non-empty string
+        self.assertIsInstance(complete_graph_signature, str)
+        self.assertGreater(len(complete_graph_signature), 0)
+
+    def test_invalid_node_attributes(self):
+        """Test for missing node attributes"""
+        self.rc.add_node(4)  # Missing 'element' and 'charge'
+
+        with self.assertRaises(ValueError) as context:
+            invalid_graph_signature = GraphSignature(self.rc)
+            invalid_graph_signature._validate_graph()
+
+        self.assertIn(
+            "Node 4 is missing the 'element' attribute", str(context.exception)
         )
 
+    def test_invalid_edge_order(self):
+        """Test for invalid edge 'order' attribute"""
+        self.its.add_edge(
+            3, 4, order="invalid_order", state="steady"
+        )  # Invalid 'order' type
+
+        with self.assertRaises(ValueError) as context:
+            invalid_graph_signature = GraphSignature(self.its)
+            invalid_graph_signature._validate_graph()
+
+        self.assertIn("Edge (3, 4) has an invalid 'order'", str(context.exception))
+
+    def test_invalid_edge_state(self):
+        """Test for invalid edge 'state' attribute"""
+        self.its.add_edge(2, 4, order=1.0, state="invalid_state")  # Invalid 'state'
+
+        with self.assertRaises(ValueError) as context:
+            invalid_graph_signature = GraphSignature(self.its)
+            invalid_graph_signature._validate_graph()
+
+        self.assertIn("Edge (2, 4) has an invalid 'state'", str(context.exception))
+
 
-# Running the tests
 if __name__ == "__main__":
     unittest.main()

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synutility"
-version = "0.0.12"
+version = "0.0.13"
 authors = [
     {name="Tieu Long Phan", email="tieu@bioinf.uni-leipzig.de"}
 ]
@@ -22,6 +22,7 @@ dependencies = [
     "rdkit>=2024.3.3",
     "networkx>=3.3",
     "seaborn>=0.13.2",
+    "requests>=2.32.3",
 ]
 
 [project.optional-dependencies]

requirements.txt

@@ -7,4 +7,6 @@ rxn-chem-utils==1.5.0
 rxn-utils==2.0.0
 rxnmapper==0.3.0
 rdkit >= 2024.3.3
-pandas>=2.2.0
+pandas>=2.2.0
+requests>=2.32.3
+torch==2.0.1

synutility/SynGraph/Descriptor/graph_descriptors.py

@@ -180,12 +180,7 @@ def get_descriptors(
         )
 
         GraphDescriptor._adjust_cycle_and_step(entry, "cycle", entry["topo"])
-        entry["signature_rc"] = GraphSignature(graph).create_graph_signature(
-            topo=entry["topo"],
-            cycle=entry["cycle"],
-            rstep=entry["rstep"],
-            condensed=condensed,
-        )
+        entry["signature_rc"] = GraphSignature(graph).create_graph_signature()
 
         # Initialize ITS descriptors and call adjust
         topo_its = GraphDescriptor.check_graph_type(its_graph)
@@ -195,12 +190,7 @@ def get_descriptors(
             entry, "cycle_its", topo_its, its_prefix="its"
         )
 
-        entry["signature_its"] = GraphSignature(its_graph).create_graph_signature(
-            topo=topo_its,
-            cycle=entry["cycle_its"],
-            rstep=entry["rstep_its"],
-            condensed=condensed,
-        )
+        entry["signature_its"] = GraphSignature(its_graph).create_graph_signature()
 
         return entry