Updated tests for scaffold network + tree

Author: OliverBScott

tests/__init__.py

@@ -5,6 +5,7 @@
 import os
 
 import pytest
+from rdkit import Chem
 from rdkit import rdBase
 
 rdBase.DisableLog('rdApp.*')
@@ -15,10 +16,44 @@ def test_root_dir():
 
 
 @pytest.fixture(name='sdf_file')
-def mock_sdf():
-    return
+def mock_sdf(tmp_path):
+    d = tmp_path / "test_data"
+    d.mkdir()
+    p = d / "test.sdf"
+    writer = Chem.SDWriter(str(p))
+    writer.write(Chem.MolFromSmiles('CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3'))
+    writer.write(Chem.MolFromSmiles('CCC1=CC2=C(S1)N(C(=O)CN=C2C3=CC=CC=C3Cl)C'))
+    writer.close()
+    return str(p)
+
+
+@pytest.fixture(name='sdf_file_2')
+def mock_sdf_2(tmp_path):
+    d = tmp_path / "test_data"
+    try:
+        d.mkdir()
+    except FileExistsError:
+        pass
+    p = d / "test_2.sdf"
+    writer = Chem.SDWriter(str(p))
+    writer.write(Chem.MolFromSmiles('C1C(=O)NC2=C(C=C(C=C2)Br)C(=N1)C3=CC=CC=N3'))
+    writer.write(Chem.MolFromSmiles('CC1=NN(C2=C1C(=NCC(=O)N2C)C3=CC=CC=C3F)C'))
+    writer.close()
+    return str(p)
 
 
 @pytest.fixture(name='smiles_file')
-def mock_smiles_file():
-    return
+def mock_smiles_file(tmp_path):
+    d = tmp_path / "test_data"
+    d.mkdir()
+    p = d / "test.smi"
+    writer = Chem.SmilesWriter(str(p))
+    writer.write(Chem.MolFromSmiles('CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3'))
+    writer.write(Chem.MolFromSmiles('CCC1=CC2=C(S1)N(C(=O)CN=C2C3=CC=CC=C3Cl)C'))
+    writer.close()
+    return str(p)
+
+
+def canon(smiles):
+    """Canonicalize SMILES for safety. If canonicalization ever changes this should remain consistent"""
+    return Chem.MolToSmiles(Chem.MolFromSmiles(smiles))

tests/io/test_smiles.py

@@ -0,0 +1,35 @@
+"""
+scaffoldgraph tests.test_network
+"""
+
+import pytest
+
+import scaffoldgraph as sg
+
+
+@pytest.fixture(name='test_net')
+def test_network(sdf_file):
+    network = sg.ScaffoldNetwork.from_sdf(sdf_file)
+    return network
+
+
+def test_network_from_sdf(sdf_file):
+    network = sg.ScaffoldNetwork.from_sdf(sdf_file)
+    assert network.num_scaffold_nodes == 8
+    assert network.num_molecule_nodes == 2
+
+
+def test_network_from_smiles(smiles_file):
+    network = sg.ScaffoldNetwork.from_smiles_file(smiles_file)
+    assert network.num_scaffold_nodes == 8
+    assert network.num_molecule_nodes == 2
+
+
+def test_hiers(sdf_file):
+    network = sg.HierS.from_sdf(sdf_file)
+    assert network.num_scaffold_nodes == 5
+    assert network.num_molecule_nodes == 2
+
+
+def test_repr(test_net):
+    assert repr(test_net) == '<ScaffoldNetwork at {}>'.format(hex(id(test_net)))

tests/io/test_supplier.py

@@ -0,0 +1,32 @@
+"""
+scaffoldgraph tests.test_tree
+"""
+
+import networkx as nx
+import pytest
+
+import scaffoldgraph as sg
+
+
+@pytest.fixture(name='test_tree')
+def test_tree_graph(sdf_file):
+    tree = sg.ScaffoldTree.from_sdf(sdf_file)
+    return tree
+
+
+def test_tree_from_sdf(sdf_file):
+    tree = sg.ScaffoldTree.from_sdf(sdf_file)
+    assert tree.num_scaffold_nodes == 5
+    assert tree.num_molecule_nodes == 2
+    assert nx.is_tree(tree)
+
+
+def test_tree_from_smiles(smiles_file):
+    tree = sg.ScaffoldTree.from_smiles_file(smiles_file)
+    assert tree.num_scaffold_nodes == 5
+    assert tree.num_molecule_nodes == 2
+    assert nx.is_tree(tree)
+
+
+def test_repr(test_tree):
+    assert repr(test_tree) == '<ScaffoldTree at {}>'.format(hex(id(test_tree)))