fix

devtools/conda-envs/spyrmsd-test-obabel-rx.yaml

@@ -0,0 +1,26 @@
+name: spyrmsd
+channels:
+  - conda-forge
+dependencies:
+  # Base
+  - python
+  - setuptools
+
+  # Maths
+  - numpy
+  - scipy
+  - rustworkx
+
+  # Chemistry
+  - openbabel
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov

devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml

@@ -0,0 +1,27 @@
+name: spyrmsd
+channels:
+  - conda-forge
+  - rdkit
+dependencies:
+  # Base
+  - python
+  - setuptools
+
+  # Maths
+  - numpy
+  - scipy
+  - rustworkx
+
+  # Chemistry
+  - rdkit
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov

devtools/conda-envs/spyrmsd.yaml

@@ -10,3 +10,4 @@ dependencies:
   - numpy
   - scipy
   - rustworkx
+  - networkx

setup.py

@@ -33,6 +33,7 @@
         "bib": ["duecredit"],
         "rdkit": ["rdkit"],
         "openbabel": ["openbabel"],
+        "networkx": ["networkx"],
     },
     platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
     python_requires=">=3.9",

tests/test_graph.py

@@ -157,6 +157,10 @@ def test_build_graph_node_features(property) -> None:
     assert graph.num_edges(G) == 3
 
 
+@pytest.mark.skipif(
+    spyrmsd.get_backend() != "graph_tool",
+    reason="NetworkX supports all Python objects as node properties.",
+)
 def test_build_graph_node_features_unsupported() -> None:
     if spyrmsd.get_backend() != "graph-tool":
         pytest.skip(
@@ -169,3 +173,37 @@ def test_build_graph_node_features_unsupported() -> None:
 
     with pytest.raises(ValueError, match="Unsupported property type:"):
         _ = graph.graph_from_adjacency_matrix(A, property)
+
+
+@pytest.mark.skipif(
+    # Run test if all supported backends are installed
+    not set(spyrmsd.graph._supported_backends) <= set(spyrmsd.available_backends),
+    reason="Not all of the required backends are installed",
+)
+def test_set_backend() -> None:
+    import graph_tool as gt
+    import networkx as nx
+    import rustworkx as rx
+
+    A = np.array([[0, 1, 1], [1, 0, 0], [1, 0, 1]])
+
+    spyrmsd.set_backend("networkx")
+    assert spyrmsd.get_backend() == "networkx"
+
+    Gnx = graph.graph_from_adjacency_matrix(A)
+    assert isinstance(Gnx, nx.Graph)
+
+    spyrmsd.set_backend("graph-tool")
+    assert spyrmsd.get_backend() == "graph_tool"
+
+    Ggt = graph.graph_from_adjacency_matrix(A)
+    assert isinstance(Ggt, gt.Graph)
+
+    spyrmsd.set_backend("rustworkx")
+    assert spyrmsd.get_backend() == "rustworkx"
+
+    Grx = graph.graph_from_adjacency_matrix(A)
+    assert isinstance(Grx, rx.PyGraph)
+
+    with pytest.raises(ValueError, match="backend is not recognized or supported"):
+        spyrmsd.set_backend("unknown")

tests/test_molecule.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pytest
 
+import spyrmsd
 from spyrmsd import constants, graph, io, molecule, utils
 
 
@@ -205,3 +206,38 @@ def test_from_rdmol(molpath, adjacency):
             with pytest.raises(AttributeError):
                 # No adjacency_matrix attribute
                 mol.adjacency_matrix
+
+
+@pytest.mark.skipif(
+    # Run test if all supported backends are installed
+    not set(spyrmsd.graph._supported_backends) <= set(spyrmsd.available_backends),
+    reason="Not all of the required backends are installed",
+)
+def test_molecule_graph_cache(mol) -> None:
+    import graph_tool as gt
+    import networkx as nx
+    import rustworkx as rx
+
+    ## Graph cache persists from previous tests, manually reset them
+    mol.G = {}
+    spyrmsd.set_backend("networkx")
+    mol.to_graph()
+
+    assert isinstance(mol.G["networkx"], nx.Graph)
+    assert "graph_tool" not in mol.G.keys()
+
+    spyrmsd.set_backend("graph-tool")
+    mol.to_graph()
+
+    spyrmsd.set_backend("rustworkx")
+    mol.to_graph()
+
+    ## Make sure all backends (still) have a cache
+    assert isinstance(mol.G["networkx"], nx.Graph)
+    assert isinstance(mol.G["graph_tool"], gt.Graph)
+    assert isinstance(mol.G["rustworkx"], rx.PyGraph)
+
+    ## Strip the molecule to ensure the cache is reset
+    mol.strip()
+
+    assert len(mol.G.items()) == 0