Merge branch 'main' into ligandnet-to-alchnet

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - pint <0.22  # https://github.com/openforcefield/openff-units/issues/69
   - openff-models >=0.0.5
   - pip
-  - pydantic
+  - pydantic <2.0.0
   - pytest
   - pytest-cov
   - pytest-xdist
@@ -20,5 +20,6 @@ dependencies:
   # docs
   - pydata-sphinx-theme
   - sphinx-jsonschema==1.15
+  - sphinx <7.1.2
   - pip:
-    - autodoc_pydantic
+    - autodoc_pydantic<2.0.0

gufe/ligandnetwork.py

@@ -2,6 +2,7 @@
 # For details, see https://github.com/OpenFreeEnergy/gufe
 from __future__ import annotations
 
+from itertools import chain
 import json
 import networkx as nx
 from typing import FrozenSet, Iterable, Optional
@@ -31,7 +32,8 @@ def __init__(
             nodes = []
 
         self._edges = frozenset(edges)
-        edge_nodes = set.union(*[{edge.componentA, edge.componentB} for edge in edges])
+        edge_nodes = set(chain.from_iterable((e.componentA, e.componentB)
+                                             for e in edges))
         self._nodes = frozenset(edge_nodes) | frozenset(nodes)
         self._graph = None
 
@@ -47,7 +49,7 @@ def _from_dict(cls, dct: dict):
         return cls.from_graphml(dct['graphml'])
 
     @property
-    def graph(self) -> nx.Graph:
+    def graph(self) -> nx.MultiDiGraph:
         """NetworkX graph for this network"""
         if self._graph is None:
             graph = nx.MultiDiGraph()
@@ -306,3 +308,11 @@ def to_rbfe_alchemical_network(
     #         autoname=autoname,
     #         autoname_prefix=autoname_prefix
     #     )
+
+    def is_connected(self) -> bool:
+        """Are all ligands in the network (indirectly) connected to each other
+
+        A "False" value indicates that either some ligands have no edges or that
+        there are separate networks that do not link to each other.
+        """
+        return nx.is_weakly_connected(self.graph)

gufe/tests/test_ligand_network.py

@@ -428,3 +428,16 @@ def test_to_rhfe_alchemical_network(self, real_molecules_network,
             assert list(edge.mapping) == ['ligand']
             assert edge.mapping['ligand'] in real_molecules_network.edges
 
+    def test_is_connected(self, simple_network):
+        assert simple_network.network.is_connected()
+
+    def test_is_not_connected(self, singleton_node_network):
+        assert not singleton_node_network.network.is_connected()
+
+
+def test_empty_ligand_network(mols):
+    # issue #217
+    n = LigandNetwork(edges=[], nodes=[mols[0]])
+
+    assert len(n.edges) == 0
+    assert len(n.nodes) == 1

gufe/tokenization.py

@@ -61,6 +61,24 @@ def __call__(cls, *args, **kwargs):
         instance = TOKENIZABLE_REGISTRY[key]
         return instance
 
+    def __init__(cls, clsname, bases, attrs):
+        """
+        Restore the signature of __init__ or __new__
+        """
+        if inspect.signature(cls.__new__) != inspect.signature(object.__new__):
+            sig = inspect.signature(cls.__new__)
+        elif inspect.signature(cls.__init__) != inspect.signature(object.__init__):
+            sig = inspect.signature(cls.__init__)
+        else:
+            # No __new__ or __init__ method defined
+            return super().__init__(clsname, bases, attrs)
+
+        # Remove the first parameter (cls/self)
+        parameters = tuple(sig.parameters.values())
+        cls.__signature__ = sig.replace(parameters=parameters[1:])
+
+        return super().__init__(clsname, bases, attrs)
+
 
 class _ABCGufeClassMeta(_GufeTokenizableMeta, abc.ABCMeta):
     # required to make use of abc.ABC in classes that use _ComponentMeta