attempt to improve node info subclass typing

method from #26 (comment)

nxontology/imports.py

@@ -11,7 +11,7 @@
 
 from nxontology import NXOntology
 from nxontology.exceptions import NodeNotFound
-from nxontology.node import Node
+from nxontology.node import NodeT
 
 logger = logging.getLogger(__name__)
 
@@ -86,21 +86,21 @@ def from_file(handle: BinaryIO | str | PathLike[AnyStr]) -> NXOntology[str]:
 
 def _pronto_edges_for_term(
  term: Term, default_rel_type: str = "is a"
-) -> list[tuple[Node, Node, str]]:
+) -> list[tuple[NodeT, NodeT, str]]:
  """
  Extract edges including "is a" relationships for a Pronto term.
  https://github.com/althonos/pronto/issues/119#issuecomment-956541286
  """
  rels = []
- source_id = cast(Node, term.id)
+ source_id = cast(NodeT, term.id)
  for target in term.superclasses(distance=1, with_self=False):
- rels.append((source_id, cast(Node, target.id), default_rel_type))
+ rels.append((source_id, cast(NodeT, target.id), default_rel_type))
  for rel_type, targets in term.relationships.items():
  for target in sorted(targets):
  rels.append(
  (
- cast(Node, term.id),
- cast(Node, target.id),
+ cast(NodeT, term.id),
+ cast(NodeT, target.id),
  rel_type.name or rel_type.id,
  )
  )

nxontology/node.py

@@ -15,10 +15,11 @@
 
 # Type definitions. networkx does not declare types.
 # https://github.com/networkx/networkx/issues/3988#issuecomment-639969263
-Node = TypeVar("Node", bound=Hashable)
+NodeT = TypeVar("NodeT", bound=Hashable)
+NodeInfoT = TypeVar("NodeInfoT")
 
 
-class Node_Info(Freezable, Generic[Node]):
+class Node_Info(Freezable, Generic[NodeT]):
  """
  Compute metrics and values for a node of an NXOntology.
  Includes intrinsic information content (IC) metrics.
@@ -35,7 +36,7 @@ class Node_Info(Freezable, Generic[Node]):
  Each ic_metric has a scaled version accessible by adding a _scaled suffix.
  """
 
- def __init__(self, nxo: NXOntology[Node], node: Node):
+ def __init__(self, nxo: NXOntology[NodeT, NodeInfoT], node: NodeT):
  if node not in nxo.graph:
  raise NodeNotFound(f"{node} not in graph.")
  self.nxo = nxo
@@ -98,12 +99,12 @@ def data(self) -> dict[Any, Any]:
  return data
 
  @property
- def parents(self) -> set[Node]:
+ def parents(self) -> set[NodeT]:
  """Direct parent nodes of this node."""
  return set(self.nxo.graph.predecessors(self.node))
 
  @property
- def parent(self) -> Node | None:
+ def parent(self) -> NodeT | None:
  """
  Sole parent of this node, or None if this node is a root.
  If this node has multiple parents, raise ValueError.
@@ -118,13 +119,13 @@ def parent(self) -> Node | None:
  raise ValueError(f"Node {self!r} has multiple parents.")
 
  @property
- def children(self) -> set[Node]:
+ def children(self) -> set[NodeT]:
  """Direct child nodes of this node."""
  return set(self.nxo.graph.successors(self.node))
 
  @property
  @cache_on_frozen
- def ancestors(self) -> set[Node]:
+ def ancestors(self) -> set[NodeT]:
  """
  Get ancestors of node in graph, including the node itself.
  Ancestors refers to more general concepts in an ontology,
@@ -137,7 +138,7 @@ def ancestors(self) -> set[Node]:
 
  @property
  @cache_on_frozen
- def descendants(self) -> set[Node]:
+ def descendants(self) -> set[NodeT]:
  """
  Get descendants of node in graph, including the node itself.
  Descendants refers to more specific concepts in an ontology,
@@ -160,12 +161,12 @@ def n_descendants(self) -> int:
 
  @property
  @cache_on_frozen
- def roots(self) -> set[Node]:
+ def roots(self) -> set[NodeT]:
  """Ancestors of this node that are roots (top-level)."""
  return self.ancestors & self.nxo.roots
 
  @property
- def leaves(self) -> set[Node]:
+ def leaves(self) -> set[NodeT]:
  """Descendents of this node that are leaves."""
  return self.descendants & self.nxo.leaves
 
@@ -181,14 +182,14 @@ def depth(self) -> int:
  return depth
 
  @property
- def paths_from_roots(self) -> Iterator[list[Node]]:
+ def paths_from_roots(self) -> Iterator[list[NodeT]]:
  for root in self.roots:
  yield from nx.all_simple_paths(
  self.nxo.graph, source=root, target=self.node
  )
 
  @property
- def paths_to_leaves(self) -> Iterator[list[Node]]:
+ def paths_to_leaves(self) -> Iterator[list[NodeT]]:
  yield from nx.all_simple_paths(
  self.nxo.graph, source=self.node, target=self.leaves
  )

nxontology/ontology.py

@@ -3,6 +3,7 @@
 import itertools
 import json
 import logging
+from abc import abstractmethod
 from os import PathLike, fspath
 from typing import Any, Generic, Iterable, cast
 
@@ -12,7 +13,7 @@
 from networkx.algorithms.isolate import isolates
 from networkx.readwrite.json_graph import node_link_data, node_link_graph
 
-from nxontology.node import Node
+from nxontology.node import NodeInfoT, NodeT
 
 from .exceptions import DuplicateError, NodeNotFound
 from .node import Node_Info
@@ -22,7 +23,7 @@
 logger = logging.getLogger(__name__)
 
 
-class NXOntology(Freezable, Generic[Node]):
+class NXOntologyBase(Freezable, Generic[NodeT, NodeInfoT]):
  """
  Encapsulate a networkx.DiGraph to represent an ontology.
  Regarding edge directionality, parent terms should point to child term.
@@ -39,7 +40,7 @@ def __init__(
  # in case there are compatability issues in the future.
  self._add_nxontology_metadata()
  self.check_is_dag()
- self._node_info_cache: dict[Node, Node_Info[Node]] = {}
+ self._node_info_cache: dict[NodeT, Node_Info[NodeT]] = {}
 
  def _add_nxontology_metadata(self) -> None:
  self.graph.graph["nxontology_version"] = get_nxontology_version()
@@ -77,7 +78,7 @@ def write_node_link_json(self, path: str | PathLike[str]) -> None:
  write_file.write("\n") # json.dump does not include a trailing newline
 
  @classmethod
- def read_node_link_json(cls, path: str | PathLike[str]) -> NXOntology[Node]:
+ def read_node_link_json(cls, path: str | PathLike[str]) -> NXOntologyBase[NodeT]:
  """
  Retrun a new graph from node-link format as written by `write_node_link_json`.
  """
@@ -90,7 +91,7 @@ def read_node_link_json(cls, path: str | PathLike[str]) -> NXOntology[Node]:
  nxo = cls(digraph)
  return nxo
 
- def add_node(self, node_for_adding: Node, **attr: Any) -> None:
+ def add_node(self, node_for_adding: NodeT, **attr: Any) -> None:
  """
  Like networkx.DiGraph.add_node but raises a DuplicateError
  if the node already exists.
@@ -99,7 +100,7 @@ def add_node(self, node_for_adding: Node, **attr: Any) -> None:
  raise DuplicateError(f"node already in graph: {node_for_adding}")
  self.graph.add_node(node_for_adding, **attr)
 
- def add_edge(self, u_of_edge: Node, v_of_edge: Node, **attr: Any) -> None:
+ def add_edge(self, u_of_edge: NodeT, v_of_edge: NodeT, **attr: Any) -> None:
  """
  Like networkx.DiGraph.add_edge but
  raises a NodeNotFound if either node does not exist
@@ -116,7 +117,7 @@ def add_edge(self, u_of_edge: Node, v_of_edge: Node, **attr: Any) -> None:
 
  @property
  @cache_on_frozen
- def roots(self) -> set[Node]:
+ def roots(self) -> set[NodeT]:
  """
  Return all top-level nodes, including isolates.
  """
@@ -127,7 +128,7 @@ def roots(self) -> set[Node]:
  return roots
 
  @property
- def root(self) -> Node:
+ def root(self) -> NodeT:
  """
  Sole root of this directed acyclic graph.
  If this ontology has multiple roots, raise ValueError.
@@ -142,7 +143,7 @@ def root(self) -> Node:
 
  @property
  @cache_on_frozen
- def leaves(self) -> set[Node]:
+ def leaves(self) -> set[NodeT]:
  """
  Return all bottom-level nodes, including isolates.
  """
@@ -154,7 +155,7 @@ def leaves(self) -> set[Node]:
 
  @property
  @cache_on_frozen
- def isolates(self) -> set[Node]:
+ def isolates(self) -> set[NodeT]:
  """
  Return disconnected nodes.
  """
@@ -175,17 +176,17 @@ def frozen(self) -> bool:
 
  def similarity(
  self,
- node_0: Node,
- node_1: Node,
+ node_0: NodeT,
+ node_1: NodeT,
  ic_metric: str = "intrinsic_ic_sanchez",
- ) -> SimilarityIC[Node]:
+ ) -> SimilarityIC[NodeT]:
  """SimilarityIC instance for the specified nodes"""
  return SimilarityIC(self, node_0, node_1, ic_metric)
 
  def similarity_metrics(
  self,
- node_0: Node,
- node_1: Node,
+ node_0: NodeT,
+ node_1: NodeT,
  ic_metric: str = "intrinsic_ic_sanchez",
  keys: list[str] | None = None,
  ) -> dict[str, Any]:
@@ -197,8 +198,8 @@ def similarity_metrics(
 
  def compute_similarities(
  self,
- source_nodes: Iterable[Node],
- target_nodes: Iterable[Node],
+ source_nodes: Iterable[NodeT],
+ target_nodes: Iterable[NodeT],
  ic_metrics: list[str] | tuple[str, ...] = ("intrinsic_ic_sanchez",),
  ) -> Iterable[dict[str, Any]]:
  """
@@ -213,16 +214,17 @@ def compute_similarities(
  yield metrics
 
  @classmethod
- def _get_node_info_cls(cls) -> type[Node_Info[Node]]:
+ @abstractmethod
+ def _get_node_info_cls(cls) -> type[NodeInfoT]:
  """
  Return the Node_Info class to use for this ontology.
  Subclasses can override this to use a custom Node_Info class.
  For the complexity of typing this method, see
  <https://github.com/related-sciences/nxontology/pull/26>.
  """
- return Node_Info
+ ...
 
- def node_info(self, node: Node) -> Node_Info[Node]:
+ def node_info(self, node: NodeT) -> NodeInfoT:
  """
  Return Node_Info instance for `node`.
  If frozen, cache node info in `self._node_info_cache`.
@@ -235,8 +237,8 @@ def node_info(self, node: Node) -> Node_Info[Node]:
  return self._node_info_cache[node]
 
  @cache_on_frozen
- def _get_name_to_node_info(self) -> dict[str, Node_Info[Node]]:
- name_to_node_info: dict[str, Node_Info[Node]] = {}
+ def _get_name_to_node_info(self) -> dict[str, Node_Info[NodeT]]:
+ name_to_node_info: dict[str, Node_Info[NodeT]] = {}
  for node in self.graph:
  info = self.node_info(node)
  name = info.name
@@ -249,7 +251,7 @@ def _get_name_to_node_info(self) -> dict[str, Node_Info[Node]]:
  name_to_node_info[name] = info
  return name_to_node_info
 
- def node_info_by_name(self, name: str) -> Node_Info[Node]:
+ def node_info_by_name(self, name: str) -> Node_Info[NodeT]:
  """
  Return Node_Info instance using a lookup by name.
  """
@@ -306,3 +308,9 @@ def set_graph_attributes(
  self.graph.graph["node_identifier_attribute"] = node_identifier_attribute
  if node_url_attribute:
  self.graph.graph["node_url_attribute"] = node_url_attribute
+
+
+class NXOntology(NXOntologyBase[NodeT, Node_Info[NodeT]]):
+ @classmethod
+ def _get_node_info_cls(cls) -> type[Node_Info[NodeT]]:
+ return Node_Info