pre-commit: pyupgrade with __future__.annotations

.pre-commit-config.yaml

@@ -1,28 +1,33 @@
+default_language_version:
+ python: python3
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.0.1
+ rev: v4.1.0
  hooks:
  - id: check-merge-conflict
  - id: debug-statements
  - id: mixed-line-ending
  - id: check-case-conflict
  - id: check-yaml
+ - repo: https://github.com/asottile/pyupgrade
+ rev: v2.31.0
+ hooks:
+ - id: pyupgrade
+ args: [--py37-plus]
  - repo: https://github.com/timothycrosley/isort
- rev: 5.9.3
+ rev: 5.10.1
  hooks:
  - id: isort
  - repo: https://github.com/python/black
- rev: 21.10b0
+ rev: 22.1.0
  hooks:
  - id: black
- language_version: python3
  - repo: https://gitlab.com/pycqa/flake8
  rev: 3.9.2
  hooks:
  - id: flake8
- language_version: python3
  - repo: https://github.com/pre-commit/mirrors-mypy
- rev: v0.910-1
+ rev: v0.931
  hooks:
  - id: mypy
  args: ["--strict", "--show-error-codes"]

nxontology/imports.py

@@ -1,7 +1,9 @@
+from __future__ import annotations
+
 import logging
 from datetime import date
 from os import PathLike
-from typing import AnyStr, BinaryIO, Counter, List, Optional, Tuple, Union, cast
+from typing import AnyStr, BinaryIO, Counter, cast
 
 import networkx as nx
 from pronto import Ontology as Prontology # type: ignore [attr-defined]
@@ -70,7 +72,7 @@ def from_obo_library(slug: str) -> NXOntology[str]:
  return nxo
 
 
-def from_file(handle: Union[BinaryIO, str, "PathLike[AnyStr]"]) -> NXOntology[str]:
+def from_file(handle: BinaryIO | str | PathLike[AnyStr]) -> NXOntology[str]:
  """
  Read ontology in OBO, OWL, or JSON (OBO Graphs) format via pronto.
 
@@ -84,7 +86,7 @@ def from_file(handle: Union[BinaryIO, str, "PathLike[AnyStr]"]) -> NXOntology[st
 
 def _pronto_edges_for_term(
  term: Term, default_rel_type: str = "is a"
-) -> List[Tuple[Node, Node, str]]:
+) -> list[tuple[Node, Node, str]]:
  """
  Extract edges including "is a" relationships for a Pronto term.
  https://github.com/althonos/pronto/issues/119#issuecomment-956541286
@@ -158,7 +160,7 @@ def pronto_to_multidigraph(
 
 def multidigraph_to_digraph(
  graph: nx.MultiDiGraph,
- rel_types: Optional[List[str]] = None,
+ rel_types: list[str] | None = None,
  reverse: bool = True,
  reduce: bool = False,
 ) -> nx.DiGraph:
@@ -216,7 +218,8 @@ def multidigraph_to_digraph(
 def read_gene_ontology(
  release: str = "current",
  source_file: str = "go-basic.json.gz",
- rel_types: Optional[List[str]] = [
+ rel_types: list[str]
+ | None = [
  "is a",
  "part of",
  "regulates",

nxontology/node.py

@@ -2,18 +2,7 @@
 
 import math
 import warnings
-from typing import (
- TYPE_CHECKING,
- Any,
- Dict,
- Generic,
- Hashable,
- Iterator,
- List,
- Optional,
- Set,
- TypeVar,
-)
+from typing import TYPE_CHECKING, Any, Generic, Hashable, Iterator, TypeVar
 
 import networkx as nx
 
@@ -37,7 +26,7 @@ class Node_Info(Freezable, Generic[Node]):
  without requiring an external corpus to ascertain term frequency.
  """
 
- ic_metrics: List[str] = [
+ ic_metrics: list[str] = [
  "intrinsic_ic",
  "intrinsic_ic_sanchez",
  ]
@@ -53,7 +42,7 @@ def __init__(self, nxo: NXOntology[Node], node: Node):
  self.node = node
 
  @property
- def name(self) -> Optional[str]:
+ def name(self) -> str | None:
  """Human readable name / label."""
  value = self._get_node_attribute(
  custom_field="node_name_attribute", default="name"
@@ -66,7 +55,7 @@ def name(self) -> Optional[str]:
  return None if value is None else str(value)
 
  @property
- def label(self) -> Optional[str]:
+ def label(self) -> str | None:
  """Human readable node name / label."""
  warnings.warn(
  "Node_Info.label is deprecated and will be removed. Use Node_Info.name instead.",
@@ -76,14 +65,14 @@ def label(self) -> Optional[str]:
  return self.name
 
  @property
- def identifier(self) -> Optional[Any]:
+ def identifier(self) -> Any | None:
  """Database / machine identifier."""
  return self._get_node_attribute(
  custom_field="node_identifier_attribute", default="identifier"
  )
 
  @property
- def url(self) -> Optional[str]:
+ def url(self) -> str | None:
  """Uniform Resource Locator (URL)"""
  value = self._get_node_attribute(
  custom_field="node_url_attribute", default="url"
@@ -102,19 +91,19 @@ def frozen(self) -> bool:
  return self.nxo.frozen
 
  @property
- def data(self) -> Dict[Any, Any]:
+ def data(self) -> dict[Any, Any]:
  """Dictionary of node data (properties) for `self.node` in the networkx graph."""
  data = self.nxo.graph.nodes[self.node]
  assert isinstance(data, dict)
  return data
 
  @property
- def parents(self) -> Set[Node]:
+ def parents(self) -> set[Node]:
  """Direct parent nodes of this node."""
  return set(self.nxo.graph.predecessors(self.node))
 
  @property
- def parent(self) -> Optional[Node]:
+ def parent(self) -> Node | None:
  """
  Sole parent of this node, or None if this node is a root.
  If this node has multiple parents, raise ValueError.
@@ -129,13 +118,13 @@ def parent(self) -> Optional[Node]:
  raise ValueError(f"Node {self!r} has multiple parents.")
 
  @property
- def children(self) -> Set[Node]:
+ def children(self) -> set[Node]:
  """Direct child nodes of this node."""
  return set(self.nxo.graph.successors(self.node))
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def ancestors(self) -> Set[Node]:
+ def ancestors(self) -> set[Node]:
  """
  Get ancestors of node in graph, including the node itself.
  Ancestors refers to more general concepts in an ontology,
@@ -148,7 +137,7 @@ def ancestors(self) -> Set[Node]:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def descendants(self) -> Set[Node]:
+ def descendants(self) -> set[Node]:
  """
  Get descendants of node in graph, including the node itself.
  Descendants refers to more specific concepts in an ontology,
@@ -171,12 +160,12 @@ def n_descendants(self) -> int:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def roots(self) -> Set[Node]:
+ def roots(self) -> set[Node]:
  """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[Node]:
  """Descendents of this node that are leaves."""
  return self.descendants & self.nxo.leaves
 

nxontology/ontology.py

@@ -3,7 +3,7 @@
 import itertools
 import json
 import logging
-from typing import Any, Dict, Generic, Iterable, List, Optional, Set, cast
+from typing import Any, Generic, Iterable, cast
 
 import fsspec
 import networkx as nx
@@ -28,10 +28,10 @@ class NXOntology(Freezable, Generic[Node]):
  Edges should go from general to more specific.
  """
 
- def __init__(self, graph: Optional[nx.DiGraph] = None):
+ def __init__(self, graph: nx.DiGraph | None = None):
  self.graph = nx.DiGraph(graph)
  self.check_is_dag()
- self._node_info_cache: Dict[Node, Node_Info[Node]] = {}
+ self._node_info_cache: dict[Node, Node_Info[Node]] = {}
 
  def check_is_dag(self) -> None:
  if nx.is_directed_acyclic_graph(self.graph):
@@ -46,7 +46,7 @@ def check_is_dag(self) -> None:
  )
 
  @property
- def name(self) -> Optional[str]:
+ def name(self) -> str | None:
  """Short human-readable name for the ontology."""
  key = self.graph.graph.get("graph_name_attribute", "name")
  name = self.graph.graph.get(key)
@@ -101,7 +101,7 @@ def add_edge(self, u_of_edge: Node, v_of_edge: Node, **attr: Any) -> None:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def roots(self) -> Set[Node]:
+ def roots(self) -> set[Node]:
  """
  Return all top-level nodes, including isolates.
  """
@@ -127,7 +127,7 @@ def root(self) -> Node:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def leaves(self) -> Set[Node]:
+ def leaves(self) -> set[Node]:
  """
  Return all bottom-level nodes, including isolates.
  """
@@ -139,7 +139,7 @@ def leaves(self) -> Set[Node]:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def isolates(self) -> Set[Node]:
+ def isolates(self) -> set[Node]:
  """
  Return disconnected nodes.
  """
@@ -172,8 +172,8 @@ def similarity_metrics(
  node_0: Node,
  node_1: Node,
  ic_metric: str = "intrinsic_ic_sanchez",
- keys: Optional[List[str]] = None,
- ) -> Dict[str, Any]:
+ keys: list[str] | None = None,
+ ) -> dict[str, Any]:
  """
  Compute intrinsic similarity metrics for two nodes.
  """
@@ -184,8 +184,8 @@ def compute_similarities(
  self,
  source_nodes: Iterable[Node],
  target_nodes: Iterable[Node],
- ic_metrics: List[str] = ["intrinsic_ic_sanchez"],
- ) -> Iterable[Dict[str, Any]]:
+ ic_metrics: list[str] = ["intrinsic_ic_sanchez"],
+ ) -> Iterable[dict[str, Any]]:
  """
  Yield similarity metric dictionaries for all combinations of
  source_node-target_node-ic_metric.
@@ -251,10 +251,10 @@ def n_edges(self) -> int:
  def set_graph_attributes(
  self,
  *,
- graph_name_attribute: Optional[str] = None,
- node_name_attribute: Optional[str] = None,
- node_identifier_attribute: Optional[str] = None,
- node_url_attribute: Optional[str] = None,
+ graph_name_attribute: str | None = None,
+ node_name_attribute: str | None = None,
+ node_identifier_attribute: str | None = None,
+ node_url_attribute: str | None = None,
  ) -> None:
  """
  Convenience method to set attributes on the graph that are recognized by nxontology.

nxontology/similarity.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import math
-from typing import TYPE_CHECKING, Any, Dict, Generic, List, Optional, Set, Tuple
+from typing import TYPE_CHECKING, Any, Generic
 
 if TYPE_CHECKING:
  from nxontology.ontology import NXOntology
@@ -49,12 +49,12 @@ def node_1_subsumes_0(self) -> bool:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def common_ancestors(self) -> Set[Node]:
+ def common_ancestors(self) -> set[Node]:
  return self.info_0.ancestors & self.info_1.ancestors
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def union_ancestors(self) -> Set[Node]:
+ def union_ancestors(self) -> set[Node]:
  return self.info_0.ancestors | self.info_1.ancestors
 
  @property
@@ -91,7 +91,7 @@ def batet_log(self) -> float:
  # replace negative sign with abs to avoid returning -0.0.
  return abs(math.log(1 - self.batet) / math.log(self.n_union_ancestors))
 
- def results(self, keys: Optional[List[str]] = None) -> Dict[str, Any]:
+ def results(self, keys: list[str] | None = None) -> dict[str, Any]:
  if keys is None:
  keys = self.default_results
  return {key: getattr(self, key) for key in keys}
@@ -155,7 +155,7 @@ def node_1_ic_scaled(self) -> float:
 
  @property # type: ignore [misc]
  @cache_on_frozen
- def _resnik_mica(self) -> Tuple[float, Optional[Node]]:
+ def _resnik_mica(self) -> tuple[float, Node | None]:
  if not self.common_ancestors:
  return 0.0, None
  resnik, mica = max(
@@ -166,7 +166,7 @@ def _resnik_mica(self) -> Tuple[float, Optional[Node]]:
  return resnik, mica
 
  @property
- def mica(self) -> Optional[Node]:
+ def mica(self) -> Node | None:
  """
  Most informative common ancestor.
  None if no common ancestors exist.

nxontology/utils.py

@@ -1,6 +1,8 @@
+from __future__ import annotations
+
 import abc
 import functools
-from typing import Callable, Dict, TypeVar
+from typing import Callable, TypeVar
 
 
 class Freezable(abc.ABC):
@@ -30,9 +32,9 @@ def wrapped(self: T_Freezable) -> T:
  if not self.frozen:
  return func(self)
  try:
- method_cache: Dict[str, T] = getattr(self, "__method_cache")
+ method_cache: dict[str, T] = getattr(self, "__method_cache")
  except AttributeError:
- method_cache: Dict[str, T] = {} # type: ignore [no-redef]
+ method_cache: dict[str, T] = {} # type: ignore [no-redef]
  setattr(self, "__method_cache", method_cache)
  if fname not in method_cache:
  method_cache[fname] = func(self)