pre-commit: switch to ruff

.pre-commit-config.yaml

@@ -9,23 +9,15 @@ repos:
  - id: mixed-line-ending
  - id: check-case-conflict
  - id: check-yaml
- - repo: https://github.com/asottile/pyupgrade
- rev: v3.3.1
+ - repo: https://github.com/charliermarsh/ruff-pre-commit
+ rev: v0.0.253
  hooks:
- - id: pyupgrade
- args: [--py38-plus]
- - repo: https://github.com/timothycrosley/isort
- rev: 5.12.0
- hooks:
- - id: isort
+ - id: ruff
+ args: ["--fix"]
  - repo: https://github.com/python/black
  rev: 23.1.0
  hooks:
  - id: black
- - repo: https://github.com/pycqa/flake8
- rev: 6.0.0
- hooks:
- - id: flake8
  - repo: https://github.com/pre-commit/mirrors-mypy
  rev: v1.0.1
  hooks:

nxontology/imports.py

@@ -91,7 +91,7 @@ def _pronto_edges_for_term(
  Extract edges including "is a" relationships for a Pronto term.
  https://github.com/althonos/pronto/issues/119#issuecomment-956541286
  """
- rels = list()
+ rels = []
  source_id = cast(Node, term.id)
  for target in term.superclasses(distance=1, with_self=False):
  rels.append((source_id, cast(Node, target.id), default_rel_type))
@@ -160,7 +160,7 @@ def pronto_to_multidigraph(
 
 def multidigraph_to_digraph(
  graph: nx.MultiDiGraph,
- rel_types: list[str] | None = None,
+ rel_types: list[str] | tuple[str, ...] | None = None,
  reverse: bool = True,
  reduce: bool = False,
 ) -> nx.DiGraph:
@@ -219,13 +219,14 @@ def read_gene_ontology(
  release: str = "current",
  source_file: str = "go-basic.json.gz",
  rel_types: list[str]
- | None = [
+ | tuple[str, ...]
+ | None = (
  "is a",
  "part of",
  "regulates",
  "negatively regulates",
  "positively regulates",
- ],
+ ),
  reduce: bool = True,
 ) -> NXOntology[str]:
  """

nxontology/ontology.py

@@ -192,7 +192,7 @@ def compute_similarities(
  self,
  source_nodes: Iterable[Node],
  target_nodes: Iterable[Node],
- ic_metrics: list[str] = ["intrinsic_ic_sanchez"],
+ ic_metrics: list[str] | tuple[str, ...] = ("intrinsic_ic_sanchez",),
  ) -> Iterable[dict[str, Any]]:
  """
  Yield similarity metric dictionaries for all combinations of
@@ -218,7 +218,7 @@ def node_info(self, node: Node) -> Node_Info[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]] = dict()
+ name_to_node_info: dict[str, Node_Info[Node]] = {}
  for node in self.graph:
  info = self.node_info(node)
  name = info.name

pyproject.toml

@@ -5,18 +5,30 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 # including this section enables version inference
 
-# https://pycqa.github.io/isort/docs/configuration/config_files.html
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-line_length = 88
-
 [tool.black]
 target-version = ['py38', 'py39', 'py310', 'py311']
 
+[tool.ruff]
+target-version = "py38"
+line-length = 88
+ignore = [
+ "E402", # ignore import-at-top-of-file violations
+ "E501", # ignore line-length violations
+ "F811", # ignore redefinition of a function
+ "B019", # ignore functools cache/lru_cache
+ "UP030", # allow explicit positional string formatting
+]
+select = [
+ "B", # flake8-bugbear
+ "C", # flake8-comprehensions
+ "C90", # mccabe
+ "E", # pycodestyle errors
+ "F", # pyflakes
+ "I", # isort
+ "UP", # pyupgrade
+ "W", # pycode warnings
+]
+
 # https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file
 [tool.mypy]
 python_version = "3.8"

setup.cfg

@@ -41,11 +41,3 @@ dev =
  pytest
 viz =
  pygraphviz
-
-[flake8]
-ignore =
- E203
- E402
- E501
- E731
- W503