update config & pre-commit dependencies

move isort and mypy config to pyproject.toml

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v3.3.0
+ rev: v4.0.1
  hooks:
  - id: check-merge-conflict
  - id: debug-statements
  - id: mixed-line-ending
  - id: check-case-conflict
  - id: check-yaml
  - repo: https://github.com/timothycrosley/isort
- rev: 5.6.4
+ rev: 5.9.3
  hooks:
  - id: isort
  - repo: https://github.com/python/black
- rev: 20.8b1
+ rev: 21.10b0
  hooks:
  - id: black
  language_version: python3
  - repo: https://gitlab.com/pycqa/flake8
- rev: 3.8.4
+ rev: 3.9.2
  hooks:
  - id: flake8
  language_version: python3
  - repo: https://github.com/pre-commit/mirrors-mypy
- rev: v0.790
+ rev: v0.910-1
  hooks:
  - id: mypy
  args: ["--strict", "--show-error-codes"]

nxontology/tests/ontology_test.py

@@ -277,8 +277,7 @@ def test_similarities(ontology: Ontology) -> None:
  ```
  Confirm the changes to ontology_utils_test_metal_sim.tsv are desired before committing.
  """
- # type ignored due to https://github.com/python/mypy/issues/6910
- nxo = ontology.ctor() # type: ignore [misc]
+ nxo = ontology.ctor()
  nxo.freeze()
  tsv = get_similarity_tsv(nxo)
  expect_tsv = ontology.sim_path.read_text()
@@ -290,7 +289,7 @@ def export_similarity_tsvs() -> None:
  Regenerate ontology_utils_test_metal_sim.tsv
  """
  for ontology in test_ontologies:
- nxo = ontology.ctor() # type: ignore [misc]
+ nxo = ontology.ctor()
  tsv = get_similarity_tsv(nxo)
  ontology.sim_path.write_text(tsv)
 

pyproject.toml

@@ -4,3 +4,36 @@ 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
+
+# https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file
+[tool.mypy]
+python_version = "3.7"
+
+[[tool.mypy.overrides]]
+module = [
+ "*.tests.*",
+]
+disallow_untyped_defs = false
+disallow_untyped_decorators = false
+
+[[tool.mypy.overrides]]
+module = [
+ "fire.*",
+ "fsspec.*",
+ "networkx.*",
+ "setuptools.*",
+ "pandas.*",
+ "pytest.*",
+ "_pytest.*",
+ "pygraphviz.*",
+]
+ignore_missing_imports = true

setup.cfg

@@ -49,17 +49,3 @@ ignore =
  E501
  E731
  W503
-
-[isort]
-profile = black
-multi_line_output = 3
-include_trailing_comma = True
-force_grid_wrap = 0
-use_parentheses = True
-line_length = 88
-
-[mypy-fire.*,fsspec.*,networkx.*,setuptools.*,pandas.*,pytest.*,_pytest.*,pygraphviz.*]
-ignore_missing_imports = True
-[mypy-*.tests.*]
-disallow_untyped_defs = False
-disallow_untyped_decorators = False