style: use ruff

.github/workflows/checks.yaml

@@ -19,3 +19,19 @@ jobs:
         run: |
           python -m pip install pipenv
           pipenv install --skip-lock  # this is what Elastic beanstalk uses
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: python3 -m pip install ".[dev]"
+
+      - name: Check style
+        run: python3 -m ruff check . && python3 -m ruff format --check .

.pre-commit-config.yaml

@@ -1,12 +1,14 @@
-# See https://pre-commit.com for more information
-# See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.4.0
     hooks:
-    - id: flake8
-      additional_dependencies: [flake8-docstrings]
-    - id: check-added-large-files
-      args: ['--maxkb=1024']
-      exclude: ^tests/data
-    - id: detect-private-key
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.0  # ruff version
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [ --fix, --exit-non-zero-on-fix ]

Pipfile

@@ -27,7 +27,6 @@ pytest-cov = "*"
 pytest-asyncio = "*"
 mock = "*"
 pre-commit = "*"
-flake8 = "*"
-flake8-docstrings = "*"
+ruff = "==0.2.0"
 ipykernel = "*"
 jupyterlab = "*"

README.md

@@ -152,10 +152,10 @@ python3 -m pytest
 
 ### And coding style tests
 
-Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.
+Code style is managed by [ruff](https://astral.sh/ruff) and checked prior to commit.
 
 ```
-see .flake8
+python3 -m ruff check --fix . && python3 -m ruff format .
 
 ```
 

pyproject.toml

@@ -45,7 +45,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "mock", "pytest-asyncio"]
-dev = ["pre-commit", "flake8", "flake8-docstrings"]
+dev = ["pre-commit", "ruff==0.2.0"]
 notebooks = ["ipykernel", "jupyterlab"]
 
 [project.urls]
@@ -73,3 +73,85 @@ testpaths = ["tests"]
 
 [tool.coverage.run]
 branch = true
+
+[tool.ruff]
+src = ["src"]
+exclude = ["docs/*", "analysis/*", "codebuild/*"]
+
+[tool.ruff.lint]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+fixable = [
+    "I",
+    "F401",
+    "D",
+    "UP",
+    "ANN",
+    "B",
+    "C4",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "SIM",
+    "RUF"
+]
+# ANN101 - missing-type-self
+# ANN003 - missing-type-kwargs
+# D203 - one-blank-line-before-class
+# D205 - blank-line-after-summary
+# D206 - indent-with-spaces*
+# D213 - multi-line-summary-second-line
+# D300 - triple-single-quotes*
+# D400 - ends-in-period
+# D415 - ends-in-punctuation
+# E111 - indentation-with-invalid-multiple*
+# E114 - indentation-with-invalid-multiple-comment*
+# E117 - over-indented*
+# E501 - line-too-long*
+# W191 - tab-indentation*
+# S321 - suspicious-ftp-lib-usage
+# *ignored for compatibility with formatter
+ignore = [
+    "ANN101", "ANN003",
+    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
+    "E111", "E114", "E117", "E501",
+    "W191",
+    "S321",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# ANN001 - missing-type-function-argument
+# ANN2 - missing-return-type
+# ANN102 - missing-type-cls
+# S101 - assert
+# B011 - assert-false
+# N815 -
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
+"src/metakb/schemas/*" = ["ANN102", "N815"]

src/metakb/__init__.py

@@ -1,36 +1,33 @@
 """The MetaKB package."""
-from pathlib import Path
 import logging
 from os import environ
+from pathlib import Path
 
 APP_ROOT = Path(__file__).resolve().parents[0]
 PROJECT_ROOT = Path(__file__).resolve().parents[1]
 
-if 'METAKB_NORM_EB_PROD' in environ:
-    LOG_FN = "/tmp/metakb.log"
-else:
-    LOG_FN = "metakb.log"
+LOG_FN = "/tmp/metakb.log" if "METAKB_NORM_EB_PROD" in environ else "metakb.log"  # noqa: S108
 
 logging.basicConfig(
-    filename=LOG_FN,
-    format='[%(asctime)s] - %(name)s - %(levelname)s : %(message)s')
-logger = logging.getLogger('metakb')
+    filename=LOG_FN, format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"
+)
+logger = logging.getLogger("metakb")
 logger.setLevel(logging.DEBUG)
 logging.getLogger("boto3").setLevel(logging.INFO)
 logging.getLogger("botocore").setLevel(logging.INFO)
 logging.getLogger("urllib3").setLevel(logging.INFO)
 logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
 logging.getLogger("hgvs.parser").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)  # noqa: E501
-logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)  # noqa: E501
+logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)
+logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)
 logging.getLogger("requests_cache.patcher").setLevel(logging.INFO)
 logging.getLogger("bioregistry.resource_manager").setLevel(logging.INFO)
 logging.getLogger("blib2to3.pgen2.driver").setLevel(logging.INFO)
 logging.getLogger("neo4j").setLevel(logging.INFO)
 logging.getLogger("asyncio").setLevel(logging.INFO)
 logger.handlers = []
 
-if 'METAKB_NORM_EB_PROD' in environ:
+if "METAKB_NORM_EB_PROD" in environ:
     ch = logging.StreamHandler()
     ch.setLevel(logging.DEBUG)
     logger.addHandler(ch)