style: pin ruff version from template (#323)

Note that we are taking on a LOT of linting/formatting failures here -- these have been fixed in a separate branch, but I want to get these pins onto main for now.

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
   - id: trailing-whitespace
   - id: end-of-file-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.9
+  rev: v0.2.0
   hooks:
     - id: ruff
     - id: ruff-format

pyproject.toml

@@ -38,7 +38,7 @@ dynamic = ["version"]
 pg = ["psycopg[binary]"]
 etl = ["gffutils", "biocommons.seqrepo", "wags-tails>=0.1.1"]
 test = ["pytest>=6.0", "pytest-cov", "mock", "httpx"]
-dev = ["pre-commit", "ruff>=0.1.9"]
+dev = ["pre-commit", "ruff==0.2.0"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -90,41 +90,87 @@ extend-exclude = "^/docs/source/conf.py"
 [tool.ruff]
 src = ["src"]
 exclude = ["docs/source/conf.py"]
-# pycodestyle (E, W)
-# Pyflakes (F)
-# flake8-annotations (ANN)
-# flake8-quotes (Q)
-# pydocstyle (D)
-# pep8-naming (N)
-# isort (I)
-select = ["E", "W", "F", "ANN", "Q", "D", "N", "I"]
-
-fixable = ["I", "F401"]
 
+[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
-# ANN101 - missing-type-self
-# ANN003 - missing-type-kwargs
-# E501 - line-too-long
-ignore = ["D203", "D205", "D213", "D400", "D415", "ANN101", "ANN003", "E501"]
-
-[tool.ruff.flake8-quotes]
-docstring-quotes = "double"
+# 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.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# ANN201 - Missing type annotation
 # ANN102 - missing-type-cls
-# D103 - Missing docstring in public function
-# F821 - undefined-name
 # F401 - unused-import
-# I001 - Import block unsorted or unformatted
 # N805 - invalid-first-argument-name-for-method
-"tests/*" = ["ANN001", "ANN102", "ANN2"]
+# S101 - assert
+# B011 - assert-false
+# D100 - undocumented-public-module
+# D103 - undocumented-public-function
+# I001 - unsorted-imports
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
 "*__init__.py" = ["F401"]
 "gene/schemas.py" = ["ANN001", "ANN201", "N805"]
 "docs/source/conf.py" = ["D100", "I001", "D103", "ANN201", "ANN001"]