Update linting (#15)

Co-authored-by: Michael Franklin <[email protected]>

.pre-commit-config.yaml

@@ -1,5 +1,3 @@
-default_language_version:
-  python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -20,22 +18,18 @@ repos:
     hooks:
       - id: markdownlint
 
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+  - repo: https://github.com/populationgenomics/pre-commits
+    rev: "v0.1.3"
     hooks:
-      - id: isort
-        name: isort (python)
-
-  - repo: https://github.com/ambv/black
-    rev: 23.12.1
-    hooks:
-      - id: black
+      - id: cpg-id-checker
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.11
+    rev: v0.6.2
     hooks:
       - id: ruff
+        args: ["--fix"]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.8.0

pyproject.toml

@@ -1,33 +1,10 @@
-[tool.black]
-line-length = 88
-skip-string-normalization = true
-
-[tool.isort]
-py_version = 311
-profile = "black"
-line_length = 88
-sections = ["FUTURE", "STDLIB", "THIRDPARTY", "HAIL", "CPG", "FIRSTPARTY", "LOCALFOLDER"]
-known_hail = [
-    "hail",
-    "hailtop",
-]
-# Adjust these for each repository, e.g., removing those that should be
-# local rather than CPG. Also fill in extend_skip below if there are any
-# subdirectories that should be ignored.
-known_cpg = [
-    "analysis_runner",
-    "cpg_infra",
-    "cpg_utils",
-    "cpg_workflows",
-    "gnomad",
-    "hail_scripts",
-    "metamist",
-]
-# extend_skip = ["list", "submodules", "etc", here"]
-
 [tool.ruff]
-line-length = 88
+line-length = 120
+
+[tool.ruff.format]
+quote-style = "single"
 
+[tool.ruff.lint]
 # ignore pydocstyle, flake8-boolean-trap (FBT)
 select = ["A", "B", "C",  "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
 
@@ -36,17 +13,28 @@ fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN
 ignore = [
     "ANN101",  # Missing type annotation for self in method
     "ANN201",  # Missing return type annotation for public function
-    "E501",    # Line length too long
-    "E731",    # Do not assign a lambda expression, use a def
-    "E741",    # Ambiguous variable name
+    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
     "G004",    # Logging statement uses f-string
-    "PLR0911", # Too many return statements
-    "PLR0912", # Too many branches
-    "PLR0913", # Too many arguments to function call
-    "PLR0915", # Too many statements
     "PLW0603", # Using the global statement to update `<VAR>` is discouraged
     "PT018",   # Assertion should be broken down into multiple parts
     "Q000",    # Single quotes found but double quotes preferred
     "S101",    # Use of assert detected
-    "I001", # Import block is un-sorted (we use isort directly as ruff sort isn't fully supported)
+]
+
+[tool.ruff.lint.isort]
+section-order = ["future", "standard-library", "third-party", "hail", "cpg", "first-party", "local-folder"]
+
+[tool.ruff.lint.isort.sections]
+hail = ["hail", "hailtop"]
+
+# Adjust these for each repository, e.g., removing those that should be
+# local rather than CPG. Also fill in extend_skip below if there are any
+# subdirectories that should be ignored.
+cpg = [
+    "analysis_runner",
+    "cpg_infra",
+    "cpg_utils",
+    "cpg_workflows",
+    "gnomad",
+    "metamist",
 ]