Remove isort + update ruff

.pre-commit-config.yaml

@@ -1,8 +1,6 @@
-default_language_version:
-  python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.4.0
     hooks:
       - id: check-yaml
         exclude: '\.*conda/.*'
@@ -19,21 +17,19 @@ repos:
     rev: v0.38.0
     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)
+      - id: cpg-id-checker
 
   - repo: https://github.com/ambv/black
-    rev: 23.12.1
+    rev: 24.2.0
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.11
+    rev: v0.3.0
     hooks:
       - id: ruff
 
@@ -51,3 +47,8 @@ repos:
             --non-interactive,
           ]
         additional_dependencies: [types-PyYAML==6.0.4, types-toml]
+
+  - repo: https://github.com/koalaman/shellcheck-precommit
+    rev: v0.9.0
+    hooks:
+      - id: shellcheck

pyproject.toml

@@ -2,32 +2,10 @@
 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
 
+[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"]
 
@@ -36,6 +14,7 @@ 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
+    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
     "E501",    # Line length too long
     "E731",    # Do not assign a lambda expression, use a def
     "E741",    # Ambiguous variable name
@@ -48,5 +27,26 @@ ignore = [
     "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",
+    "hail_scripts",
+    "metamist",
 ]