Fully pin lint workflow

Author: jeromekelleher

.github/workflows/lint.yml

@@ -5,4 +5,4 @@ on:
 
 jobs:
   Lint:
-    uses: tskit-dev/.github/.github/workflows/lint.yml@main
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v11

prek.toml

@@ -1,6 +1,20 @@
-# Configuration file for `prek`, a git hook framework written in Rust.
-# See https://prek.j178.dev for more information.
-#:schema https://www.schemastore.org/prek.json
+# The prek configuration defining linting requirements. This 
+# setup is optimised for long-term stability and determinism,
+# and therefore only uses either "builtin" rules or "local"
+# rules implementing lint workflows.  We do not use any remote
+# workflow repos.
+
+files = { glob = [
+    "msprime/**",
+    "benchmarks/**",
+    "tests/**",
+    "*.toml",
+    "docs/**",
+    "lib/*.[c,h]",
+    "lib/tests/*.[c,h]",
+]}
+
+exclude = { glob = ["lib/avl.*"]}
 
 [[repos]]
 repo = "builtin"
@@ -16,46 +30,38 @@ hooks = [
 ]
 
 [[repos]]
-repo = "https://github.com/pre-commit/pre-commit-hooks"
-rev = "v6.0.0"
-hooks = [
-  { id = "debug-statements" },
-]
-
-[[repos]]
-repo = "https://github.com/astral-sh/uv-pre-commit"
-rev = "0.10.3"
-hooks = [
-  { id = "uv-lock" }
-]
-
-[[repos]]
-repo = "https://github.com/benjeffery/pre-commit-clang-format"
-rev = "1.0"
+repo = "local"
 hooks = [
   {
-    id = "clang-format",
-    exclude = "avl|subprojects|dev-tools",
-    verbose = true
-  }
+    id = "ruff-check",
+    name = "ruff check",
+    language = "system",
+    entry = "ruff check --fix --force-exclude",
+    types = ["python"],
+  },
 ]
 
 [[repos]]
-repo = "https://github.com/asottile/blacken-docs"
-rev = "1.20.0"
+repo = "local"
 hooks = [
   {
-    id = "blacken-docs",
-    args = ["--skip-errors"],
-    additional_dependencies = ["black==22.3.0"],
-    language_version = "python3"
-  }
+    id = "ruff-format",
+    name = "ruff format",
+    language = "system",
+    entry = "ruff format --force-exclude",
+    types = ["python"],
+  },
 ]
 
 [[repos]]
-repo = "https://github.com/astral-sh/ruff-pre-commit"
-rev = "v0.15.0" # Ruff version.
+repo = "local"
 hooks = [
-  { id = "ruff-check", args = ["--fix"], types_or = ["python", "pyi"] },
-  { id = "ruff-format", types_or = ["python", "pyi"] },
+  {
+    id = "clang-format",
+    name = "clang-format",
+    language = "system",
+    entry = "clang-format -i",
+    types = ["c", "header"],
+    verbose = true,
+  },
 ]

pyproject.toml

@@ -98,9 +98,11 @@ docs = [
     "scipy"
 ]
 
+# Fully pin lint requirements for determinism. 
 lint = [
     "clang-format==21.1.8",
-    "prek",
+    "ruff==0.15.1",
+    "prek==0.3.3",
 ]
 
 dev = [
@@ -154,15 +156,15 @@ ignore = [
     "PT009", # pytest.raises(ValueError) too broad
     "PT011", # pytest.raises(ValueError) too broad
     "PT012", # pytest.raises() block should contain a single simple statement
-    "B018", # Found useless expression. Either assign it
     "B028", # No stacklevel for warnings
+    "B018", # Found useless expression. Either assign it
 ]
 
 fixable = ["ALL"]
 unfixable = []
 
 [tool.ruff.lint.isort]
-known-first-party = ["_msprime", "msprime"]
+known-first-party = ["_msprime", "msprime", "lwt_interface"]
 known-third-party = [
   "tskit",
   "numpy",

tests/test_dict_encoding.py

@@ -1,9 +1,9 @@
 # Test cases for the low-level dictionary encoding used to move
 # data around in C.
 import lwt_interface.dict_encoding_testlib
-from msprime import _msprime
+import msprime
 
-lwt_interface.dict_encoding_testlib.lwt_module = _msprime
+lwt_interface.dict_encoding_testlib.lwt_module = msprime._msprime
 
 # Bring the tests defined in dict_encoding_testlib into the current namespace
 # so pytest will find and execute them.