STYLE: Apply pre-commit hook fixes across the repository

Run the full pre-commit suite repo-wide (black, ruff, shfmt, taplo) and
resolve shellcheck findings: egrep -> grep -E, guard rm with
${MODULES_DIR:?}, and count wheels with find instead of ls.

Author: CavRiley

Utilities/Hooks/kw-commit-msg.py

@@ -21,10 +21,8 @@
 import re
 import subprocess
 import sys
-
 from pathlib import Path
 
-
 DEFAULT_LINE_LENGTH: int = 78
 
 
@@ -116,7 +114,7 @@ def main():
         r"^(Merge|Revert|BUG:|COMP:|DOC:|ENH:|PERF:|STYLE:|WIP:)\s", subject_line
     ):
         die(
-            f"""Start ITK commit messages with a standard prefix (and a space):
+            """Start ITK commit messages with a standard prefix (and a space):
   BUG:    - fix for runtime crash or incorrect result
   COMP:   - compiler error or warning fix
   DOC:    - documentation change

Utilities/Hooks/prepare-commit-msg

@@ -18,7 +18,7 @@
 #==========================================================================
 
 egrep-q() {
-  egrep "$@" >/dev/null 2>/dev/null
+  grep -E "$@" >/dev/null 2>/dev/null
 }
 
 # First argument is file containing commit message.
@@ -45,9 +45,9 @@ instructions='#\
 # Follow the first line commit summary with an empty line, then a detailed\
 # description in one or more paragraphs.\
 #' &&
-sed '/^# On branch.*$/ a\
+  sed '/^# On branch.*$/ a\
 '"$instructions"'
 /^# Not currently on any branch.*$/ a\
 '"$instructions"'
-' "$commit_msg" > "$commit_msg_tmp" &&
-mv "$commit_msg_tmp" "$commit_msg"
+' "$commit_msg" >"$commit_msg_tmp" &&
+  mv "$commit_msg_tmp" "$commit_msg"

Utilities/scripts/build-all-latest-wheels.sh

@@ -19,12 +19,30 @@ IPP_BRANCH="python-build-system"
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
-    --platform-env) PLATFORM_ENV="$2"; shift 2 ;;
-    --itk-ref)      ITK_REF="$2"; shift 2 ;;
-    --itk-repo)     ITK_REPO="$2"; shift 2 ;;
-    --ipp-branch)   IPP_BRANCH="$2"; shift 2 ;;
-    --ipp-repo)     IPP_REPO="$2"; shift 2 ;;
-    *) echo "Unknown option: $1"; exit 1 ;;
+  --platform-env)
+    PLATFORM_ENV="$2"
+    shift 2
+    ;;
+  --itk-ref)
+    ITK_REF="$2"
+    shift 2
+    ;;
+  --itk-repo)
+    ITK_REPO="$2"
+    shift 2
+    ;;
+  --ipp-branch)
+    IPP_BRANCH="$2"
+    shift 2
+    ;;
+  --ipp-repo)
+    IPP_REPO="$2"
+    shift 2
+    ;;
+  *)
+    echo "Unknown option: $1"
+    exit 1
+    ;;
   esac
 done
 
@@ -63,7 +81,7 @@ for rc in "${WORKDIR}"/ITK/Modules/Remote/*.remote.cmake; do
     if [ -d "${MODULES_DIR}/${name}/wrapping" ] && [ -f "${MODULES_DIR}/${name}/pyproject.toml" ]; then
       module_list+=("${name}")
     else
-      rm -rf "${MODULES_DIR}/${name}"
+      rm -rf "${MODULES_DIR:?}/${name}"
     fi
   else
     echo "  WARNING: Failed to clone ${name}, skipping"
@@ -111,7 +129,7 @@ done
 echo ""
 echo "=== Build complete ==="
 echo "Wheels: ${DIST_DIR}"
-ls -1 "${DIST_DIR}"/*.whl 2>/dev/null | wc -l
+find "${DIST_DIR}" -maxdepth 1 -name '*.whl' | wc -l
 echo "total wheels produced"
 
 if [ ${#failed_modules[@]} -gt 0 ]; then

Utilities/scripts/build_all_latest_wheels.py

@@ -21,7 +21,9 @@ def run(cmd: list[str], **kwargs) -> subprocess.CompletedProcess:
     return subprocess.run(cmd, check=True, **kwargs)
 
 
-def clone(repo: str, dest: Path, branch: str | None = None, depth: int | None = 1) -> bool:
+def clone(
+    repo: str, dest: Path, branch: str | None = None, depth: int | None = 1
+) -> bool:
     cmd = ["git", "clone"]
     if depth is not None:
         cmd += ["--depth", str(depth)]

pyproject.toml

@@ -33,7 +33,14 @@ bump_map = { "ENH" = "MINOR", "BUG" = "PATCH", "COMP" = "PATCH", "PERF" = "PATCH
 commit_parser = "^(?P<change_type>BUG|COMP|DOC|ENH|PERF|STYLE): (?P<message>.*)"
 changelog_pattern = "^(BUG|COMP|DOC|ENH|PERF|STYLE)?(!)?"
 change_type_map = { "ENH" = "Enhancements", "BUG" = "Bug Fixes", "COMP" = "Build Fixes", "DOC" = "Documentation", "PERF" = "Performance", "STYLE" = "Style" }
-change_type_order = ["Enhancements", "Bug Fixes", "Build Fixes", "Performance", "Documentation", "Style"]
+change_type_order = [
+  "Enhancements",
+  "Bug Fixes",
+  "Build Fixes",
+  "Performance",
+  "Documentation",
+  "Style",
+]
 info = """
 ITK commit message convention: PREFIX: Description
 

scripts/build_python_instance_base.py

@@ -728,9 +728,7 @@ def _update_module_itk_deps(pyproject_path: Path, itk_version: str) -> bool:
             pyproject_data = tomllib.load(f)
 
         # --- Strategy 3: module declares dynamic dependencies -----------------
-        dynamic_fields = (
-            pyproject_data.get("project", {}).get("dynamic", [])
-        )
+        dynamic_fields = pyproject_data.get("project", {}).get("dynamic", [])
         if "dependencies" in dynamic_fields:
             # The module has opted into dynamic dependency resolution.
             # Set ITK_PACKAGE_VERSION in the environment so the
@@ -739,7 +737,7 @@ def _update_module_itk_deps(pyproject_path: Path, itk_version: str) -> bool:
             os.environ["ITK_PACKAGE_VERSION"] = itk_version
             print(
                 f"Strategy 3: {pyproject_path.name} declares "
-                f"dynamic=[\"dependencies\"]; set ITK_PACKAGE_VERSION="
+                f'dynamic=["dependencies"]; set ITK_PACKAGE_VERSION='
                 f"{itk_version} for metadata provider"
             )
             return False  # no file modification needed
@@ -760,9 +758,7 @@ def _update_module_itk_deps(pyproject_path: Path, itk_version: str) -> bool:
             "itk-segmentation",
         )
         _base_pkg_alt = "|".join(re.escape(p) for p in _ITK_BASE_PACKAGES)
-        pattern = re.compile(
-            rf'"({_base_pkg_alt})\s*==\s*[\d]+\.[\d]+\.\*"'
-        )
+        pattern = re.compile(rf'"({_base_pkg_alt})\s*==\s*[\d]+\.[\d]+\.\*"')
 
         # Warn about pinned remote-module cross-deps that may also need
         # attention but should not be auto-rewritten.
@@ -790,6 +786,7 @@ def _update_module_itk_deps(pyproject_path: Path, itk_version: str) -> bool:
             min_floor = itk_version
 
         changed = False
+
         def _replace(m: re.Match) -> str:
             nonlocal changed
             changed = True
@@ -822,9 +819,7 @@ def build_external_module_python_wheel(self):
             itk_ver = self.package_env_config.get("ITK_PACKAGE_VERSION", "")
             if itk_ver:
                 shutil.copy2(module_pyproject, pyproject_orig)
-                deps_rewritten = self._update_module_itk_deps(
-                    module_pyproject, itk_ver
-                )
+                deps_rewritten = self._update_module_itk_deps(module_pyproject, itk_ver)
 
         # Ensure venv tools are first in PATH
         py_exe = str(self.package_env_config["PYTHON_EXECUTABLE"])  # Python3_EXECUTABLE