From 7f79060de07b22eaf9c2c24f1ee1fc5b91745016 Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Thu, 4 Jun 2026 12:26:56 -0700
Subject: [PATCH 1/7] Added commit pre hooks for clang-format + clang-tidy

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 .clang-tidy                 |  42 ++++++++++
 .githooks/pre-commit        | 150 ++++++++++++++++++++++++++++++++++++
 CMakeLists.txt              |   2 +
 cmake/setup-git-hooks.cmake |  23 ++++++
 4 files changed, 217 insertions(+)
 create mode 100644 .clang-tidy
 create mode 100755 .githooks/pre-commit
 create mode 100644 cmake/setup-git-hooks.cmake

diff --git a/.clang-tidy b/.clang-tidy
new file mode 100644
index 00000000..bec9f7d7
--- /dev/null
+++ b/.clang-tidy
@@ -0,0 +1,42 @@
+---
+# AMS clang-tidy configuration
+#
+# Run manually:  clang-tidy -p build/ src/AMSlib/wf/workflow.hpp
+# Integrated via the pre-commit git hook.
+
+Checks: >
+  -*,
+  bugprone-*,
+  -bugprone-easily-swappable-parameters,
+  -bugprone-narrowing-conversions,
+  misc-*,
+  -misc-non-private-member-variables-in-classes,
+  -misc-no-recursion,
+  modernize-*,
+  -modernize-use-trailing-return-type,
+  -modernize-avoid-c-arrays,
+  -modernize-use-nodiscard,
+  performance-*,
+  readability-identifier-naming,
+  readability-redundant-*,
+  readability-simplify-*,
+  readability-braces-around-statements,
+
+WarningsAsErrors: ''
+
+HeaderFilterRegex: 'src/AMSlib/.*'
+
+CheckOptions:
+  - key: readability-identifier-naming.ClassCase
+    value: CamelCase
+  - key: readability-identifier-naming.PrivateMemberPrefix
+    value: '_'
+  - key: readability-identifier-naming.FunctionCase
+    value: camelBack
+  - key: readability-identifier-naming.NamespaceCase
+    value: lower_case
+  - key: modernize-use-override.AllowOverrideAndFinal
+    value: false
+  - key: performance-unnecessary-value-param.AllowedTypes
+    value: 'std::shared_ptr;std::unique_ptr'
+
diff --git a/.githooks/pre-commit b/.githooks/pre-commit
new file mode 100755
index 00000000..9c5c29a4
--- /dev/null
+++ b/.githooks/pre-commit
@@ -0,0 +1,150 @@
+#!/usr/bin/env bash
+#
+# Git pre-commit hook for AMS:
+#   1. Runs clang-format on staged C/C++ files (auto-fixes and re-stages)
+#   2. Runs clang-tidy on staged .cpp files (reports errors, blocks commit)
+#
+# Install (automatic via cmake/setup-git-hooks.cmake):
+#   .githooks/pre-commit
+#
+# Skip temporarily:
+#   git commit --no-verify
+#
+# Skip only clang-tidy (format still runs):
+#   AMS_SKIP_TIDY=1 git commit
+#
+# Requires: clang-format, clang-tidy on PATH
+# clang-tidy requires compile_commands.json (generated by cmake)
+
+set -euo pipefail
+
+# ---------------------------------------------------------------------------
+# Find tools
+# ---------------------------------------------------------------------------
+
+find_tool() {
+  local base="$1"
+  for candidate in "${base}-18" "${base}-17" "${base}-16" "${base}-15" "${base}-14" "${base}"; do
+    if command -v "$candidate" &>/dev/null; then
+      echo "$candidate"
+      return
+    fi
+  done
+}
+
+CLANG_FORMAT=$(find_tool clang-format)
+CLANG_TIDY=$(find_tool clang-tidy)
+
+# File extensions to process
+EXTENSIONS='\.(cpp|hpp|cc|hh|h|c|cxx|hxx)$'
+# clang-tidy only on translation units (not headers)
+TIDY_EXTENSIONS='\.(cpp|cc|c|cxx)$'
+
+# ---------------------------------------------------------------------------
+# Collect staged files
+# ---------------------------------------------------------------------------
+
+STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "$EXTENSIONS" || true)
+
+if [[ -z "$STAGED_FILES" ]]; then
+  exit 0
+fi
+
+# ---------------------------------------------------------------------------
+# Phase 1: clang-format (auto-fix + re-stage)
+# ---------------------------------------------------------------------------
+
+if [[ -n "$CLANG_FORMAT" ]]; then
+  REFORMATTED=0
+
+  for file in $STAGED_FILES; do
+    [[ -f "$file" ]] || continue
+
+    "$CLANG_FORMAT" -i -style=file "$file"
+
+    if ! git diff --quiet -- "$file"; then
+      echo "  clang-format: reformatted $file"
+      git add "$file"
+      REFORMATTED=1
+    fi
+  done
+
+  if [[ "$REFORMATTED" -eq 1 ]]; then
+    echo ""
+    echo "clang-format: reformatted files have been re-staged."
+    echo ""
+  fi
+else
+  echo "WARNING: clang-format not found, skipping format check."
+fi
+
+# ---------------------------------------------------------------------------
+# Phase 2: clang-tidy (lint, block on errors)
+# ---------------------------------------------------------------------------
+
+# Allow skipping clang-tidy via environment variable
+if [[ "${AMS_SKIP_TIDY:-0}" == "1" ]]; then
+  exit 0
+fi
+
+if [[ -z "$CLANG_TIDY" ]]; then
+  echo "WARNING: clang-tidy not found, skipping lint check."
+  exit 0
+fi
+
+# Find compile_commands.json — check common build directory names
+COMPILE_DB=""
+for dir in build build-* cmake-build-* out; do
+  candidate=$(find . -maxdepth 2 -path "./${dir}/compile_commands.json" -print -quit 2>/dev/null)
+  if [[ -n "$candidate" ]]; then
+    COMPILE_DB="$candidate"
+    break
+  fi
+done
+
+if [[ -z "$COMPILE_DB" ]]; then
+  echo "WARNING: compile_commands.json not found, skipping clang-tidy."
+  echo "         Run cmake first to generate it."
+  exit 0
+fi
+
+COMPILE_DB_DIR=$(dirname "$COMPILE_DB")
+
+# Filter to translation units only
+TIDY_FILES=$(echo "$STAGED_FILES" | grep -E "$TIDY_EXTENSIONS" || true)
+
+if [[ -z "$TIDY_FILES" ]]; then
+  exit 0
+fi
+
+TIDY_ERRORS=0
+
+for file in $TIDY_FILES; do
+  [[ -f "$file" ]] || continue
+
+  # Only run on files that appear in compile_commands.json
+  # (headers and test files outside the build may not be there)
+  if ! grep -q "\"file\".*$(basename "$file")\"" "$COMPILE_DB" 2>/dev/null; then
+    continue
+  fi
+
+  echo "  clang-tidy: checking $file"
+
+  if ! "$CLANG_TIDY" -p "$COMPILE_DB_DIR" --quiet "$file" 2>&1 | \
+       grep -v "^$" | grep -v "warnings generated" ; then
+    : # clean
+  else
+    TIDY_ERRORS=1
+  fi
+done
+
+if [[ "$TIDY_ERRORS" -eq 1 ]]; then
+  echo ""
+  echo "clang-tidy: issues found (see above)."
+  echo "Fix them, or skip with: AMS_SKIP_TIDY=1 git commit"
+  echo "Or skip all hooks with: git commit --no-verify"
+  exit 1
+fi
+
+exit 0
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
index a04fd71d..fb71fd02 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,6 +14,8 @@ cmake_policy(SET CMP0074 NEW)
 
 project(AMS VERSION 0.1.1 LANGUAGES CXX C)
 
+# We insall AMS githook to run clang-format etc when commiting
+include(cmake/setup-git-hooks.cmake)
 
 # NOTE: This may break some of our integrations with the applications. But flux requires > C++20, RMQ requires C++17 and although AMS does not have 
 # any restrictions on the CXX standard the application may impose those. The solution would be to compile RMQ with an older GCC version  (8) and 
diff --git a/cmake/setup-git-hooks.cmake b/cmake/setup-git-hooks.cmake
new file mode 100644
index 00000000..a342cc65
--- /dev/null
+++ b/cmake/setup-git-hooks.cmake
@@ -0,0 +1,23 @@
+# Automatically configure git hooks when the project is configured.
+# Place in cmake/setup-git-hooks.cmake and include from the top-level CMakeLists.txt.
+
+find_package(Git QUIET)
+
+if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
+  # Only set if not already configured (respects developer overrides)
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} config --get core.hooksPath
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE _current_hooks_path
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    RESULT_VARIABLE _rc
+  )
+
+  if(NOT _rc EQUAL 0 OR NOT _current_hooks_path STREQUAL ".githooks")
+    message(STATUS "Setting git hooks path to .githooks/")
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} config core.hooksPath .githooks
+      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    )
+  endif()
+endif()

From 754e13a85490f79e3f68b8c75b266466f9ec29db Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Thu, 4 Jun 2026 15:38:52 -0700
Subject: [PATCH 2/7] Fixed clang tidy support

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 .clang-tidy          |  5 +----
 .githooks/pre-commit | 34 +++++++++++++++++++++-------------
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index bec9f7d7..e4269c07 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -17,10 +17,7 @@ Checks: >
   -modernize-avoid-c-arrays,
   -modernize-use-nodiscard,
   performance-*,
-  readability-identifier-naming,
-  readability-redundant-*,
-  readability-simplify-*,
-  readability-braces-around-statements,
+  readability-identifier-naming
 
 WarningsAsErrors: ''
 
diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index 9c5c29a4..1be05145 100755
--- a/.githooks/pre-commit
+++ b/.githooks/pre-commit
@@ -13,6 +13,9 @@
 # Skip only clang-tidy (format still runs):
 #   AMS_SKIP_TIDY=1 git commit
 #
+# Specify build directory (for compile_commands.json):
+#   export AMS_BUILD_DIR=/path/to/build
+#
 # Requires: clang-format, clang-tidy on PATH
 # clang-tidy requires compile_commands.json (generated by cmake)
 
@@ -38,13 +41,14 @@ CLANG_TIDY=$(find_tool clang-tidy)
 # File extensions to process
 EXTENSIONS='\.(cpp|hpp|cc|hh|h|c|cxx|hxx)$'
 # clang-tidy only on translation units (not headers)
-TIDY_EXTENSIONS='\.(cpp|cc|c|cxx)$'
+TIDY_EXTENSIONS='\.(cpp|cc|c|cxx|hpp|h|hh|hxx)$'
 
 # ---------------------------------------------------------------------------
 # Collect staged files
 # ---------------------------------------------------------------------------
 
-STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "$EXTENSIONS" || true)
+REPO_ROOT=$(git rev-parse --show-toplevel)
+STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "$EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
 
 if [[ -z "$STAGED_FILES" ]]; then
   exit 0
@@ -92,19 +96,25 @@ if [[ -z "$CLANG_TIDY" ]]; then
   exit 0
 fi
 
-# Find compile_commands.json — check common build directory names
+# Find compile_commands.json
+# Priority: AMS_BUILD_DIR env var > common build directory names
 COMPILE_DB=""
-for dir in build build-* cmake-build-* out; do
-  candidate=$(find . -maxdepth 2 -path "./${dir}/compile_commands.json" -print -quit 2>/dev/null)
-  if [[ -n "$candidate" ]]; then
-    COMPILE_DB="$candidate"
-    break
-  fi
-done
+
+if [[ -n "${AMS_BUILD_DIR:-}" && -f "${AMS_BUILD_DIR}/compile_commands.json" ]]; then
+  COMPILE_DB="${AMS_BUILD_DIR}/compile_commands.json"
+else
+  for dir in build build-* cmake-build-* out; do
+    candidate=$(find . -maxdepth 2 -path "./${dir}/compile_commands.json" -print -quit 2>/dev/null)
+    if [[ -n "$candidate" ]]; then
+      COMPILE_DB="$candidate"
+      break
+    fi
+  done
+fi
 
 if [[ -z "$COMPILE_DB" ]]; then
   echo "WARNING: compile_commands.json not found, skipping clang-tidy."
-  echo "         Run cmake first to generate it."
+  echo "         Run cmake first, or set AMS_BUILD_DIR to your build directory."
   exit 0
 fi
 
@@ -120,8 +130,6 @@ fi
 TIDY_ERRORS=0
 
 for file in $TIDY_FILES; do
-  [[ -f "$file" ]] || continue
-
   # Only run on files that appear in compile_commands.json
   # (headers and test files outside the build may not be there)
   if ! grep -q "\"file\".*$(basename "$file")\"" "$COMPILE_DB" 2>/dev/null; then

From d399cd736bd828e6e03350f8a401427bccbd421e Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Thu, 4 Jun 2026 17:36:09 -0700
Subject: [PATCH 3/7] Added python linting to the pre-hook (ruff-based)

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 .githooks/pre-commit | 143 +++++++++++++++++++++++++++----------------
 pyproject.toml       |  60 ++++--------------
 2 files changed, 104 insertions(+), 99 deletions(-)

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index 1be05145..ce35de63 100755
--- a/.githooks/pre-commit
+++ b/.githooks/pre-commit
@@ -1,8 +1,9 @@
 #!/usr/bin/env bash
 #
 # Git pre-commit hook for AMS:
-#   1. Runs clang-format on staged C/C++ files (auto-fixes and re-stages)
-#   2. Runs clang-tidy on staged .cpp files (reports errors, blocks commit)
+#   Phase 1: clang-format on staged C/C++ files (auto-fixes, re-stages)
+#   Phase 2: ruff on staged Python files (auto-fixes, re-stages)
+#   Phase 3: clang-tidy on staged .cpp files (reports errors, blocks commit)
 #
 # Install (automatic via cmake/setup-git-hooks.cmake):
 #   .githooks/pre-commit
@@ -10,21 +11,17 @@
 # Skip temporarily:
 #   git commit --no-verify
 #
-# Skip only clang-tidy (format still runs):
+# Skip only clang-tidy (format + ruff still run):
 #   AMS_SKIP_TIDY=1 git commit
 #
 # Specify build directory (for compile_commands.json):
 #   export AMS_BUILD_DIR=/path/to/build
 #
-# Requires: clang-format, clang-tidy on PATH
+# Requires: clang-format, clang-tidy, ruff on PATH
 # clang-tidy requires compile_commands.json (generated by cmake)
 
 set -euo pipefail
 
-# ---------------------------------------------------------------------------
-# Find tools
-# ---------------------------------------------------------------------------
-
 find_tool() {
   local base="$1"
   for candidate in "${base}-18" "${base}-17" "${base}-16" "${base}-15" "${base}-14" "${base}"; do
@@ -37,54 +34,99 @@ find_tool() {
 
 CLANG_FORMAT=$(find_tool clang-format)
 CLANG_TIDY=$(find_tool clang-tidy)
+RUFF=$(command -v ruff 2>/dev/null || true)
 
-# File extensions to process
-EXTENSIONS='\.(cpp|hpp|cc|hh|h|c|cxx|hxx)$'
-# clang-tidy only on translation units (not headers)
-TIDY_EXTENSIONS='\.(cpp|cc|c|cxx|hpp|h|hh|hxx)$'
-
-# ---------------------------------------------------------------------------
-# Collect staged files
-# ---------------------------------------------------------------------------
+CPP_EXTENSIONS='\.(cpp|hpp|cc|hh|h|c|cxx|hxx)$'
+TIDY_EXTENSIONS='\.(cpp|cc|c|cxx)$'
+PY_EXTENSIONS='\.py$'
 
 REPO_ROOT=$(git rev-parse --show-toplevel)
-STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "$EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
 
-if [[ -z "$STAGED_FILES" ]]; then
+ALL_STAGED=$(git diff --cached --name-only --diff-filter=ACM || true)
+
+CPP_FILES=$(echo "$ALL_STAGED" | grep -E "$CPP_EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
+PY_FILES=$(echo "$ALL_STAGED" | grep -E "$PY_EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
+
+if [[ -z "$CPP_FILES" && -z "$PY_FILES" ]]; then
   exit 0
 fi
 
-# ---------------------------------------------------------------------------
-# Phase 1: clang-format (auto-fix + re-stage)
-# ---------------------------------------------------------------------------
+if [[ -n "$CPP_FILES" ]]; then
+  if [[ -n "$CLANG_FORMAT" ]]; then
+    REFORMATTED=0
 
-if [[ -n "$CLANG_FORMAT" ]]; then
-  REFORMATTED=0
+    for file in $CPP_FILES; do
+      "$CLANG_FORMAT" -i -style=file "$file"
 
-  for file in $STAGED_FILES; do
-    [[ -f "$file" ]] || continue
+      if ! git diff --quiet -- "$file"; then
+        echo "  clang-format: reformatted $file"
+        git add "$file"
+        REFORMATTED=1
+      fi
+    done
 
-    "$CLANG_FORMAT" -i -style=file "$file"
+    if [[ "$REFORMATTED" -eq 1 ]]; then
+      echo ""
+      echo "clang-format: reformatted files have been re-staged."
+      echo ""
+    fi
+  else
+    echo "WARNING: clang-format not found, skipping C/C++ format check."
+  fi
+fi
 
-    if ! git diff --quiet -- "$file"; then
-      echo "  clang-format: reformatted $file"
-      git add "$file"
-      REFORMATTED=1
+if [[ -n "$PY_FILES" ]]; then
+  if [[ -n "$RUFF" ]]; then
+    PY_REFORMATTED=0
+
+    # Format (equivalent to black)
+    for file in $PY_FILES; do
+      "$RUFF" format --quiet "$file"
+    done
+
+    # Lint with auto-fix (import sorting, safe fixes)
+    for file in $PY_FILES; do
+      "$RUFF" check --fix --quiet "$file" 2>/dev/null || true
+    done
+
+    # Re-stage any modified files
+    for file in $PY_FILES; do
+      if ! git diff --quiet -- "$file"; then
+        echo "  ruff: reformatted $file"
+        git add "$file"
+        PY_REFORMATTED=1
+      fi
+    done
+
+    if [[ "$PY_REFORMATTED" -eq 1 ]]; then
+      echo ""
+      echo "ruff: reformatted files have been re-staged."
+      echo ""
     fi
-  done
 
-  if [[ "$REFORMATTED" -eq 1 ]]; then
-    echo ""
-    echo "clang-format: reformatted files have been re-staged."
-    echo ""
+    # Lint check (report remaining issues — unfixable ones)
+    RUFF_ERRORS=0
+    for file in $PY_FILES; do
+      if ! "$RUFF" check --quiet "$file" 2>/dev/null; then
+        RUFF_ERRORS=1
+      fi
+    done
+
+    if [[ "$RUFF_ERRORS" -eq 1 ]]; then
+      echo ""
+      echo "ruff: lint errors found (see above). Fix them before committing."
+      echo "Or skip all hooks with: git commit --no-verify"
+      exit 1
+    fi
+  else
+    echo "WARNING: ruff not found, skipping Python format/lint check."
+    echo "         Install with: pip install ruff"
   fi
-else
-  echo "WARNING: clang-format not found, skipping format check."
 fi
 
-# ---------------------------------------------------------------------------
-# Phase 2: clang-tidy (lint, block on errors)
-# ---------------------------------------------------------------------------
+if [[ -z "$CPP_FILES" ]]; then
+  exit 0
+fi
 
 # Allow skipping clang-tidy via environment variable
 if [[ "${AMS_SKIP_TIDY:-0}" == "1" ]]; then
@@ -92,19 +134,18 @@ if [[ "${AMS_SKIP_TIDY:-0}" == "1" ]]; then
 fi
 
 if [[ -z "$CLANG_TIDY" ]]; then
-  echo "WARNING: clang-tidy not found, skipping lint check."
+  echo "WARNING: clang-tidy not found, skipping C++ lint check."
   exit 0
 fi
 
 # Find compile_commands.json
-# Priority: AMS_BUILD_DIR env var > common build directory names
 COMPILE_DB=""
 
 if [[ -n "${AMS_BUILD_DIR:-}" && -f "${AMS_BUILD_DIR}/compile_commands.json" ]]; then
   COMPILE_DB="${AMS_BUILD_DIR}/compile_commands.json"
 else
   for dir in build build-* cmake-build-* out; do
-    candidate=$(find . -maxdepth 2 -path "./${dir}/compile_commands.json" -print -quit 2>/dev/null)
+    candidate=$(find "${REPO_ROOT}" -maxdepth 2 -path "${REPO_ROOT}/${dir}/compile_commands.json" -print -quit 2>/dev/null)
     if [[ -n "$candidate" ]]; then
       COMPILE_DB="$candidate"
       break
@@ -121,7 +162,7 @@ fi
 COMPILE_DB_DIR=$(dirname "$COMPILE_DB")
 
 # Filter to translation units only
-TIDY_FILES=$(echo "$STAGED_FILES" | grep -E "$TIDY_EXTENSIONS" || true)
+TIDY_FILES=$(echo "$CPP_FILES" | grep -E "$TIDY_EXTENSIONS" || true)
 
 if [[ -z "$TIDY_FILES" ]]; then
   exit 0
@@ -131,28 +172,26 @@ TIDY_ERRORS=0
 
 for file in $TIDY_FILES; do
   # Only run on files that appear in compile_commands.json
-  # (headers and test files outside the build may not be there)
   if ! grep -q "\"file\".*$(basename "$file")\"" "$COMPILE_DB" 2>/dev/null; then
     continue
   fi
 
   echo "  clang-tidy: checking $file"
 
-  if ! "$CLANG_TIDY" -p "$COMPILE_DB_DIR" --quiet "$file" 2>&1 | \
-       grep -v "^$" | grep -v "warnings generated" ; then
-    : # clean
-  else
+  # clang-tidy exits non-zero when WarningsAsErrors checks fire.
+  # Warnings (not promoted to errors) print but don't affect the exit code.
+  if ! "$CLANG_TIDY" -p "$COMPILE_DB_DIR" --quiet "$file"; then
     TIDY_ERRORS=1
   fi
 done
 
 if [[ "$TIDY_ERRORS" -eq 1 ]]; then
   echo ""
-  echo "clang-tidy: issues found (see above)."
-  echo "Fix them, or skip with: AMS_SKIP_TIDY=1 git commit"
+  echo "clang-tidy: errors found (see above)."
+  echo "Warnings are informational and do not block the commit."
+  echo "Fix errors, or skip with: AMS_SKIP_TIDY=1 git commit"
   echo "Or skip all hooks with: git commit --no-verify"
   exit 1
 fi
 
 exit 0
-
diff --git a/pyproject.toml b/pyproject.toml
index 4fa48839..4a2a949b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,6 +32,7 @@ classifiers = [
   "Programming Language :: Python :: 3 :: Only",
 ]
 dependencies = [
+  "ruff",
   "h5py",
   "argparse",
   "SQLAlchemy",
@@ -56,51 +57,11 @@ AMSDeploy = "ams_wf.AMSDeploy:main"
 package-dir = {"" = "src/AMSWorkflow"}
 packages = ["ams_wf", "ams"]
 
-# Black formatting
-[tool.black]
-line-length = 120
-include = '\.pyi?$'
-exclude = '''
-/(
-      .eggs         # exclude a few common directories in the
-    | .git          # root of the project
-    | .hg
-    | .mypy_cache
-    | .tox
-    | venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-'''
-
-# iSort
-[tool.isort]
-profile = "black"
-line_length = 120
-multi_line_output = 3
-include_trailing_comma = true
-virtual_env = "venv"
-
-# flake8
-[tool.flake8]
-ignore = ["E501", "W503", "E226", "BLK100", "E203"]
-max-line-length = 120
-exclude = [
-    # No need to traverse our git directory
-    ".git",
-    # There's no value in checking cache directories
-    "__pycache__",
-    "*.egg-info",
-    "build"
-]
 # E501: Line too long
 # W503: Line break occurred before binary operator
 # E226: Missing white space around arithmetic operator
-
 [tool.ruff]
-lint.ignore = ["E501", "E226", "E203"]
+line-length = 120
 show-fixes = true
 exclude = [
   ".git",
@@ -108,10 +69,15 @@ exclude = [
   "*.egg-info",
   "build"
 ]
-# change the default line length number or characters.
-line-length = 120
-lint.select = ['E', 'F', 'W', 'A', 'PLC', 'PLE', 'PLW', 'I', 'N', 'Q']
 
-[tool.yapf]
-ignore = ["E501", "W503", "E226", "BLK100", "E203"]
-column_limit = 120
+[tool.ruff.lint]
+select = ['E', 'F', 'W', 'A', 'PLC', 'PLE', 'PLW', 'I', 'N', 'Q', 'B', 'UP', 'SIM', 'RUF']
+ignore = ["E501", "E226", "E203"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["ams", "ams_wf"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+

From 430bcad00ec27e65cd98a5087a80c63565836e9e Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Wed, 10 Jun 2026 10:33:11 -0700
Subject: [PATCH 4/7] Removed installing hook in CMake and made ruff a dev
 dependencies

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 CMakeLists.txt              |  3 ---
 cmake/setup-git-hooks.cmake | 23 -----------------------
 pyproject.toml              |  6 +++++-
 3 files changed, 5 insertions(+), 27 deletions(-)
 delete mode 100644 cmake/setup-git-hooks.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fb71fd02..e43f0c7b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,9 +14,6 @@ cmake_policy(SET CMP0074 NEW)
 
 project(AMS VERSION 0.1.1 LANGUAGES CXX C)
 
-# We insall AMS githook to run clang-format etc when commiting
-include(cmake/setup-git-hooks.cmake)
-
 # NOTE: This may break some of our integrations with the applications. But flux requires > C++20, RMQ requires C++17 and although AMS does not have 
 # any restrictions on the CXX standard the application may impose those. The solution would be to compile RMQ with an older GCC version  (8) and 
 # have flux to be an external of the system environment
diff --git a/cmake/setup-git-hooks.cmake b/cmake/setup-git-hooks.cmake
deleted file mode 100644
index a342cc65..00000000
--- a/cmake/setup-git-hooks.cmake
+++ /dev/null
@@ -1,23 +0,0 @@
-# Automatically configure git hooks when the project is configured.
-# Place in cmake/setup-git-hooks.cmake and include from the top-level CMakeLists.txt.
-
-find_package(Git QUIET)
-
-if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
-  # Only set if not already configured (respects developer overrides)
-  execute_process(
-    COMMAND ${GIT_EXECUTABLE} config --get core.hooksPath
-    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-    OUTPUT_VARIABLE _current_hooks_path
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-    RESULT_VARIABLE _rc
-  )
-
-  if(NOT _rc EQUAL 0 OR NOT _current_hooks_path STREQUAL ".githooks")
-    message(STATUS "Setting git hooks path to .githooks/")
-    execute_process(
-      COMMAND ${GIT_EXECUTABLE} config core.hooksPath .githooks
-      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-    )
-  endif()
-endif()
diff --git a/pyproject.toml b/pyproject.toml
index 4a2a949b..d940a7b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,6 @@ classifiers = [
   "Programming Language :: Python :: 3 :: Only",
 ]
 dependencies = [
-  "ruff",
   "h5py",
   "argparse",
   "SQLAlchemy",
@@ -42,6 +41,11 @@ dependencies = [
   "flux-python>=0.75.0"
 ]
 
+[project.optional-dependencies]
+dev = [
+  "ruff",
+]
+
 [project.scripts]
 AMSBroker = "ams_wf.AMSBroker:main"
 AMSDBStage = "ams_wf.AMSDBStage:main"

From cbaf3e0620dba8405417dd7e185240789e436ebf Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Tue, 23 Jun 2026 13:26:27 -0700
Subject: [PATCH 5/7] Adding an explicit scripts to reformat the codebase

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 .githooks/pre-commit        | 181 +----------------
 scripts/run-code-quality.sh | 394 ++++++++++++++++++++++++++++++++++++
 2 files changed, 403 insertions(+), 172 deletions(-)
 create mode 100755 scripts/run-code-quality.sh

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index ce35de63..f2320852 100755
--- a/.githooks/pre-commit
+++ b/.githooks/pre-commit
@@ -1,9 +1,7 @@
 #!/usr/bin/env bash
 #
 # Git pre-commit hook for AMS:
-#   Phase 1: clang-format on staged C/C++ files (auto-fixes, re-stages)
-#   Phase 2: ruff on staged Python files (auto-fixes, re-stages)
-#   Phase 3: clang-tidy on staged .cpp files (reports errors, blocks commit)
+#   Runs non-mutating checks on staged C/C++ and Python files.
 #
 # Install (automatic via cmake/setup-git-hooks.cmake):
 #   .githooks/pre-commit
@@ -11,187 +9,26 @@
 # Skip temporarily:
 #   git commit --no-verify
 #
-# Skip only clang-tidy (format + ruff still run):
+# Skip only clang-tidy:
 #   AMS_SKIP_TIDY=1 git commit
 #
 # Specify build directory (for compile_commands.json):
 #   export AMS_BUILD_DIR=/path/to/build
 #
+# Apply fixes explicitly:
+#   scripts/run-code-quality.sh --fix
+#
 # Requires: clang-format, clang-tidy, ruff on PATH
 # clang-tidy requires compile_commands.json (generated by cmake)
 
 set -euo pipefail
 
-find_tool() {
-  local base="$1"
-  for candidate in "${base}-18" "${base}-17" "${base}-16" "${base}-15" "${base}-14" "${base}"; do
-    if command -v "$candidate" &>/dev/null; then
-      echo "$candidate"
-      return
-    fi
-  done
-}
-
-CLANG_FORMAT=$(find_tool clang-format)
-CLANG_TIDY=$(find_tool clang-tidy)
-RUFF=$(command -v ruff 2>/dev/null || true)
-
-CPP_EXTENSIONS='\.(cpp|hpp|cc|hh|h|c|cxx|hxx)$'
-TIDY_EXTENSIONS='\.(cpp|cc|c|cxx)$'
-PY_EXTENSIONS='\.py$'
-
 REPO_ROOT=$(git rev-parse --show-toplevel)
+SCRIPT="${REPO_ROOT}/scripts/run-code-quality.sh"
 
-ALL_STAGED=$(git diff --cached --name-only --diff-filter=ACM || true)
-
-CPP_FILES=$(echo "$ALL_STAGED" | grep -E "$CPP_EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
-PY_FILES=$(echo "$ALL_STAGED" | grep -E "$PY_EXTENSIONS" | sed "s|^|${REPO_ROOT}/|" || true)
-
-if [[ -z "$CPP_FILES" && -z "$PY_FILES" ]]; then
-  exit 0
-fi
-
-if [[ -n "$CPP_FILES" ]]; then
-  if [[ -n "$CLANG_FORMAT" ]]; then
-    REFORMATTED=0
-
-    for file in $CPP_FILES; do
-      "$CLANG_FORMAT" -i -style=file "$file"
-
-      if ! git diff --quiet -- "$file"; then
-        echo "  clang-format: reformatted $file"
-        git add "$file"
-        REFORMATTED=1
-      fi
-    done
-
-    if [[ "$REFORMATTED" -eq 1 ]]; then
-      echo ""
-      echo "clang-format: reformatted files have been re-staged."
-      echo ""
-    fi
-  else
-    echo "WARNING: clang-format not found, skipping C/C++ format check."
-  fi
-fi
-
-if [[ -n "$PY_FILES" ]]; then
-  if [[ -n "$RUFF" ]]; then
-    PY_REFORMATTED=0
-
-    # Format (equivalent to black)
-    for file in $PY_FILES; do
-      "$RUFF" format --quiet "$file"
-    done
-
-    # Lint with auto-fix (import sorting, safe fixes)
-    for file in $PY_FILES; do
-      "$RUFF" check --fix --quiet "$file" 2>/dev/null || true
-    done
-
-    # Re-stage any modified files
-    for file in $PY_FILES; do
-      if ! git diff --quiet -- "$file"; then
-        echo "  ruff: reformatted $file"
-        git add "$file"
-        PY_REFORMATTED=1
-      fi
-    done
-
-    if [[ "$PY_REFORMATTED" -eq 1 ]]; then
-      echo ""
-      echo "ruff: reformatted files have been re-staged."
-      echo ""
-    fi
-
-    # Lint check (report remaining issues — unfixable ones)
-    RUFF_ERRORS=0
-    for file in $PY_FILES; do
-      if ! "$RUFF" check --quiet "$file" 2>/dev/null; then
-        RUFF_ERRORS=1
-      fi
-    done
-
-    if [[ "$RUFF_ERRORS" -eq 1 ]]; then
-      echo ""
-      echo "ruff: lint errors found (see above). Fix them before committing."
-      echo "Or skip all hooks with: git commit --no-verify"
-      exit 1
-    fi
-  else
-    echo "WARNING: ruff not found, skipping Python format/lint check."
-    echo "         Install with: pip install ruff"
-  fi
-fi
-
-if [[ -z "$CPP_FILES" ]]; then
-  exit 0
-fi
-
-# Allow skipping clang-tidy via environment variable
-if [[ "${AMS_SKIP_TIDY:-0}" == "1" ]]; then
-  exit 0
-fi
-
-if [[ -z "$CLANG_TIDY" ]]; then
-  echo "WARNING: clang-tidy not found, skipping C++ lint check."
-  exit 0
-fi
-
-# Find compile_commands.json
-COMPILE_DB=""
-
-if [[ -n "${AMS_BUILD_DIR:-}" && -f "${AMS_BUILD_DIR}/compile_commands.json" ]]; then
-  COMPILE_DB="${AMS_BUILD_DIR}/compile_commands.json"
-else
-  for dir in build build-* cmake-build-* out; do
-    candidate=$(find "${REPO_ROOT}" -maxdepth 2 -path "${REPO_ROOT}/${dir}/compile_commands.json" -print -quit 2>/dev/null)
-    if [[ -n "$candidate" ]]; then
-      COMPILE_DB="$candidate"
-      break
-    fi
-  done
-fi
-
-if [[ -z "$COMPILE_DB" ]]; then
-  echo "WARNING: compile_commands.json not found, skipping clang-tidy."
-  echo "         Run cmake first, or set AMS_BUILD_DIR to your build directory."
-  exit 0
-fi
-
-COMPILE_DB_DIR=$(dirname "$COMPILE_DB")
-
-# Filter to translation units only
-TIDY_FILES=$(echo "$CPP_FILES" | grep -E "$TIDY_EXTENSIONS" || true)
-
-if [[ -z "$TIDY_FILES" ]]; then
-  exit 0
-fi
-
-TIDY_ERRORS=0
-
-for file in $TIDY_FILES; do
-  # Only run on files that appear in compile_commands.json
-  if ! grep -q "\"file\".*$(basename "$file")\"" "$COMPILE_DB" 2>/dev/null; then
-    continue
-  fi
-
-  echo "  clang-tidy: checking $file"
-
-  # clang-tidy exits non-zero when WarningsAsErrors checks fire.
-  # Warnings (not promoted to errors) print but don't affect the exit code.
-  if ! "$CLANG_TIDY" -p "$COMPILE_DB_DIR" --quiet "$file"; then
-    TIDY_ERRORS=1
-  fi
-done
-
-if [[ "$TIDY_ERRORS" -eq 1 ]]; then
-  echo ""
-  echo "clang-tidy: errors found (see above)."
-  echo "Warnings are informational and do not block the commit."
-  echo "Fix errors, or skip with: AMS_SKIP_TIDY=1 git commit"
-  echo "Or skip all hooks with: git commit --no-verify"
+if [[ ! -f "$SCRIPT" ]]; then
+  echo "ERROR: missing helper script: $SCRIPT"
   exit 1
 fi
 
-exit 0
+exec bash "$SCRIPT" --check --staged --fail-on-partial
diff --git a/scripts/run-code-quality.sh b/scripts/run-code-quality.sh
new file mode 100755
index 00000000..a7cd40eb
--- /dev/null
+++ b/scripts/run-code-quality.sh
@@ -0,0 +1,394 @@
+#!/usr/bin/env bash
+# 
+# Copyright 2021-2026 Lawrence Livermore National Security, LLC and other
+# AMSLib Project Developers
+#
+# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
+#
+# Developer utility for AMS code-quality checks and explicit fixes.
+#
+# Examples:
+#   scripts/run-code-quality.sh
+#   scripts/run-code-quality.sh --fix
+#   scripts/run-code-quality.sh --ruff --fix
+#   scripts/run-code-quality.sh --clang-format --clang-tidy src tests
+#   scripts/run-code-quality.sh --check --staged
+
+set -euo pipefail
+
+usage() {
+  cat <<'EOF'
+Usage: scripts/run-code-quality.sh [options] [paths...]
+
+Run code-quality tools across the repository or a selected subset of files.
+By default, this runs check-only mode on tracked files under:
+  src tests examples tools scripts .githooks
+
+Options:
+  --check              Run non-mutating checks only (default)
+  --fix                Apply clang-format and ruff fixes explicitly
+  --staged             Operate on staged files instead of the full codebase
+  --fail-on-partial    Refuse staged runs when relevant files also have unstaged changes
+  --ruff               Run ruff format/check on Python files
+  --clang-format       Run clang-format on C/C++ files
+  --clang-tidy         Run clang-tidy on C/C++ translation units
+  --build-dir DIR      Build directory containing compile_commands.json
+  --help               Show this help text
+
+Notes:
+  - If no tool is selected, the script runs ruff, clang-format, and clang-tidy.
+  - --fix does not apply clang-tidy fixes; clang-tidy remains check-only.
+  - AMS_SKIP_TIDY=1 skips clang-tidy.
+  - AMS_BUILD_DIR can be used instead of --build-dir.
+EOF
+}
+
+find_tool() {
+  local base="$1"
+  local candidate=""
+
+  for candidate in "${base}-18" "${base}-17" "${base}-16" "${base}-15" "${base}-14" "${base}"; do
+    if command -v "$candidate" >/dev/null 2>&1; then
+      printf '%s\n' "$candidate"
+      return 0
+    fi
+  done
+
+  return 1
+}
+
+warn() {
+  printf 'WARNING: %s\n' "$*"
+}
+
+die() {
+  printf 'ERROR: %s\n' "$*" >&2
+  exit 1
+}
+
+append_if_exists() {
+  local path="$1"
+
+  if [[ -e "$path" ]]; then
+    RELEVANT_FILES+=("$path")
+  fi
+}
+
+is_cpp_file() {
+  local path="$1"
+  [[ "$path" =~ \.(cpp|hpp|cc|hh|h|c|cxx|hxx)$ ]]
+}
+
+is_tidy_file() {
+  local path="$1"
+  [[ "$path" =~ \.(cpp|cc|c|cxx)$ ]]
+}
+
+is_python_file() {
+  local path="$1"
+  [[ "$path" =~ \.py$ ]]
+}
+
+collect_files() {
+  local target=""
+
+  if [[ "$USE_STAGED" -eq 1 ]]; then
+    while IFS= read -r -d '' target; do
+      append_if_exists "$target"
+    done < <(git diff --cached --name-only -z --diff-filter=ACM -- "${TARGETS[@]}")
+    return
+  fi
+
+  while IFS= read -r -d '' target; do
+    append_if_exists "$target"
+  done < <(git ls-files -z -- "${TARGETS[@]}")
+}
+
+detect_partial_staging() {
+  local file=""
+  local partial_files=()
+
+  [[ "$USE_STAGED" -eq 1 && "$FAIL_ON_PARTIAL" -eq 1 ]] || return 0
+
+  for file in "${RELEVANT_FILES[@]}"; do
+    if ! git diff --quiet -- "$file"; then
+      partial_files+=("$file")
+    fi
+  done
+
+  if [[ "${#partial_files[@]}" -eq 0 ]]; then
+    return 0
+  fi
+
+  printf 'ERROR: refusing to run on partially staged files.\n' >&2
+  printf 'Stage or stash the remaining edits first:\n' >&2
+  for file in "${partial_files[@]}"; do
+    printf '  %s\n' "$file" >&2
+  done
+  return 1
+}
+
+find_compile_db() {
+  local candidate=""
+  local dir=""
+
+  if [[ -n "$BUILD_DIR" && -f "$BUILD_DIR/compile_commands.json" ]]; then
+    printf '%s\n' "$BUILD_DIR/compile_commands.json"
+    return 0
+  fi
+
+  for dir in build build-* cmake-build-* out; do
+    while IFS= read -r candidate; do
+      if [[ -n "$candidate" ]]; then
+        printf '%s\n' "$candidate"
+        return 0
+      fi
+    done < <(find "$REPO_ROOT" -maxdepth 2 -path "$REPO_ROOT/$dir/compile_commands.json" -print 2>/dev/null)
+  done
+
+  return 1
+}
+
+run_clang_format() {
+  local file=""
+  local failed=0
+
+  if [[ "${#CPP_FILES[@]}" -eq 0 ]]; then
+    return 0
+  fi
+
+  if [[ -z "$CLANG_FORMAT" ]]; then
+    warn "clang-format not found, skipping C/C++ formatting."
+    return 0
+  fi
+
+  if [[ "$APPLY_FIXES" -eq 1 ]]; then
+    for file in "${CPP_FILES[@]}"; do
+      "$CLANG_FORMAT" -i -style=file "$file"
+      printf 'clang-format: updated %s\n' "$file"
+    done
+    return 0
+  fi
+
+  for file in "${CPP_FILES[@]}"; do
+    if ! "$CLANG_FORMAT" --dry-run -Werror -style=file "$file"; then
+      failed=1
+    fi
+  done
+
+  if [[ "$failed" -eq 1 ]]; then
+    printf '\nclang-format: formatting issues found.\n'
+    printf 'Apply them explicitly with: scripts/run-code-quality.sh --clang-format --fix\n'
+    return 1
+  fi
+
+  return 0
+}
+
+run_ruff() {
+  local failed=0
+
+  if [[ "${#PY_FILES[@]}" -eq 0 ]]; then
+    return 0
+  fi
+
+  if [[ -z "$RUFF" ]]; then
+    warn "ruff not found, skipping Python checks."
+    warn "Install with: pip install ruff"
+    return 0
+  fi
+
+  if [[ "$APPLY_FIXES" -eq 1 ]]; then
+    "$RUFF" format "${PY_FILES[@]}"
+    "$RUFF" check --fix "${PY_FILES[@]}" || true
+  else
+    if ! "$RUFF" format --check "${PY_FILES[@]}"; then
+      failed=1
+    fi
+  fi
+
+  if ! "$RUFF" check "${PY_FILES[@]}"; then
+    failed=1
+  fi
+
+  if [[ "$failed" -eq 1 ]]; then
+    printf '\nruff: Python formatting or lint issues found.\n'
+    printf 'Apply fixes explicitly with: scripts/run-code-quality.sh --ruff --fix\n'
+    return 1
+  fi
+
+  return 0
+}
+
+run_clang_tidy() {
+  local compile_db=""
+  local compile_db_dir=""
+  local file=""
+  local failed=0
+  local rel_file=""
+  local abs_file=""
+
+  if [[ "$SKIP_TIDY" -eq 1 || "${#TIDY_FILES[@]}" -eq 0 ]]; then
+    return 0
+  fi
+
+  if [[ -z "$CLANG_TIDY" ]]; then
+    warn "clang-tidy not found, skipping C/C++ lint checks."
+    return 0
+  fi
+
+  if ! compile_db=$(find_compile_db); then
+    warn "compile_commands.json not found, skipping clang-tidy."
+    warn "Run cmake first, or set AMS_BUILD_DIR / --build-dir."
+    return 0
+  fi
+
+  compile_db_dir=$(dirname "$compile_db")
+
+  for file in "${TIDY_FILES[@]}"; do
+    rel_file="$file"
+    abs_file="$REPO_ROOT/$file"
+
+    if ! grep -Fq "\"$rel_file\"" "$compile_db" && ! grep -Fq "\"$abs_file\"" "$compile_db"; then
+      continue
+    fi
+
+    printf 'clang-tidy: checking %s\n' "$file"
+    if ! "$CLANG_TIDY" -p "$compile_db_dir" --quiet "$file"; then
+      failed=1
+    fi
+  done
+
+  if [[ "$failed" -eq 1 ]]; then
+    printf '\nclang-tidy: errors found.\n'
+    printf 'Fix the reported issues, or skip tidy with: AMS_SKIP_TIDY=1 ...\n'
+    return 1
+  fi
+
+  return 0
+}
+
+REPO_ROOT=$(git rev-parse --show-toplevel)
+cd "$REPO_ROOT"
+
+DEFAULT_TARGETS=(src tests examples tools scripts .githooks)
+TARGETS=()
+RELEVANT_FILES=()
+CPP_FILES=()
+PY_FILES=()
+TIDY_FILES=()
+
+USE_STAGED=0
+FAIL_ON_PARTIAL=0
+APPLY_FIXES=0
+RUN_RUFF=0
+RUN_CLANG_FORMAT=0
+RUN_CLANG_TIDY=0
+BUILD_DIR="${AMS_BUILD_DIR:-}"
+SKIP_TIDY=0
+
+if [[ "${AMS_SKIP_TIDY:-0}" == "1" ]]; then
+  SKIP_TIDY=1
+fi
+
+while [[ "$#" -gt 0 ]]; do
+  case "$1" in
+    --check)
+      APPLY_FIXES=0
+      ;;
+    --fix)
+      APPLY_FIXES=1
+      ;;
+    --staged)
+      USE_STAGED=1
+      ;;
+    --fail-on-partial)
+      FAIL_ON_PARTIAL=1
+      ;;
+    --ruff)
+      RUN_RUFF=1
+      ;;
+    --clang-format)
+      RUN_CLANG_FORMAT=1
+      ;;
+    --clang-tidy)
+      RUN_CLANG_TIDY=1
+      ;;
+    --build-dir)
+      shift
+      [[ "$#" -gt 0 ]] || die "--build-dir requires a value"
+      BUILD_DIR="$1"
+      ;;
+    --help|-h)
+      usage
+      exit 0
+      ;;
+    --)
+      shift
+      while [[ "$#" -gt 0 ]]; do
+        TARGETS+=("$1")
+        shift
+      done
+      break
+      ;;
+    -*)
+      die "unknown option: $1"
+      ;;
+    *)
+      TARGETS+=("$1")
+      ;;
+  esac
+  shift
+done
+
+if [[ "$RUN_RUFF" -eq 0 && "$RUN_CLANG_FORMAT" -eq 0 && "$RUN_CLANG_TIDY" -eq 0 ]]; then
+  RUN_RUFF=1
+  RUN_CLANG_FORMAT=1
+  RUN_CLANG_TIDY=1
+fi
+
+if [[ "${#TARGETS[@]}" -eq 0 ]]; then
+  TARGETS=("${DEFAULT_TARGETS[@]}")
+fi
+
+CLANG_FORMAT=$(find_tool clang-format || true)
+CLANG_TIDY=$(find_tool clang-tidy || true)
+RUFF=$(command -v ruff 2>/dev/null || true)
+
+collect_files
+
+for file in "${RELEVANT_FILES[@]}"; do
+  if [[ "$RUN_CLANG_FORMAT" -eq 1 ]] && is_cpp_file "$file"; then
+    CPP_FILES+=("$file")
+  fi
+
+  if [[ "$RUN_RUFF" -eq 1 ]] && is_python_file "$file"; then
+    PY_FILES+=("$file")
+  fi
+
+  if [[ "$RUN_CLANG_TIDY" -eq 1 ]] && is_tidy_file "$file"; then
+    TIDY_FILES+=("$file")
+  fi
+done
+
+if [[ "${#CPP_FILES[@]}" -eq 0 && "${#PY_FILES[@]}" -eq 0 && "${#TIDY_FILES[@]}" -eq 0 ]]; then
+  exit 0
+fi
+
+detect_partial_staging
+
+status=0
+
+if [[ "$RUN_CLANG_FORMAT" -eq 1 ]] && ! run_clang_format; then
+  status=1
+fi
+
+if [[ "$RUN_RUFF" -eq 1 ]] && ! run_ruff; then
+  status=1
+fi
+
+if [[ "$RUN_CLANG_TIDY" -eq 1 ]] && ! run_clang_tidy; then
+  status=1
+fi
+
+exit "$status"

From 98f40132b8a8c9c2d3f23cdcd70a01eae12afc24 Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Tue, 23 Jun 2026 13:30:25 -0700
Subject: [PATCH 6/7] Fixing typo in comments

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 .githooks/pre-commit | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index f2320852..8c220f45 100755
--- a/.githooks/pre-commit
+++ b/.githooks/pre-commit
@@ -3,8 +3,8 @@
 # Git pre-commit hook for AMS:
 #   Runs non-mutating checks on staged C/C++ and Python files.
 #
-# Install (automatic via cmake/setup-git-hooks.cmake):
-#   .githooks/pre-commit
+# Install:
+#   git config core.hooksPath .githooks
 #
 # Skip temporarily:
 #   git commit --no-verify

From a2ab9d1760937e991775ffa5e1a030432bc98d06 Mon Sep 17 00:00:00 2001
From: Loic Pottier <pottier1@llnl.gov>
Date: Wed, 8 Jul 2026 17:31:46 -0700
Subject: [PATCH 7/7] Fixed scripts/run-code-quality.sh for clang-tidy

Signed-off-by: Loic Pottier <pottier1@llnl.gov>
---
 scripts/run-code-quality.sh | 222 ++++++++++++++++++++++++++++++++----
 1 file changed, 198 insertions(+), 24 deletions(-)

diff --git a/scripts/run-code-quality.sh b/scripts/run-code-quality.sh
index a7cd40eb..86ff30c5 100755
--- a/scripts/run-code-quality.sh
+++ b/scripts/run-code-quality.sh
@@ -11,8 +11,8 @@
 #   scripts/run-code-quality.sh
 #   scripts/run-code-quality.sh --fix
 #   scripts/run-code-quality.sh --ruff --fix
-#   scripts/run-code-quality.sh --clang-format --clang-tidy src tests
-#   scripts/run-code-quality.sh --check --staged
+#   scripts/run-code-quality.sh --all --clang-format --clang-tidy src tests
+#   scripts/run-code-quality.sh --check
 
 set -euo pipefail
 
@@ -20,14 +20,15 @@ usage() {
   cat <<'EOF'
 Usage: scripts/run-code-quality.sh [options] [paths...]
 
-Run code-quality tools across the repository or a selected subset of files.
-By default, this runs check-only mode on tracked files under:
+Run code-quality tools on staged files by default, or across the repository
+with --all. Full-codebase runs use tracked files under:
   src tests examples tools scripts .githooks
 
 Options:
   --check              Run non-mutating checks only (default)
   --fix                Apply clang-format and ruff fixes explicitly
-  --staged             Operate on staged files instead of the full codebase
+  --staged             Operate on staged files (default)
+  --all                Operate on the full codebase instead of staged files
   --fail-on-partial    Refuse staged runs when relevant files also have unstaged changes
   --ruff               Run ruff format/check on Python files
   --clang-format       Run clang-format on C/C++ files
@@ -76,17 +77,25 @@ append_if_exists() {
 
 is_cpp_file() {
   local path="$1"
-  [[ "$path" =~ \.(cpp|hpp|cc|hh|h|c|cxx|hxx)$ ]]
+  local lower="${path,,}"
+  [[ "$lower" =~ \.(cpp|hpp|cc|hh|h|c|cxx|hxx)$ ]]
 }
 
 is_tidy_file() {
   local path="$1"
-  [[ "$path" =~ \.(cpp|cc|c|cxx)$ ]]
+  local lower="${path,,}"
+  [[ "$lower" =~ \.(cpp|cc|c|cxx)$ ]]
+}
+
+is_dependency_file() {
+  local path="$1"
+  [[ "$path" == _deps/* || "$path" == */_deps/* ]]
 }
 
 is_python_file() {
   local path="$1"
-  [[ "$path" =~ \.py$ ]]
+  local lower="${path,,}"
+  [[ "$lower" =~ \.py$ ]]
 }
 
 collect_files() {
@@ -149,6 +158,162 @@ find_compile_db() {
   return 1
 }
 
+append_unique_compile_db_tidy_file() {
+  local candidate="$1"
+  local file=""
+
+  for file in "${COMPILE_DB_TIDY_FILES[@]}"; do
+    if [[ "$file" == "$candidate" ]]; then
+      return 0
+    fi
+  done
+
+  COMPILE_DB_TIDY_FILES+=("$candidate")
+}
+
+tidy_file_in_compile_db() {
+  local candidate="$1"
+  local file=""
+
+  for file in "${COMPILE_DB_TIDY_FILES[@]}"; do
+    if [[ "$file" == "$candidate" ]]; then
+      return 0
+    fi
+  done
+
+  return 1
+}
+
+collect_compile_db_tidy_files() {
+  local file=""
+  local parsed_files=""
+
+  [[ "$RUN_CLANG_TIDY" -eq 1 && "$SKIP_TIDY" -eq 0 ]] || return 0
+
+  if ! COMPILE_DB=$(find_compile_db); then
+    return 0
+  fi
+
+  COMPILE_DB_DIR=$(dirname "$COMPILE_DB")
+
+  if ! command -v python3 >/dev/null 2>&1; then
+    warn "python3 not found, cannot read compile_commands.json for clang-tidy discovery."
+    return 0
+  fi
+
+  if ! parsed_files=$(python3 - "$REPO_ROOT" "$COMPILE_DB" "${TARGETS[@]}" <<'PY'
+import json
+import os
+import sys
+
+repo_root = os.path.realpath(sys.argv[1])
+compile_db = sys.argv[2]
+targets = sys.argv[3:]
+tidy_extensions = (".cpp", ".cc", ".c", ".cxx")
+
+
+def repo_relative(path):
+    abs_path = os.path.realpath(path)
+    try:
+        rel_path = os.path.relpath(abs_path, repo_root)
+    except ValueError:
+        return None
+    if rel_path == os.pardir or rel_path.startswith(os.pardir + os.sep):
+        return None
+    return rel_path.replace(os.sep, "/")
+
+
+def normalize_target(target):
+    if target in ("", "."):
+        return ""
+    if os.path.isabs(target):
+        rel_target = repo_relative(target)
+    else:
+        rel_target = repo_relative(os.path.join(repo_root, target))
+    if rel_target in (None, "."):
+        return ""
+    return rel_target.rstrip("/")
+
+
+target_filters = [normalize_target(target) for target in targets]
+target_filters = [target for target in target_filters if target is not None]
+
+
+def target_matches(rel_path):
+    for target in target_filters:
+        if target == "" or rel_path == target or rel_path.startswith(target + "/"):
+            return True
+    return False
+
+
+def is_dependency_path(rel_path):
+    return "_deps" in rel_path.split("/")
+
+
+with open(compile_db, encoding="utf-8") as handle:
+    entries = json.load(handle)
+
+seen = set()
+for entry in entries:
+    raw_file = entry.get("file")
+    if not isinstance(raw_file, str):
+        continue
+
+    if os.path.isabs(raw_file):
+        source_path = raw_file
+    else:
+        directory = entry.get("directory")
+        if not isinstance(directory, str):
+            directory = os.path.dirname(compile_db)
+        source_path = os.path.join(directory, raw_file)
+
+    rel_path = repo_relative(source_path)
+    if rel_path is None or rel_path in seen:
+        continue
+    if is_dependency_path(rel_path):
+        continue
+    if not rel_path.lower().endswith(tidy_extensions):
+        continue
+    if not target_matches(rel_path):
+        continue
+
+    seen.add(rel_path)
+    print(rel_path)
+PY
+); then
+    warn "failed to read $COMPILE_DB for clang-tidy discovery."
+    return 0
+  fi
+
+  COMPILE_DB_PARSED=1
+
+  while IFS= read -r file; do
+    if [[ -n "$file" ]]; then
+      append_unique_compile_db_tidy_file "$file"
+    fi
+  done <<< "$parsed_files"
+}
+
+sync_tidy_files_with_compile_db() {
+  local file=""
+  local staged_tidy_files=()
+
+  [[ "$RUN_CLANG_TIDY" -eq 1 && "$COMPILE_DB_PARSED" -eq 1 ]] || return 0
+
+  if [[ "$USE_STAGED" -eq 0 ]]; then
+    TIDY_FILES=("${COMPILE_DB_TIDY_FILES[@]}")
+    return 0
+  fi
+
+  for file in "${TIDY_FILES[@]}"; do
+    if tidy_file_in_compile_db "$file"; then
+      staged_tidy_files+=("$file")
+    fi
+  done
+
+  TIDY_FILES=("${staged_tidy_files[@]}")
+}
+
 run_clang_format() {
   local file=""
   local failed=0
@@ -221,12 +386,10 @@ run_ruff() {
 }
 
 run_clang_tidy() {
-  local compile_db=""
-  local compile_db_dir=""
+  local compile_db="$COMPILE_DB"
+  local compile_db_dir="$COMPILE_DB_DIR"
   local file=""
   local failed=0
-  local rel_file=""
-  local abs_file=""
 
   if [[ "$SKIP_TIDY" -eq 1 || "${#TIDY_FILES[@]}" -eq 0 ]]; then
     return 0
@@ -237,19 +400,20 @@ run_clang_tidy() {
     return 0
   fi
 
-  if ! compile_db=$(find_compile_db); then
-    warn "compile_commands.json not found, skipping clang-tidy."
-    warn "Run cmake first, or set AMS_BUILD_DIR / --build-dir."
-    return 0
+  if [[ -z "$compile_db" ]]; then
+    if ! compile_db=$(find_compile_db); then
+      warn "compile_commands.json not found, skipping clang-tidy."
+      warn "Run cmake first, or set AMS_BUILD_DIR / --build-dir."
+      return 0
+    fi
+    compile_db_dir=$(dirname "$compile_db")
   fi
-
-  compile_db_dir=$(dirname "$compile_db")
-
   for file in "${TIDY_FILES[@]}"; do
-    rel_file="$file"
-    abs_file="$REPO_ROOT/$file"
+    if is_dependency_file "$file"; then
+      continue
+    fi
 
-    if ! grep -Fq "\"$rel_file\"" "$compile_db" && ! grep -Fq "\"$abs_file\"" "$compile_db"; then
+    if [[ "$COMPILE_DB_PARSED" -eq 1 ]] && ! tidy_file_in_compile_db "$file"; then
       continue
     fi
 
@@ -277,8 +441,12 @@ RELEVANT_FILES=()
 CPP_FILES=()
 PY_FILES=()
 TIDY_FILES=()
+COMPILE_DB_TIDY_FILES=()
+COMPILE_DB=""
+COMPILE_DB_DIR=""
+COMPILE_DB_PARSED=0
 
-USE_STAGED=0
+USE_STAGED=1
 FAIL_ON_PARTIAL=0
 APPLY_FIXES=0
 RUN_RUFF=0
@@ -302,6 +470,9 @@ while [[ "$#" -gt 0 ]]; do
     --staged)
       USE_STAGED=1
       ;;
+    --all)
+      USE_STAGED=0
+      ;;
     --fail-on-partial)
       FAIL_ON_PARTIAL=1
       ;;
@@ -366,11 +537,14 @@ for file in "${RELEVANT_FILES[@]}"; do
     PY_FILES+=("$file")
   fi
 
-  if [[ "$RUN_CLANG_TIDY" -eq 1 ]] && is_tidy_file "$file"; then
+  if [[ "$RUN_CLANG_TIDY" -eq 1 ]] && is_tidy_file "$file" && ! is_dependency_file "$file"; then
     TIDY_FILES+=("$file")
   fi
 done
 
+collect_compile_db_tidy_files
+sync_tidy_files_with_compile_db
+
 if [[ "${#CPP_FILES[@]}" -eq 0 && "${#PY_FILES[@]}" -eq 0 && "${#TIDY_FILES[@]}" -eq 0 ]]; then
   exit 0
 fi