Add Git hooks to format code automically

.clang-tidy

@@ -0,0 +1,39 @@
+---
+# 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
+
+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'
+

.githooks/pre-commit

@@ -0,0 +1,197 @@
+#!/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)
+#
+# Install (automatic via cmake/setup-git-hooks.cmake):
+#   .githooks/pre-commit
+#
+# Skip temporarily:
+#   git commit --no-verify
+#
+# 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, 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)
+
+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"
+  exit 1
+fi
+
+exit 0

.gitlab/custom-jobs-and-variables.yml

@@ -14,25 +14,25 @@ variables:
 
   # Dane
   # Arguments for top level allocation
-  DANE_SHARED_ALLOC: "--exclusive --reservation=ci --time=45 --nodes=1"
+  DANE_SHARED_ALLOC: "--account=lpbf --exclusive --reservation=ci --time=45 --nodes=1"
   # Arguments for job level allocation
-  DANE_JOB_ALLOC: "--mpi=none --reservation=ci --nodes=1"
+  DANE_JOB_ALLOC: "--account=lpbf --mpi=none --reservation=ci --nodes=1"
   # Add variables that should apply to all the jobs on a machine:
   #  DANE_MY_VAR: "..."
 
   # Tioga
   # Arguments for top level allocation
   # OPTIONAL: "-o per-resource.count=2" allows to get 2 jobs running on each node.
-  TIOGA_SHARED_ALLOC: "--queue=pci --exclusive --time-limit=1h --nodes=1 -o per-resource.count=4"
+  TIOGA_SHARED_ALLOC: "--bank=asccasc --queue=pci --exclusive --time-limit=1h --nodes=1 -o per-resource.count=4"
   # Arguments for job level allocation, we need to match the time limit. Otherwise it immediately exits
-  TIOGA_JOB_ALLOC: "--nodes=1 --begin-time=+5s --time-limit=1h"
+  TIOGA_JOB_ALLOC: "--bank=asccasc --nodes=1 --begin-time=+5s --time-limit=1h"
   # Add variables that should apply to all the jobs on a machine:
   #  TIOGA_MY_VAR: "..."
 
   # Tuo
-  TUOLUMNE_SHARED_ALLOC: "--queue=pci --exclusive --time-limit=1h --nodes=1 -o per-resource.count=4"
+  TUOLUMNE_SHARED_ALLOC: "--bank=lpbf --queue=pci --exclusive --time-limit=1h --nodes=1 -o per-resource.count=4"
   # Arguments for job level allocation
-  TUOLUMNE_JOB_ALLOC: "--nodes=1 --begin-time=+5s --time-limit=1h"
+  TUOLUMNE_JOB_ALLOC: "--bank=lpbf --nodes=1 --begin-time=+5s --time-limit=1h"
 
 # Configuration shared by build and test jobs specific to this project.
 # Not all configuration can be shared. Here projects can fine tune the

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 

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()

pyproject.toml

@@ -32,6 +32,7 @@ classifiers = [
   "Programming Language :: Python :: 3 :: Only",
 ]
 dependencies = [
+  "ruff",
   "h5py",
   "argparse",
   "SQLAlchemy",
@@ -56,62 +57,27 @@ 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",
   "__pycache__",
   "*.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"
+