add clang-tidy

.clang-tidy

----
-Checks:  
-	'clang-diagnostic-*,clang-analyzer-*,-*,        
-	*
-	-android-*
-	-bugprone-bool-pointer-implicit-conversion
-	-cert-env33-c
-	-cert-dcl50-cpp
-	-cert-dcl59-cpp
-	-cppcoreguidelines-no-malloc
-	-cppcoreguidelines-owning-memory
-	-cppcoreguidelines-pro-bounds-array-to-pointer-decay
-	-cppcoreguidelines-pro-bounds-constant-array-index
-	-cppcoreguidelines-pro-bounds-pointer-arithmetic
-	-cppcoreguidelines-pro-type-const-cast
-	-cppcoreguidelines-pro-type-cstyle-cast
-	-cppcoreguidelines-pro-type-reinterpret-cast
-	-cppcoreguidelines-pro-type-union-access
-	-cppcoreguidelines-pro-type-vararg
-	-cppcoreguidelines-special-member-functions
-	-fuchsia-*
-	-google-*
-	google-default-arguments
-	google-explicit-constructor
-	google-runtime-member-string-references
-	google-runtime-operator
-	-hicpp-braces-around-statements
-	-hicpp-named-parameter
-	-hicpp-no-array-decay
-	-hicpp-no-assembler
-	-hicpp-no-malloc
-	-hicpp-function-size
-	-hicpp-special-member-functions
-	-hicpp-vararg
-	-llvm-*
-	-objc-*
-	-readability-else-after-return
-	-readability-implicit-bool-conversion
-	-readability-named-parameter
-	-readability-simplify-boolean-expr
-	-readability-braces-around-statements
-	-readability-identifier-naming
-	-readability-function-size
-	-readability-redundant-member-init
-	-misc-bool-pointer-implicit-conversion
-	-misc-definitions-in-headers
-	-misc-unused-alias-decls
-	-misc-unused-parameters
-	-misc-unused-using-decls
-	-modernize-use-using
-	-modernize-use-default-member-init
-	-clang-diagnostic-*
-	-clang-analyzer-*'
-...
-
+Checks: >
+  *
+  -android-*
+  -bugprone-bool-pointer-implicit-conversion
+  -cert-env33-c
+  -cert-dcl50-cpp
+  -cert-dcl59-cpp
+  -cppcoreguidelines-*
+  -fuchsia-*
+  -google-*
+  google-default-arguments
+  google-explicit-constructor
+  google-runtime-member-string-references
+  google-runtime-operator
+  -hicpp-braces-around-statements
+  -hicpp-named-parameter
+  -hicpp-no-array-decay
+  -hicpp-no-assembler
+  -hicpp-no-malloc
+  -hicpp-function-size
+  -hicpp-special-member-functions
+  -hicpp-vararg
+  -llvm-*
+  -objc-*
+  -readability-else-after-return
+  -readability-implicit-bool-conversion
+  -readability-named-parameter
+  -readability-simplify-boolean-expr
+  -readability-braces-around-statements
+  -readability-identifier-naming
+  -readability-function-size
+  -readability-redundant-member-init
+  -misc-bool-pointer-implicit-conversion
+  -misc-definitions-in-headers
+  -misc-unused-alias-decls
+  -misc-unused-parameters
+  -misc-unused-using-decls
+  -modernize-use-using
+  -modernize-use-default-member-init
+  -clang-diagnostic-*
+  -clang-analyzer-*
+WarningsAsErrors: ''
+HeaderFilterRegex: ''
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+User:            allonli
+CheckOptions:    
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'

.travis.yml

@@ -7,7 +7,6 @@ os:
   - linux
 env:
   global:
-    - JOB=check_style
     - CMAKE_URL=https://cmake.org/files/v3.11/cmake-3.11.1-Linux-x86_64.tar.gz
 addons:
   apt:
@@ -19,8 +18,11 @@ addons:
       - python
       - python-pip
       - python2.7-dev
-      - clang-6.0
       - libc6-i386
+      - clang-6.0
+      - libclang-6.0
+      - llvm-6.0
+      - llvm-6.0-dev
       - curl
 
 compiler:
@@ -37,16 +39,21 @@ before_install:
       export PATH=${DEPS_DIR}/cmake/bin:${PATH}
     fi
 
-install:
-  - if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi
-  - if [ "$CXX" = "clang++" ]; then export CXX="clang++-6.0" CC="clang-6.0"; fi
+#install:
+#  - if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi
+#  - if [ "$CXX" = "clang++" ]; then export CXX="clang++-6.0" CC="clang-6.0"; fi
 
-script:
+before_script:
   - |
-    
+    echo "cmake generate compile_commands.json for clang-tidy"
+    ls -l -a
+    clang-tidy -version 
+    clang-format -version
+script:
+  - | 
     function timeout() { perl -e 'alarm shift; exec @ARGV' "$@"; }
   - |
-    timeout 600 .travis/${JOB}.sh # 10min timeout
+    timeout 600 .travis/pre-commit-job.sh # 10min timeout
     RESULT=$?; if [ $RESULT -eq 0 ] || [ $RESULT -eq 142 ]; then true; else exit 1; fi;
 
 notifications:

build.sh

 #!/bin/bash
 
 build_for_linux() {
-    echo "linux"
+	if [ ! `which brew` ]; then
+        echo "building failed! homebrew not found, please install homebrew."
+        return
+    fi
+    if [ ! `which cmake` ]; then
+        echo "installing cmake."
+        brew install cmake
+        if [ ! $? ]; then
+            echo "cmake install failed."
+            return
+        fi
+    fi
+    PLATFORM="x86"
+    MODE="Release"
+    CXX_FLAGS="-std=c++11 -O3 -s"
+    BUILD_DIR=build/release/"${PLATFORM}"
+    mkdir -p ${BUILD_DIR}/build
+
+    mkdir -p ${BUILD_DIR}/test
+    cp -r test/models ${BUILD_DIR}/test/models
+
+    cmake . \
+        -B"${BUILD_DIR}" \
+    	-DCMAKE_BUILD_TYPE="${MODE}" \
+    	-DCMAKE_CXX_FLAGS="${CXX_FLAGS}" \
+    	-DIS_MAC=true
+
+    cd ${BUILD_DIR}
+    make -j 8
 }
 
 build_for_mac() {

tools/pre-commit.hooks/.clang-tidy.hook

 #!/bin/bash
-set -e
 
 echo "allonli clang-tidy formating init"
-clang-tidy -checks="-*,misc-unused-using-decls" -fix src/framework/data_type.h --
 
-TOTAL_ERRORS=0
+cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+clang-foramt -version
+clang-tidy -version
+python ./tools/pre-commit.hooks/run-clang-tidy.py
+#TOTAL_ERRORS=0
 
 # The trick to remove deleted files: https://stackoverflow.com/a/2413151
-for file in $(git diff --cached --name-status | awk '$1 != "D" {print $2}' | grep "src" | grep -v ".pb."); do
-    echo "clang-tidy formating $file" 
-    clang-tidy $file 
-    TOTAL_ERRORS=$(expr $TOTAL_ERRORS + $?);
-done
-
-exit $TOTAL_ERRORS
+#for file in $(git diff --cached --name-status | awk '$1 != "D" {print $2}' | grep "src" | grep -v ".pb."); do
+#    echo "clang-tidy formating $file" 
+#    clang-tidy $file 
+#    TOTAL_ERRORS=$(expr $TOTAL_ERRORS + $?);
+#done
+#
+#exit $TOTAL_ERRORS

tools/pre-commit.hooks/run-clang-tidy.py

+#!/usr/bin/env python
+#
+#===- run-clang-tidy.py - Parallel clang-tidy runner ---------*- python -*--===#
+#
+#                     The LLVM Compiler Infrastructure
+#
+# This file is distributed under the University of Illinois Open Source
+# License. See LICENSE.TXT for details.
+#
+#===------------------------------------------------------------------------===#
+# FIXME: Integrate with clang-tidy-diff.py
+
+"""
+Parallel clang-tidy runner
+==========================
+
+Runs clang-tidy over all files in a compilation database. Requires clang-tidy
+and clang-apply-replacements in $PATH.
+
+Example invocations.
+- Run clang-tidy on all files in the current working directory with a default
+  set of checks and show warnings in the cpp files and all project headers.
+    run-clang-tidy.py $PWD
+
+- Fix all header guards.
+    run-clang-tidy.py -fix -checks=-*,llvm-header-guard
+
+- Fix all header guards included from clang-tidy and header guards
+  for clang-tidy headers.
+    run-clang-tidy.py -fix -checks=-*,llvm-header-guard extra/clang-tidy \
+                      -header-filter=extra/clang-tidy
+
+Compilation database setup:
+http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html
+"""
+
+from __future__ import print_function
+
+import argparse
+import glob
+import json
+import multiprocessing
+import os
+import re
+import shutil
+import subprocess
+import sys
+import tempfile
+import threading
+import traceback
+import yaml
+
+is_py2 = sys.version[0] == '2'
+
+if is_py2:
+    import Queue as queue
+else:
+    import queue as queue
+
+def find_compilation_database(path):
+  """Adjusts the directory until a compilation database is found."""
+  result = './'
+  while not os.path.isfile(os.path.join(result, path)):
+    if os.path.realpath(result) == '/':
+      print('Error: could not find compilation database.')
+      sys.exit(1)
+    result += '../'
+  return os.path.realpath(result)
+
+
+def make_absolute(f, directory):
+  if os.path.isabs(f):
+    return f
+  return os.path.normpath(os.path.join(directory, f))
+
+
+def get_tidy_invocation(f, clang_tidy_binary, checks, tmpdir, build_path,
+                        header_filter, extra_arg, extra_arg_before, quiet):
+  """Gets a command line for clang-tidy."""
+  start = [clang_tidy_binary]
+  if header_filter is not None:
+    start.append('-header-filter=' + header_filter)
+  else:
+    # Show warnings in all in-project headers by default.
+    start.append('-header-filter=^' + build_path + '/.*')
+  if checks:
+    start.append('-checks=' + checks)
+  if tmpdir is not None:
+    start.append('-export-fixes')
+    # Get a temporary file. We immediately close the handle so clang-tidy can
+    # overwrite it.
+    (handle, name) = tempfile.mkstemp(suffix='.yaml', dir=tmpdir)
+    os.close(handle)
+    start.append(name)
+  for arg in extra_arg:
+      start.append('-extra-arg=%s' % arg)
+  for arg in extra_arg_before:
+      start.append('-extra-arg-before=%s' % arg)
+  start.append('-p=' + build_path)
+  if quiet:
+      start.append('-quiet')
+  start.append(f)
+  return start
+
+
+def merge_replacement_files(tmpdir, mergefile):
+  """Merge all replacement files in a directory into a single file"""
+  # The fixes suggested by clang-tidy >= 4.0.0 are given under
+  # the top level key 'Diagnostics' in the output yaml files
+  mergekey="Diagnostics"
+  merged=[]
+  for replacefile in glob.iglob(os.path.join(tmpdir, '*.yaml')):
+    content = yaml.safe_load(open(replacefile, 'r'))
+    if not content:
+      continue # Skip empty files.
+    merged.extend(content.get(mergekey, []))
+
+  if merged:
+    # MainSourceFile: The key is required by the definition inside
+    # include/clang/Tooling/ReplacementsYaml.h, but the value
+    # is actually never used inside clang-apply-replacements,
+    # so we set it to '' here.
+    output = { 'MainSourceFile': '', mergekey: merged }
+    with open(mergefile, 'w') as out:
+      yaml.safe_dump(output, out)
+  else:
+    # Empty the file:
+    open(mergefile, 'w').close()
+
+
+def check_clang_apply_replacements_binary(args):
+  """Checks if invoking supplied clang-apply-replacements binary works."""
+  try:
+    subprocess.check_call([args.clang_apply_replacements_binary, '--version'])
+  except:
+    print('Unable to run clang-apply-replacements. Is clang-apply-replacements '
+          'binary correctly specified?', file=sys.stderr)
+    traceback.print_exc()
+    sys.exit(1)
+
+
+def apply_fixes(args, tmpdir):
+  """Calls clang-apply-fixes on a given directory."""
+  invocation = [args.clang_apply_replacements_binary]
+  if args.format:
+    invocation.append('-format')
+  if args.style:
+    invocation.append('-style=' + args.style)
+  invocation.append(tmpdir)
+  subprocess.call(invocation)
+
+
+def run_tidy(args, tmpdir, build_path, queue):
+  """Takes filenames out of queue and runs clang-tidy on them."""
+  while True:
+    name = queue.get()
+    invocation = get_tidy_invocation(name, args.clang_tidy_binary, args.checks,
+                                     tmpdir, build_path, args.header_filter,
+                                     args.extra_arg, args.extra_arg_before,
+                                     args.quiet)
+    sys.stdout.write(' '.join(invocation) + '\n')
+    subprocess.call(invocation)
+    queue.task_done()
+
+
+def main():
+  parser = argparse.ArgumentParser(description='Runs clang-tidy over all files '
+                                   'in a compilation database. Requires '
+                                   'clang-tidy and clang-apply-replacements in '
+                                   '$PATH.')
+  parser.add_argument('-clang-tidy-binary', metavar='PATH',
+                      default='clang-tidy',
+                      help='path to clang-tidy binary')
+  parser.add_argument('-clang-apply-replacements-binary', metavar='PATH',
+                      default='clang-apply-replacements',
+                      help='path to clang-apply-replacements binary')
+  parser.add_argument('-checks', default=None,
+                      help='checks filter, when not specified, use clang-tidy '
+                      'default')
+  parser.add_argument('-header-filter', default=None,
+                      help='regular expression matching the names of the '
+                      'headers to output diagnostics from. Diagnostics from '
+                      'the main file of each translation unit are always '
+                      'displayed.')
+  parser.add_argument('-export-fixes', metavar='filename', dest='export_fixes',
+                      help='Create a yaml file to store suggested fixes in, '
+                      'which can be applied with clang-apply-replacements.')
+  parser.add_argument('-j', type=int, default=0,
+                      help='number of tidy instances to be run in parallel.')
+  parser.add_argument('files', nargs='*', default=['.*'],
+                      help='files to be processed (regex on path)')
+  parser.add_argument('-fix', action='store_true', help='apply fix-its')
+  parser.add_argument('-format', action='store_true', help='Reformat code '
+                      'after applying fixes')
+  parser.add_argument('-style', default='file', help='The style of reformat '
+                      'code after applying fixes')
+  parser.add_argument('-p', dest='build_path',
+                      help='Path used to read a compile command database.')
+  parser.add_argument('-extra-arg', dest='extra_arg',
+                      action='append', default=[],
+                      help='Additional argument to append to the compiler '
+                      'command line.')
+  parser.add_argument('-extra-arg-before', dest='extra_arg_before',
+                      action='append', default=[],
+                      help='Additional argument to prepend to the compiler '
+                      'command line.')
+  parser.add_argument('-quiet', action='store_true',
+                      help='Run clang-tidy in quiet mode')
+  args = parser.parse_args()
+
+  db_path = 'compile_commands.json'
+
+  if args.build_path is not None:
+    build_path = args.build_path
+  else:
+    # Find our database
+    build_path = find_compilation_database(db_path)
+
+  try:
+    invocation = [args.clang_tidy_binary, '-list-checks']
+    invocation.append('-p=' + build_path)
+    if args.checks:
+      invocation.append('-checks=' + args.checks)
+    invocation.append('-')
+    subprocess.check_call(invocation)
+  except:
+    print("Unable to run clang-tidy.", file=sys.stderr)
+    sys.exit(1)
+
+  # Load the database and extract all files.
+  database = json.load(open(os.path.join(build_path, db_path)))
+  files = [make_absolute(entry['file'], entry['directory'])
+           for entry in database]
+
+  max_task = args.j
+  if max_task == 0:
+    max_task = multiprocessing.cpu_count()
+
+  tmpdir = None
+  if args.fix or args.export_fixes:
+    check_clang_apply_replacements_binary(args)
+    tmpdir = tempfile.mkdtemp()
+
+  # Build up a big regexy filter from all command line arguments.
+  file_name_re = re.compile('|'.join(args.files))
+
+  try:
+    # Spin up a bunch of tidy-launching threads.
+    task_queue = queue.Queue(max_task)
+    for _ in range(max_task):
+      t = threading.Thread(target=run_tidy,
+                           args=(args, tmpdir, build_path, task_queue))
+      t.daemon = True
+      t.start()
+
+    # Fill the queue with files.
+    for name in files:
+      if file_name_re.search(name):
+        task_queue.put(name)
+
+    # Wait for all threads to be done.
+    task_queue.join()
+
+  except KeyboardInterrupt:
+    # This is a sad hack. Unfortunately subprocess goes
+    # bonkers with ctrl-c and we start forking merrily.
+    print('\nCtrl-C detected, goodbye.')
+    if tmpdir:
+      shutil.rmtree(tmpdir)
+    os.kill(0, 9)
+
+  return_code = 0
+  if args.export_fixes:
+    print('Writing fixes to ' + args.export_fixes + ' ...')
+    try:
+      merge_replacement_files(tmpdir, args.export_fixes)
+    except:
+      print('Error exporting fixes.\n', file=sys.stderr)
+      traceback.print_exc()
+      return_code=1
+
+  if args.fix:
+    print('Applying fixes ...')
+    try:
+      apply_fixes(args, tmpdir)
+    except:
+      print('Error applying fixes.\n', file=sys.stderr)
+      traceback.print_exc()
+      return_code=1
+
+  if tmpdir:
+    shutil.rmtree(tmpdir)
+  sys.exit(return_code)
+
+if __name__ == '__main__':
+  main()