Merge pull request #2154 from rbberger/coding_standard

include(Testing)

include(CodeCoverage)

include(CodingStandard)

###############################################################################

# Print package summary

if(CMAKE_VERSION VERSION_LESS 3.12)

    find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12

    if(PYTHONINTERP_FOUND)

        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})

        set(Python3_VERSION ${PYTHON_VERSION_STRING})

    endif()

else()

    find_package(Python3 COMPONENTS Interpreter QUIET)

endif()

if (Python3_EXECUTABLE)

    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)

        add_custom_target(

          check-whitespace

          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

          WORKING_DIRECTORY  ${LAMMPS_DIR}

          COMMENT "Check for whitespace errors")

        add_custom_target(

          check-permissions

          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .

          WORKING_DIRECTORY  ${LAMMPS_DIR}

          COMMENT "Check for permission errors")

        add_custom_target(

          fix-whitespace

          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .

          WORKING_DIRECTORY  ${LAMMPS_DIR}

          COMMENT "Fix whitespace errors")

        add_custom_target(

          fix-permissions

          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permission.py -f .

          WORKING_DIRECTORY  ${LAMMPS_DIR}

          COMMENT "Fix permission errors")

    endif()

endif()

#!/usr/bin/env python3

# Utility for detecting and fixing file permission issues in LAMMPS

#

# Written by Richard Berger (Temple University)

import os

import glob

import yaml

import argparse

import stat

DEFAULT_CONFIG = """

permission: "rw-r--r--"

recursive: true

include:

    - cmake/**

    - doc/src/**

    - python

    - src/**

    - examples/**

    - tools/coding_standard

patterns:

    - "*.c"

    - "*.cmake"

    - "*.cpp"

    - "*.h"

    - "*.jpg"

    - "*.md"

    - "*.pdf"

    - "*.png"

    - "*.rst"

    - "*.tex"

    - ".gitignore"

    - "README"

    - "in.*"

    - "requirements.txt"

"""

def check_permission(path, mask):

    st = os.stat(path)

    return bool(stat.S_IMODE(st.st_mode) == mask)

def generate_permission_mask(line):

    assert(len(line) == 9)

    mask = 0

    # USER

    if line[0] == "r":

        mask |= stat.S_IRUSR

    if line[1] == "w":

        mask |= stat.S_IWUSR

    if line[2] == "x":

        mask |= stat.S_IXUSR

    # GROUP

    if line[3] == "r":

        mask |= stat.S_IRGRP

    if line[4] == "w":

        mask |= stat.S_IWGRP

    if line[5] == "x":

        mask |= stat.S_IXGRP

    # OTHER

    if line[6] == "r":

        mask |= stat.S_IROTH

    if line[7] == "w":

        mask |= stat.S_IWOTH

    if line[8] == "x":

        mask |= stat.S_IXOTH

    return mask

def check_folder(directory, config, fix=False, verbose=False):

    files = []

    for base_path in config['include']:

        for pattern in config['patterns']:

            path = os.path.join(directory, base_path, pattern)

            files += glob.glob(path, recursive=config['recursive'])

    mask = generate_permission_mask(config['permission'])

    for f in files:

        path = os.path.normpath(f)

        if verbose:

            print("Checking file:", path)

        ok = check_permission(path, mask)

        if not ok:

            print("[Error] Wrong file permissions @ {}".format(path))

            if fix:

                if os.access(path, os.W_OK):

                    print("Changing permissions of file {} to '{}'".format(path, config['permission']))

                    os.chmod(path, mask)

                else:

                    print("[Error] Can not write permissions of file {}".format(path))

def main():

    parser = argparse.ArgumentParser(description='Utility for detecting and fixing file permission issues in LAMMPS')

    parser.add_argument('-c', '--config', metavar='CONFIG_FILE', help='location of a optional configuration file')

    parser.add_argument('-f', '--fix', action='store_true', help='automatically fix permissions')

    parser.add_argument('-v', '--verbose', action='store_true', help='verbose output')

    parser.add_argument('DIRECTORY', help='directory that should be checked')

    args = parser.parse_args()

    if args.config:

        with open(args.config, 'r') as cfile:

            config = yaml.load(cfile, Loader=yaml.FullLoader)

    else:

        config = yaml.load(DEFAULT_CONFIG, Loader=yaml.FullLoader)

    check_folder(args.DIRECTORY, config, args.fix, args.verbose)

if __name__ == "__main__":

    main()

#!/usr/bin/env python3

# Utility for detecting and fixing whitespace issues in LAMMPS

#

# Written by Richard Berger (Temple University)

import os

import glob

import re

import yaml

import argparse

import shutil

DEFAULT_CONFIG = """

recursive: true

include:

    - cmake/**

    - doc

    - doc/src/**

    - python

    - src/**

    - tools/coding_standard

patterns:

    - "*.c"

    - "*.cmake"

    - "*.cpp"

    - "*.h"

    - "*.md"

    - "*.py"

    - "*.rst"

    - "*.sh"

    - ".gitignore"

    - "README"

    - "requirements.txt"

"""

def check_trailing_whitespace(f):

    pattern = re.compile(r'\s+\n$')

    last_line = "\n"

    lineno = 1

    errors = set()

    for line in f:

        if pattern.match(line):

            errors.add(lineno)

        last_line = line

        lineno += 1

    return errors, last_line

def check_file(path):

    encoding = 'UTF-8'

    last_line = "\n"

    whitespace_errors = set()

    try:

        with open(path, 'r') as f:

            whitespace_errors, last_line = check_trailing_whitespace(f)

    except UnicodeDecodeError:

        encoding = 'ISO-8859-1'

        try:

            with open(path, 'r', encoding=encoding) as f:

                whitespace_errors, last_line = check_trailing_whitespace(f)

        except Exception:

            encoding = 'unknown'

    return {

        'whitespace_errors': whitespace_errors,

        'encoding': encoding,

        'eof_error': not last_line.endswith('\n')

    }

def fix_file(path, check_result):

    newfile = path + ".modified"

    with open(newfile, 'w', encoding='UTF-8') as out:

        with open(path, 'r', encoding=check_result['encoding']) as src:

            for line in src:

                print(line.rstrip(), file=out)

    shutil.move(newfile, path)

def check_folder(directory, config, fix=False, verbose=False):

    files = []

    for base_path in config['include']:

        for pattern in config['patterns']:

            path = os.path.join(directory, base_path, pattern)

            files += glob.glob(path, recursive=config['recursive'])

    for f in files:

        path = os.path.normpath(f)

        if verbose:

            print("Checking file:", path)

        result = check_file(path)

        has_resolvable_errors = False

        for lineno in result['whitespace_errors']:

            print("[Error] Trailing whitespace @ {}:{}".format(path, lineno))

            has_resolvable_errors = True

        if result['eof_error']:

            print("[Error] Missing newline at end of file @ {}".format(path))

            has_resolvable_errors = True

        if result['encoding'] == 'unknown':

            print("[Error] Unknown text encoding @ {}".format(path))

            has_resolvable_errors = False

        elif result['encoding'] == 'ISO-8859-1':

            print("[Error] Found ISO-8859-1 encoding instead of UTF-8 @ {}".format(path))

            has_resolvable_errors = True

        if has_resolvable_errors and fix:

            print("Applying automatic fixes to file:", path)

            fix_file(path, result)

def main():

    parser = argparse.ArgumentParser(description='Utility for detecting and fixing whitespace issues in LAMMPS')

    parser.add_argument('-c', '--config', metavar='CONFIG_FILE', help='location of a optional configuration file')

    parser.add_argument('-f', '--fix', action='store_true', help='automatically fix common issues')

    parser.add_argument('-v', '--verbose', action='store_true', help='verbose output')

    parser.add_argument('DIRECTORY', help='directory that should be checked')

    args = parser.parse_args()

    if args.config:

        with open(args.config, 'r') as cfile:

            config = yaml.load(cfile, Loader=yaml.FullLoader)

    else:

        config = yaml.load(DEFAULT_CONFIG, Loader=yaml.FullLoader)

    check_folder(args.DIRECTORY, config, args.fix, args.verbose)

if __name__ == "__main__":

    main()