From 49982e22bf7044143c7bd72a596df8f5da9c334c Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sat, 13 Jun 2020 09:54:12 -0400
Subject: [PATCH] Add check for permissions

---
 cmake/Modules/CodingStandard.cmake   |  10 +++
 tools/coding_standard/permissions.py | 118 +++++++++++++++++++++++++++
 tools/coding_standard/whitespace.py  |  17 ++--
 3 files changed, 137 insertions(+), 8 deletions(-)
 create mode 100644 tools/coding_standard/permissions.py

diff --git a/cmake/Modules/CodingStandard.cmake b/cmake/Modules/CodingStandard.cmake
index 467dbb2b16..5a9c0e1dda 100644
--- a/cmake/Modules/CodingStandard.cmake
+++ b/cmake/Modules/CodingStandard.cmake
@@ -15,10 +15,20 @@ if (Python3_EXECUTABLE)
           ${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()
diff --git a/tools/coding_standard/permissions.py b/tools/coding_standard/permissions.py
new file mode 100644
index 0000000000..d956aed58c
--- /dev/null
+++ b/tools/coding_standard/permissions.py
@@ -0,0 +1,118 @@
+#!/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()
diff --git a/tools/coding_standard/whitespace.py b/tools/coding_standard/whitespace.py
index f9923893a0..04246ec704 100644
--- a/tools/coding_standard/whitespace.py
+++ b/tools/coding_standard/whitespace.py
@@ -17,18 +17,19 @@ include:
     - doc/src/**
     - python
     - src/**
+    - tools/coding_standard
 patterns:
+    - "*.c"
+    - "*.cmake"
+    - "*.cpp"
+    - "*.h"
+    - "*.md"
+    - "*.py"
+    - "*.rst"
+    - "*.sh"
     - ".gitignore"
     - "README"
     - "requirements.txt"
-    - "*.c"
-    - "*.cpp"
-    - "*.h"
-    - "*.sh"
-    - "*.py"
-    - "*.md"
-    - "*.rst"
-    - "*.cmake"
 """
 
 def check_trailing_whitespace(f):