add python tool to detect and remove (if desired) error docs from headers

also document the tools in the manual.

tools/coding_standard/README

@@ -2,4 +2,6 @@ These Python scripts help to detect whether files in the repository
 conform to LAMMPS coding conventions or not, and can fix those issues, too.
 
 permissions.py   detects if sources have executable permissions and scripts have not
-whitespace.py    (currently) detects trailing whitespace
+whitespace.py    detects TAB characters and trailing whitespace
+homepage.py      detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
+errordocs.py     detects deprecated error docs in header files

tools/coding_standard/errordocs.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+# Utility for detecting leftover error/warning docs in header files
+#
+# Written by Axel Kohlmeyer (Temple University)
+from __future__ import print_function
+import sys
+
+if sys.version_info.major < 3:
+    sys.exit('This script must be run with Python 3.5 or later')
+
+if sys.version_info.minor < 5:
+    sys.exit('This script must be run with Python 3.5 or later')
+
+import os
+import glob
+import re
+import yaml
+import argparse
+import shutil
+
+DEFAULT_CONFIG = """
+recursive: true
+include:
+    - src/**
+patterns:
+    - "*.h"
+"""
+
+def check_errordocs(f):
+    pattern = re.compile(r'^ */\* *ERROR/WARNING messag')
+    lineno = 1
+    errors = set()
+
+    for line in f:
+        if pattern.match(line):
+            errors.add(lineno)
+        lineno += 1
+
+    return errors
+
+def check_file(path):
+    if path.find('errordocs.py') >= 0: return { 'errordocs_errors' : '' }
+    encoding = 'UTF-8'
+    errordocs_errors = set()
+    try:
+        with open(path, 'r') as f:
+            errordocs_errors = check_errordocs(f)
+    except UnicodeDecodeError:
+        encoding = 'ISO-8859-1'
+        try:
+            with open(path, 'r', encoding=encoding) as f:
+                errordocs_errors = check_errordocs(f)
+        except Exception:
+            encoding = 'unknown'
+
+    return {
+        'errordocs_errors': errordocs_errors,
+        'encoding': encoding
+    }
+
+def fix_file(path, check_result):
+    if path.find('errordocs.py') >= 0: return
+    newfile = path + ".modified"
+    pattern = re.compile(r'[\n\r ]* */\* *ERROR/WARNING *messag.*\*/', re.DOTALL)
+    with open(newfile, 'w', encoding='UTF-8') as out:
+        with open(path, 'r', encoding=check_result['encoding']) as src:
+            filetxt = re.sub(pattern,'', src.read());
+            print(filetxt, end='', file=out)
+    shutil.copymode(path, newfile)
+    shutil.move(newfile, path)
+
+def check_folder(directory, config, fix=False, verbose=False):
+    success = True
+    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['errordocs_errors']:
+            print("[Error] Found LAMMPS errordocs @ {}:{}".format(path, lineno))
+            has_resolvable_errors = True
+
+        if has_resolvable_errors:
+            if fix:
+                print("Applying automatic fixes to file:", path)
+                fix_file(path, result)
+            else:
+                success = False
+
+    return success
+
+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 URLs')
+    parser.add_argument('-v', '--verbose', action='store_true', help='verbose output')
+    parser.add_argument('DIRECTORY', help='directory (or file) that should be checked')
+    args = parser.parse_args()
+    lammpsdir = os.path.abspath(os.path.expanduser(args.DIRECTORY))
+
+    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)
+
+    if os.path.isdir(lammpsdir):
+        if not check_folder(lammpsdir, config, args.fix, args.verbose):
+           sys.exit(1)
+    else:
+        success = True
+        path = os.path.normpath(lammpsdir)
+
+        if args.verbose:
+            print("Checking file:", path)
+
+        result = check_file(path)
+
+        has_resolvable_errors = False
+
+        for lineno in result['errordocs_errors']:
+            print("[Error] Found LAMMPS errordocs @ {}:{}".format(path, lineno))
+            has_resolvable_errors = True
+
+        if has_resolvable_errors:
+            if args.fix:
+                print("Applying automatic fixes to file:", path)
+                fix_file(path, result)
+            else:
+                success = False
+
+        if not success:
+            sys.exit(1)
+
+if __name__ == "__main__":
+    main()