def main():
"""Run the checking script."""
parser = OptionParser()
parser.add_option('-S', '--source-root',
help='Source tree root directory')
parser.add_option('-B', '--build-root',
help='Build tree root directory')
parser.add_option('--installed',
help='Read list of installed files from given file')
parser.add_option('-l', '--log',
help='Write issues into a given log file in addition to stderr')
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
parser.add_option('--check-ignored', action='store_true',
help='Check documentation ignored by Doxygen')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
installedlist = []
if options.installed:
with open(options.installed, 'r') as outfile:
for line in outfile:
installedlist.append(line.strip())
reporter = Reporter(options.log)
if options.ignore:
reporter.load_filters(options.ignore)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.set_installed_file_list(installedlist)
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files()
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml()
reporter.write_pending()
if not options.quiet:
sys.stderr.write('Checking...\n')
for fileobj in tree.get_files():
check_file(fileobj, reporter)
for includedfile in fileobj.get_includes():
check_include(fileobj, includedfile, reporter)
for classobj in tree.get_classes():
check_class(classobj, reporter)
for memberobj in tree.get_members():
if memberobj.is_visible() or options.check_ignored:
check_member(memberobj, reporter)
reporter.write_pending()
reporter.report_unused_filters()
reporter.close_log()
def main():
"""Run the graph generation script."""
import os
import sys
from optparse import OptionParser
from gmxtree import GromacsTree
from reporter import Reporter
parser = OptionParser()
parser.add_option('-S', '--source-root',
help='Source tree root directory')
parser.add_option('-B', '--build-root',
help='Build tree root directory')
parser.add_option('--ignore-cycles',
help='Set file with module dependencies to ignore in cycles')
parser.add_option('-o', '--outdir', default='.',
help='Specify output directory for graphs')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_installed_file_list()
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files()
if options.ignore_cycles:
tree.load_cycle_suppression_list(options.ignore_cycles)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml(only_files=True)
if not options.quiet:
sys.stderr.write('Writing graphs...\n')
graphbuilder = GraphBuilder(tree)
if not os.path.exists(options.outdir):
os.mkdir(options.outdir)
filename = os.path.join(options.outdir, 'module-deps.dot')
graph = graphbuilder.create_modules_graph()
with open(filename, 'w') as outfile:
graph.write(outfile)
# Skip some modules that are too big to make any sense
skippedmodules = ('legacyheaders', 'gmxlib', 'mdlib', 'gmxana', 'gmxpreprocess')
for module in tree.get_modules():
if not module.get_name()[7:] in skippedmodules:
filename = '{0}-deps.dot'.format(module.get_name())
filename = os.path.join(options.outdir, filename)
graph = graphbuilder.create_module_file_graph(module)
with open(filename, 'w') as outfile:
graph.write(outfile)
def main():
"""Run the checking script."""
parser = OptionParser()
parser.add_option('-S', '--source-root', help='Source tree root directory')
parser.add_option('-B', '--build-root', help='Build tree root directory')
parser.add_option(
'-l',
'--log',
help='Write issues into a given log file in addition to stderr')
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
parser.add_option('--check-ignored',
action='store_true',
help='Issue notes for comments ignored by Doxygen')
parser.add_option('-q',
'--quiet',
action='store_true',
help='Do not write status messages')
parser.add_option('--exitcode',
action='store_true',
help='Return non-zero exit code if there are warnings')
options, args = parser.parse_args()
reporter = Reporter(options.log)
if options.ignore:
reporter.load_filters(options.ignore)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_git_attributes()
if not options.quiet:
sys.stderr.write('Reading source files...\n')
# TODO: The checking should be possible without storing everything in memory
tree.scan_files(keep_contents=True)
if not options.quiet:
sys.stderr.write(
'Finding config.h and other preprocessor macro uses...\n')
tree.find_define_file_uses()
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml()
reporter.write_pending()
if not options.quiet:
sys.stderr.write('Checking...\n')
check_all(tree, reporter, options.check_ignored)
reporter.write_pending()
reporter.report_unused_filters()
reporter.close_log()
if options.exitcode and reporter.had_warnings():
sys.exit(1)
def main():
"""Run the graph generation script."""
import os
import sys
from optparse import OptionParser
from gmxtree import GromacsTree
from reporter import Reporter
parser = OptionParser()
parser.add_option('-S', '--source-root', help='Source tree root directory')
parser.add_option('-B', '--build-root', help='Build tree root directory')
parser.add_option(
'--ignore-cycles',
help='Set file with module dependencies to ignore in cycles')
parser.add_option('-o',
'--outdir',
default='.',
help='Specify output directory for graphs')
parser.add_option('-q',
'--quiet',
action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files()
if options.ignore_cycles:
tree.load_cycle_suppression_list(options.ignore_cycles)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml(only_files=True)
if not options.quiet:
sys.stderr.write('Writing graphs...\n')
graphbuilder = GraphBuilder(tree)
if not os.path.exists(options.outdir):
os.mkdir(options.outdir)
filename = os.path.join(options.outdir, 'module-deps.dot')
graph = graphbuilder.create_modules_graph()
with open(filename, 'w') as outfile:
graph.write(outfile)
# Skip some modules that are too big to make any sense
skippedmodules = ('gmxlib', 'mdlib', 'gmxana', 'gmxpreprocess')
for module in tree.get_modules():
if not module.get_name()[7:] in skippedmodules:
filename = '{0}-deps.dot'.format(module.get_name())
filename = os.path.join(options.outdir, filename)
graph = graphbuilder.create_module_file_graph(module)
with open(filename, 'w') as outfile:
graph.write(outfile)
def main():
"""Run the include sorter script."""
import os
import sys
from optparse import OptionParser
from gmxtree import GromacsTree
from reporter import Reporter
parser = OptionParser()
parser.add_option('-S', '--source-root', help='Source tree root directory')
parser.add_option('-B', '--build-root', help='Build tree root directory')
parser.add_option('-F', '--files', help='Specify files to sort')
parser.add_option('-q',
'--quiet',
action='store_true',
help='Do not write status messages')
# This is for evaluating different options; can be removed from the final
# version.
parser.add_option('-s',
'--style',
type='choice',
default='pub-priv',
choices=('single-group', 'pub-priv', 'pub-local'),
help='Style for Gromacs includes')
parser.add_option('--absolute',
action='store_true',
help='Write all include paths relative to src/')
options, args = parser.parse_args()
filelist = args
if options.files:
if options.files == '-':
lines = sys.stdin.readlines()
else:
with open(options.files, 'r') as fp:
lines = fp.readlines()
filelist.extend([x.strip() for x in lines])
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_installed_file_list()
files = []
for filename in filelist:
fileobj = tree.get_file(os.path.abspath(filename))
if not fileobj:
sys.stderr.write(
'warning: ignoring unknown file {0}\n'.format(filename))
continue
files.append(fileobj)
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files(only_files=files, keep_contents=True)
extfiles = set(files)
for fileobj in files:
for included_file in fileobj.get_includes():
other_file = included_file.get_file()
if other_file:
extfiles.add(other_file)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml(only_files=extfiles)
if not options.quiet:
sys.stderr.write('Sorting includes...\n')
sorter = IncludeSorter(GroupedSorter(options.style, options.absolute),
options.quiet)
for fileobj in files:
sorter.sort_includes(fileobj)
def main():
"""Run the checking script."""
parser = OptionParser()
parser.add_option('-S', '--source-root',
help='Source tree root directory')
parser.add_option('-B', '--build-root',
help='Build tree root directory')
parser.add_option('-l', '--log',
help='Write issues into a given log file in addition to stderr')
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
parser.add_option('--ignore-cycles',
help='Set file with module dependencies to ignore in cycles')
parser.add_option('--check-ignored', action='store_true',
help='Issue notes for comments ignored by Doxygen')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
parser.add_option('--exitcode', action='store_true',
help='Return non-zero exit code if there are warnings')
options, args = parser.parse_args()
reporter = Reporter(options.log)
if options.ignore:
reporter.load_filters(options.ignore)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_git_attributes()
tree.load_installed_file_list()
if not options.quiet:
sys.stderr.write('Reading source files...\n')
# TODO: The checking should be possible without storing everything in memory
tree.scan_files(keep_contents=True)
if not options.quiet:
sys.stderr.write('Finding config.h and other preprocessor macro uses...\n')
tree.find_define_file_uses()
if options.ignore_cycles:
tree.load_cycle_suppression_list(options.ignore_cycles)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml()
reporter.write_pending()
if not options.quiet:
sys.stderr.write('Checking...\n')
check_all(tree, reporter, options.check_ignored)
reporter.write_pending()
reporter.report_unused_filters()
reporter.close_log()
if options.exitcode and reporter.had_warnings():
sys.exit(1)
def main():
"""Run the include sorter script."""
import os
import sys
from optparse import OptionParser
from gmxtree import GromacsTree
from reporter import Reporter
parser = OptionParser()
parser.add_option("-S", "--source-root", help="Source tree root directory")
parser.add_option("-B", "--build-root", help="Build tree root directory")
parser.add_option("-F", "--files", help="Specify files to sort")
parser.add_option("-q", "--quiet", action="store_true", help="Do not write status messages")
# This is for evaluating different options; can be removed from the final
# version.
parser.add_option(
"-s",
"--style",
type="choice",
default="pub-priv",
choices=("single-group", "pub-priv", "pub-local"),
help="Style for GROMACS includes",
)
parser.add_option("--absolute", action="store_true", help="Write all include paths relative to src/")
options, args = parser.parse_args()
filelist = args
if options.files:
if options.files == "-":
lines = sys.stdin.readlines()
else:
with open(options.files, "r") as fp:
lines = fp.readlines()
filelist.extend([x.strip() for x in lines])
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write("Scanning source tree...\n")
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_installed_file_list()
files = []
for filename in filelist:
fileobj = tree.get_file(os.path.abspath(filename))
if not fileobj:
sys.stderr.write("warning: ignoring unknown file {0}\n".format(filename))
continue
files.append(fileobj)
if not options.quiet:
sys.stderr.write("Reading source files...\n")
tree.scan_files(only_files=files, keep_contents=True)
extfiles = set(files)
for fileobj in files:
for included_file in fileobj.get_includes():
other_file = included_file.get_file()
if other_file:
extfiles.add(other_file)
if not options.quiet:
sys.stderr.write("Reading Doxygen XML files...\n")
tree.load_xml(only_files=extfiles)
if not options.quiet:
sys.stderr.write("Sorting includes...\n")
sorter = IncludeSorter(GroupedSorter(options.style, options.absolute), options.quiet)
for fileobj in files:
sorter.sort_includes(fileobj)
def main():
"""Run the include sorter script."""
import os
import sys
from optparse import OptionParser
from gmxtree import GromacsTree
from reporter import Reporter
parser = OptionParser()
parser.add_option('-S', '--source-root',
help='Source tree root directory')
parser.add_option('-B', '--build-root',
help='Build tree root directory')
parser.add_option('-F', '--files',
help='Specify files to sort')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
# This is for evaluating different options; can be removed from the final
# version.
parser.add_option('-s', '--style', type='choice', default='pub-priv',
choices=('single-group', 'pub-priv', 'pub-local'),
help='Style for GROMACS includes')
parser.add_option('--absolute', action='store_true',
help='Write all include paths relative to src/')
options, args = parser.parse_args()
filelist = args
if options.files:
if options.files == '-':
lines = sys.stdin.readlines()
else:
with open(options.files, 'r') as fp:
lines = fp.readlines()
filelist.extend([x.strip() for x in lines])
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.load_installed_file_list()
files = []
for filename in filelist:
fileobj = tree.get_file(os.path.abspath(filename))
if not fileobj:
sys.stderr.write('warning: ignoring unknown file {0}\n'.format(filename))
continue
files.append(fileobj)
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files(only_files=files, keep_contents=True)
extfiles = set(files)
for fileobj in files:
for included_file in fileobj.get_includes():
other_file = included_file.get_file()
if other_file:
extfiles.add(other_file)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml(only_files=extfiles)
if not options.quiet:
sys.stderr.write('Sorting includes...\n')
sorter = IncludeSorter(GroupedSorter(options.style, options.absolute), options.quiet)
for fileobj in files:
sorter.sort_includes(fileobj)
def main():
"""Run the checking script."""
parser = OptionParser()
parser.add_option('-S', '--source-root', help='Source tree root directory')
parser.add_option('-B', '--build-root', help='Build tree root directory')
parser.add_option('--installed',
help='Read list of installed files from given file')
parser.add_option(
'-l',
'--log',
help='Write issues into a given log file in addition to stderr')
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
parser.add_option('--check-ignored',
action='store_true',
help='Check documentation ignored by Doxygen')
parser.add_option('-q',
'--quiet',
action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
installedlist = []
if options.installed:
with open(options.installed, 'r') as outfile:
for line in outfile:
installedlist.append(line.strip())
reporter = Reporter(options.log)
if options.ignore:
reporter.load_filters(options.ignore)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
tree.set_installed_file_list(installedlist)
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files()
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml()
reporter.write_pending()
if not options.quiet:
sys.stderr.write('Checking...\n')
for fileobj in tree.get_files():
check_file(fileobj, reporter)
for includedfile in fileobj.get_includes():
check_include(fileobj, includedfile, reporter)
for classobj in tree.get_classes():
check_class(classobj, reporter)
for memberobj in tree.get_members():
if memberobj.is_visible() or options.check_ignored:
check_member(memberobj, reporter)
reporter.write_pending()
reporter.report_unused_filters()
reporter.close_log()
