def cmd_run_server(args):
setup_logging('REPROZIP-JUPYTER-SERVER', args.verbosity)
if not args.target:
sys.stderr.write("Missing experiment directory\n")
sys.exit(2)
run_server(args.target, args.jupyter_args, verbosity=args.verbosity)
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
parser = argparse.ArgumentParser(
description="Graphical user interface for reprounzip",
epilog="Please report issues to [email protected]")
parser.add_argument('--version', action='version',
version="reprounzip-qt version %s" % __version__)
parser.add_argument('-v', '--verbose', action='count', default=1,
dest='verbosity', help="augments verbosity level")
parser.add_argument('package', nargs=argparse.OPTIONAL)
parser.add_argument('--unpacked', action='append', default=[])
argv = sys.argv[1:]
i = 0
while i < len(argv):
if argv[i].startswith('-psn'):
del argv[i]
else:
i += 1
args = parser.parse_args(argv)
setup_logging('REPROUNZIP-QT', args.verbosity)
from reprounzip_qt.gui import Application, ReprounzipUi
app = Application(sys.argv)
window_args = {}
if args.package and args.unpacked:
sys.stderr.write("You can't pass both a package and a unpacked "
"directory\n")
sys.exit(2)
elif args.package:
logger.info("Got package on the command-line: %s", args.package)
record_usage(cmdline='package')
window_args = dict(unpack=dict(package=args.package))
elif len(args.unpacked) == 1:
logger.info("Got unpacked directory on the command-line: %s",
args.unpacked)
record_usage(cmdline='directory')
window_args = dict(run=dict(unpacked_directory=args.unpacked[0]),
tab=1)
elif args.unpacked:
sys.stderr.write("You may only use --unpacked once\n")
sys.exit(2)
else:
record_usage(cmdline='empty')
window = ReprounzipUi(**window_args)
app.set_first_window(window)
window.setVisible(True)
app.exec_()
submit_usage_report()
sys.exit(0)
def cmd_trace_notebook(args):
setup_logging('REPROZIP-JUPYTER-TRACE', args.verbosity)
if not args.notebook:
sys.stderr.write("missing notebook\n")
sys.exit(2)
return trace_notebook(args.notebook,
save_notebook=args.save_notebook,
verbosity=args.verbosity, dir=args.dir,
identify_packages=args.identify_packages,
find_inputs_outputs=args.find_inputs_outputs,
append=args.append)
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
# Parses command-line
# General options
def add_options(opts):
opts.add_argument('--version', action='version',
version="reprounzip version %s" % __version__)
# Loads plugins
for name, func, descr, descr_1 in get_plugins('reprounzip.plugins'):
func()
parser = RPUZArgumentParser(
description="reprounzip is the ReproZip component responsible for "
"unpacking and reproducing an experiment previously "
"packed with reprozip",
epilog="Please report issues to [email protected]")
add_options(parser)
parser.add_argument('-v', '--verbose', action='count', default=1,
dest='verbosity',
help="augments verbosity level")
subparsers = parser.add_subparsers(title="subcommands", metavar='')
# usage_report subcommand
parser_stats = subparsers.add_parser(
'usage_report',
help="Enables or disables anonymous usage reports")
add_options(parser_stats)
parser_stats.add_argument('--enable', action='store_true')
parser_stats.add_argument('--disable', action='store_true')
parser_stats.set_defaults(func=usage_report)
# Loads unpackers
for name, func, descr, descr_1 in get_plugins('reprounzip.unpackers'):
plugin_parser = subparsers.add_parser(
name, help=descr_1, description=descr,
formatter_class=argparse.RawDescriptionHelpFormatter)
add_options(plugin_parser)
info = func(plugin_parser)
plugin_parser.set_defaults(selected_unpacker=name)
if info is None:
info = {}
unpackers[name] = info
signals.pre_parse_args(parser=parser, subparsers=subparsers)
args = parser.parse_args()
signals.post_parse_args(args=args)
if getattr(args, 'func', None) is None:
parser.print_help(sys.stderr)
sys.exit(2)
signals.unpacker = getattr(args, 'selected_unpacker', None)
setup_logging('REPROUNZIP', args.verbosity)
setup_usage_report('reprounzip', __version__)
if hasattr(args, 'selected_unpacker'):
record_usage(unpacker=args.selected_unpacker)
signals.pre_setup.subscribe(lambda **kw: record_usage(setup=True))
signals.pre_run.subscribe(lambda **kw: record_usage(run=True))
try:
try:
args.func(args)
except UsageError:
raise
except Exception as e:
signals.application_finishing(reason=e)
submit_usage_report(result=type(e).__name__)
raise
else:
signals.application_finishing(reason=None)
except UsageError:
parser.print_help(sys.stderr)
sys.exit(2)
submit_usage_report(result='success')
sys.exit(0)
def run_from_vistrails():
setup_logging('REPROUNZIP-VISTRAILS', logging.INFO)
cli_version = 1
if len(sys.argv) > 1:
try:
cli_version = int(sys.argv[1])
except ValueError:
logging.info("Compatibility mode: reprounzip-vistrails didn't get "
"a version number")
if cli_version != 1:
logging.critical("Unknown interface version %d; you are probably "
"using a version of reprounzip-vistrails too old for "
"your VisTrails package. Consider upgrading.",
cli_version)
sys.exit(1)
parser = argparse.ArgumentParser()
parser.add_argument('unpacker')
parser.add_argument('directory')
parser.add_argument('run')
parser.add_argument('--input-file', action='append', default=[])
parser.add_argument('--output-file', action='append', default=[])
parser.add_argument('--cmdline', action='store')
args = parser.parse_args(sys.argv[2:])
config = load_config(Path(args.directory) / 'config.yml', canonical=True)
python = sys.executable
rpuz = [python, '-m', 'reprounzip.main', args.unpacker]
os.environ['REPROUNZIP_NON_INTERACTIVE'] = 'y'
def cmd(lst, add=None):
if add:
logging.info("cmd: %s %s", ' '.join(lst), add)
string = ' '.join(shell_escape(a) for a in (rpuz + lst))
string += ' ' + add
subprocess.check_call(string, shell=True,
cwd=args.directory)
else:
logging.info("cmd: %s", ' '.join(lst))
subprocess.check_call(rpuz + lst,
cwd=args.directory)
logging.info("reprounzip-vistrails calling reprounzip; dir=%s",
args.directory)
# Parses input files from the command-line
upload_command = []
seen_input_names = set()
for input_file in args.input_file:
input_name, filename = input_file.split(':', 1)
upload_command.append('%s:%s' % (filename, input_name))
seen_input_names.add(input_name)
# Resets the input files that are used by this run and were not given
for name, f in iteritems(config.inputs_outputs):
if name not in seen_input_names and int(args.run) in f.read_runs:
upload_command.append(':%s' % name)
# Runs the command
cmd(['upload', '.'] + upload_command)
# Runs the experiment
if args.cmdline:
cmd(['run', '.', args.run, '--cmdline'], add=args.cmdline)
else:
cmd(['run', '.', args.run])
# Gets output files
for output_file in args.output_file:
output_name, filename = output_file.split(':', 1)
cmd(['download', '.',
'%s:%s' % (output_name, filename)])
def run_from_vistrails():
setup_logging('REPROUNZIP-VISTRAILS', logging.INFO)
parser = argparse.ArgumentParser()
parser.add_argument('unpacker')
parser.add_argument('directory')
parser.add_argument('run')
parser.add_argument('--input-file', action='append', default=[])
parser.add_argument('--output-file', action='append', default=[])
parser.add_argument('--cmdline', action='store')
args = parser.parse_args()
runs, packages, other_files = load_config(Path(args.directory) /
'config.yml',
canonical=True)
run = runs[int(args.run)]
python = sys.executable
rpuz = [python, '-m', 'reprounzip.main', args.unpacker]
os.environ['REPROUNZIP_NON_INTERACTIVE'] = 'y'
def cmd(lst, add=None):
if add:
logging.info("cmd: %s %s", ' '.join(lst), add)
string = ' '.join(shell_escape(a) for a in (rpuz + lst))
string += ' ' + add
subprocess.check_call(string, shell=True, cwd=args.directory)
else:
logging.info("cmd: %s", ' '.join(lst))
subprocess.check_call(rpuz + lst, cwd=args.directory)
logging.info("reprounzip-vistrails calling reprounzip; dir=%s",
args.directory)
# Parses input files from the command-line
upload_command = []
seen_input_names = set()
for input_file in args.input_file:
input_name, filename = input_file.split(':', 1)
upload_command.append('%s:%s' % (filename, input_name))
seen_input_names.add(input_name)
# Resets the input files that were not given
for input_name in run['input_files']:
if input_name not in seen_input_names:
upload_command.append(':%s' % input_name)
# Runs the command
cmd(['upload', '.'] + upload_command)
# Runs the experiment
if args.cmdline:
cmd(['run', '.', '--cmdline'], add=args.cmdline)
else:
cmd(['run', '.'])
# Gets output files
for output_file in args.output_file:
output_name, filename = output_file.split(':', 1)
cmd(['download', '.', '%s:%s' % (output_name, filename)])
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
# Encoding for output streams
if str == bytes: # PY2
writer = codecs.getwriter(locale.getpreferredencoding())
o_stdout, o_stderr = sys.stdout, sys.stderr
sys.stdout = writer(sys.stdout)
sys.stdout.buffer = o_stdout
sys.stderr = writer(sys.stderr)
sys.stderr.buffer = o_stderr
# http://bugs.python.org/issue13676
# This prevents reprozip from reading argv and envp arrays from trace
if sys.version_info < (2, 7, 3):
sys.stderr.write("Error: your version of Python, %s, is not "
"supported\nVersions before 2.7.3 are affected by "
"bug 13676 and will not work with ReproZip\n" %
sys.version.split(' ', 1)[0])
sys.exit(1)
# Parses command-line
# General options
options = argparse.ArgumentParser(add_help=False)
options.add_argument('--version',
action='version',
version="reprounzip version %s" % __version__)
options.add_argument('-v',
'--verbose',
action='count',
default=1,
dest='verbosity',
help="augments verbosity level")
parser = argparse.ArgumentParser(
description="reprounzip is the ReproZip component responsible for "
"unpacking and reproducing an experiment previously "
"packed with reprozip",
epilog="Please report issues to [email protected]",
parents=[options])
subparsers = parser.add_subparsers(title="formats",
metavar='',
dest='selected_unpacker')
parser_info = subparsers.add_parser(
'info',
parents=[options],
help="Prints out some information about a pack")
parser_info.add_argument('pack', nargs=1, help="Pack to read")
parser_info.set_defaults(func=lambda args: print_info(args, unpackers))
parser_showfiles = subparsers.add_parser(
'showfiles',
parents=[options],
help="Prints out input and output file names")
parser_showfiles.add_argument('pack',
nargs=1,
help="Pack or directory to read from")
parser_showfiles.set_defaults(func=showfiles)
# Loads commands from plugins
for entry_point in iter_entry_points('reprounzip.unpackers'):
try:
setup_function = entry_point.load()
except Exception:
print("Plugin %s from %s %s failed to initialize!" %
(entry_point.name, entry_point.dist.project_name,
entry_point.dist.version),
file=sys.stderr)
traceback.print_exc(file=sys.stderr)
continue
name = entry_point.name
# Docstring is used as description (used for detailed help)
descr = setup_function.__doc__.strip()
# First line of docstring is the help (used for general help)
descr_1 = descr.split('\n', 1)[0]
plugin_parser = subparsers.add_parser(
name,
parents=[options],
help=descr_1,
description=descr,
formatter_class=argparse.RawDescriptionHelpFormatter)
info = setup_function(plugin_parser)
if info is None:
info = {}
unpackers[name] = info
args = parser.parse_args()
signals.unpacker = args.selected_unpacker
setup_logging('REPROUNZIP', args.verbosity)
try:
args.func(args)
except Exception as e:
signals.application_finishing(reason=e)
raise
else:
signals.application_finishing(reason=None)
sys.exit(0)
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
# Parses command-line
# General options
def add_options(opts):
opts.add_argument('--version',
action='version',
version="reprounzip version %s" % __version__)
# Loads plugins
for name, func, descr, descr_1 in get_plugins('reprounzip.plugins'):
func()
parser = RPUZArgumentParser(
description="reprounzip is the ReproZip component responsible for "
"unpacking and reproducing an experiment previously "
"packed with reprozip",
epilog="Please report issues to [email protected]")
add_options(parser)
parser.add_argument('-v',
'--verbose',
action='count',
default=1,
dest='verbosity',
help="augments verbosity level")
subparsers = parser.add_subparsers(title="subcommands", metavar='')
# usage_report subcommand
parser_stats = subparsers.add_parser(
'usage_report', help="Enables or disables anonymous usage reports")
add_options(parser_stats)
parser_stats.add_argument('--enable', action='store_true')
parser_stats.add_argument('--disable', action='store_true')
parser_stats.set_defaults(func=usage_report)
# Loads unpackers
for name, func, descr, descr_1 in get_plugins('reprounzip.unpackers'):
plugin_parser = subparsers.add_parser(
name,
help=descr_1,
description=descr,
formatter_class=argparse.RawDescriptionHelpFormatter)
add_options(plugin_parser)
info = func(plugin_parser)
plugin_parser.set_defaults(selected_unpacker=name)
if info is None:
info = {}
unpackers[name] = info
signals.pre_parse_args(parser=parser, subparsers=subparsers)
args = parser.parse_args()
signals.post_parse_args(args=args)
if getattr(args, 'func', None) is None:
parser.print_help(sys.stderr)
sys.exit(2)
signals.unpacker = getattr(args, 'selected_unpacker', None)
setup_logging('REPROUNZIP', args.verbosity)
setup_usage_report('reprounzip', __version__)
if hasattr(args, 'selected_unpacker'):
record_usage(unpacker=args.selected_unpacker)
signals.pre_setup.subscribe(lambda **kw: record_usage(setup=True))
signals.pre_run.subscribe(lambda **kw: record_usage(run=True))
try:
try:
args.func(args)
except UsageError:
raise
except Exception as e:
signals.application_finishing(reason=e)
submit_usage_report(result=type(e).__name__)
raise
else:
signals.application_finishing(reason=None)
except UsageError:
parser.print_help(sys.stderr)
sys.exit(2)
submit_usage_report(result='success')
sys.exit(0)
if self.testNames is None:
self.test = self.testLoader.discover(
start_dir=os.path.dirname(os.path.abspath(__file__)),
pattern='test_*.py')
else:
self.test = self.testLoader.loadTestsFromNames(self.testNames)
if __name__ == '__main__':
# Locale
locale.setlocale(locale.LC_ALL, '')
# Disables usage reporting
os.environ['REPROZIP_USAGE_STATS'] = 'off'
setup_logging('TESTSUITE', 999)
parser = argparse.ArgumentParser(description="reprozip tests")
parser.add_argument('--unittests', action='store_true',
dest='unittests', default=None)
parser.add_argument('--no-unittests', action='store_false',
dest='unittests', default=None)
parser.add_argument('--functests', action='store_true',
dest='functests', default=None)
parser.add_argument('--no-functests', action='store_false',
dest='functests', default=None)
parser.add_argument('--interactive', action='store_true')
parser.add_argument('--run-vagrant', action='store_true')
parser.add_argument('--run-docker', action='store_true')
parser.add_argument('arg', nargs=argparse.REMAINDER)
parser.add_argument('--no-raise-warnings', action='store_false',
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
parser = argparse.ArgumentParser(
description="Graphical user interface for reprounzip",
epilog="Please report issues to [email protected]")
parser.add_argument('--version',
action='version',
version="reprounzip-qt version %s" % __version__)
parser.add_argument('-v',
'--verbose',
action='count',
default=1,
dest='verbosity',
help="augments verbosity level")
parser.add_argument('package', nargs=argparse.OPTIONAL)
parser.add_argument('--unpacked', action='append', default=[])
argv = sys.argv[1:]
i = 0
while i < len(argv):
if argv[i].startswith('-psn'):
del argv[i]
else:
i += 1
args = parser.parse_args(argv)
setup_logging('REPROUNZIP-QT', args.verbosity)
from reprounzip_qt.gui import Application, ReprounzipUi
app = Application(sys.argv)
window_args = {}
if args.package and args.unpacked:
sys.stderr.write("You can't pass both a package and a unpacked "
"directory\n")
sys.exit(2)
elif args.package:
logger.info("Got package on the command-line: %s", args.package)
record_usage(cmdline='package')
window_args = dict(unpack=dict(package=args.package))
elif len(args.unpacked) == 1:
logger.info("Got unpacked directory on the command-line: %s",
args.unpacked)
record_usage(cmdline='directory')
window_args = dict(run=dict(unpacked_directory=args.unpacked[0]),
tab=1)
elif args.unpacked:
sys.stderr.write("You may only use --unpacked once\n")
sys.exit(2)
else:
record_usage(cmdline='empty')
window = ReprounzipUi(**window_args)
app.set_first_window(window)
window.setVisible(True)
app.exec_()
submit_usage_report()
sys.exit(0)
def main():
"""Entry point when called on the command-line.
"""
# Locale
locale.setlocale(locale.LC_ALL, '')
# Encoding for output streams
if str == bytes: # PY2
writer = codecs.getwriter(locale.getpreferredencoding())
o_stdout, o_stderr = sys.stdout, sys.stderr
sys.stdout = writer(sys.stdout)
sys.stdout.buffer = o_stdout
sys.stderr = writer(sys.stderr)
sys.stderr.buffer = o_stderr
# http://bugs.python.org/issue13676
# This prevents reprozip from reading argv and envp arrays from trace
if sys.version_info < (2, 7, 3):
sys.stderr.write("Error: your version of Python, %s, is not "
"supported\nVersions before 2.7.3 are affected by "
"bug 13676 and will not work with ReproZip\n" %
sys.version.split(' ', 1)[0])
sys.exit(1)
# Parses command-line
# General options
options = argparse.ArgumentParser(add_help=False)
options.add_argument('--version', action='version',
version="reprounzip version %s" % __version__)
options.add_argument('-v', '--verbose', action='count', default=1,
dest='verbosity',
help="augments verbosity level")
parser = argparse.ArgumentParser(
description="reprounzip is the ReproZip component responsible for "
"unpacking and reproducing an experiment previously "
"packed with reprozip",
epilog="Please report issues to [email protected]",
parents=[options])
subparsers = parser.add_subparsers(title="formats", metavar='',
dest='selected_unpacker')
parser_info = subparsers.add_parser(
'info', parents=[options],
help="Prints out some information about a pack")
parser_info.add_argument('pack', nargs=1,
help="Pack to read")
parser_info.set_defaults(func=lambda args: print_info(args, unpackers))
parser_showfiles = subparsers.add_parser(
'showfiles', parents=[options],
help="Prints out input and output file names")
parser_showfiles.add_argument('pack', nargs=1,
help="Pack or directory to read from")
parser_showfiles.set_defaults(func=showfiles)
# Loads commands from plugins
for entry_point in iter_entry_points('reprounzip.unpackers'):
try:
setup_function = entry_point.load()
except Exception:
print("Plugin %s from %s %s failed to initialize!" % (
entry_point.name,
entry_point.dist.project_name, entry_point.dist.version),
file=sys.stderr)
traceback.print_exc(file=sys.stderr)
continue
name = entry_point.name
# Docstring is used as description (used for detailed help)
descr = setup_function.__doc__.strip()
# First line of docstring is the help (used for general help)
descr_1 = descr.split('\n', 1)[0]
plugin_parser = subparsers.add_parser(
name, parents=[options],
help=descr_1, description=descr,
formatter_class=argparse.RawDescriptionHelpFormatter)
info = setup_function(plugin_parser)
if info is None:
info = {}
unpackers[name] = info
args = parser.parse_args()
signals.unpacker = args.selected_unpacker
setup_logging('REPROUNZIP', args.verbosity)
try:
args.func(args)
except Exception as e:
signals.application_finishing(reason=e)
raise
else:
signals.application_finishing(reason=None)
sys.exit(0)
def run_from_vistrails():
setup_logging('REPROUNZIP-VISTRAILS', logging.INFO)
parser = argparse.ArgumentParser()
parser.add_argument('unpacker')
parser.add_argument('directory')
parser.add_argument('run')
parser.add_argument('--input-file', action='append', default=[])
parser.add_argument('--output-file', action='append', default=[])
parser.add_argument('--cmdline', action='store')
args = parser.parse_args()
runs, packages, other_files = load_config(
Path(args.directory) / 'config.yml',
canonical=True)
run = runs[int(args.run)]
python = sys.executable
rpuz = [python, '-m', 'reprounzip.main', args.unpacker]
os.environ['REPROUNZIP_NON_INTERACTIVE'] = 'y'
def cmd(lst, add=None):
if add:
logging.info("cmd: %s %s", ' '.join(lst), add)
string = ' '.join(shell_escape(a) for a in (rpuz + lst))
string += ' ' + add
subprocess.check_call(string, shell=True,
cwd=args.directory)
else:
logging.info("cmd: %s", ' '.join(lst))
subprocess.check_call(rpuz + lst,
cwd=args.directory)
logging.info("reprounzip-vistrails calling reprounzip; dir=%s",
args.directory)
# Parses input files from the command-line
upload_command = []
seen_input_names = set()
for input_file in args.input_file:
input_name, filename = input_file.split(':', 1)
upload_command.append('%s:%s' % (filename, input_name))
seen_input_names.add(input_name)
# Resets the input files that were not given
for input_name in run['input_files']:
if input_name not in seen_input_names:
upload_command.append(':%s' % input_name)
# Runs the command
cmd(['upload', '.'] + upload_command)
# Runs the experiment
if args.cmdline:
cmd(['run', '.', '--cmdline'], add=args.cmdline)
else:
cmd(['run', '.'])
# Gets output files
for output_file in args.output_file:
output_name, filename = output_file.split(':', 1)
cmd(['download', '.',
'%s:%s' % (output_name, filename)])
