import sys, os
import argparse
from msmbuilder.License import LicenseString
from msmbuilder.Citation import CiteString
from msmbuilder.metrics import parsers as metric_parsers
from pprint import pprint
import warnings
import logging
logger = logging.getLogger(__name__)
def _iter_both_cases(string):
"""Iterate over the chars in a strings in both cases
>>> [e for e in _iter_both_cases("string")]
['s', 'S', 't', 'T', 'r', 'R', 'i', 'I', 'n', 'N', 'g', 'G']
"""
for c in string:
yield c
yield c.swapcase()
[docs]def die_if_path_exists(path):
if isinstance(path, list):
map(die_if_path_exists, path)
return None
directory = os.path.split(path)[0]
if len(directory) > 0 and not os.path.exists(directory):
logger.info('Creating directory %s', directory)
os.makedirs(directory)
if os.path.exists(path):
name = os.path.split(sys.argv[0])[1]
logger.error('%s: Error: %s already exists!. Exiting.', name, path)
sys.exit(1)
return None
[docs]def ensure_path_exists(path):
name = os.path.split(sys.argv[0])[1]
if not os.path.exists(path):
logger.error("%s: Error: Can't find %s", name, path)
sys.exit(1)
RESERVED = {'assignments': ('-a', 'Path to assignments file.', 'Data/Assignments.h5', str),
'project': ('-p', 'Path to ProjectInfo file.', 'ProjectInfo.yaml', str),
'tProb': ('-t', 'Path to transition matrix.', 'Data/tProb.mtx', str),
'output_dir': ('-o', 'Location to save results.', 'Data/', str),
'pdb': ('-s', 'Path to PDB structure file.', None, str)}
[docs]def add_argument(group, dest, help=None, type=None, choices=None, nargs=None, default=None, action=None):
"""
Wrapper around arglib.ArgumentParser.add_argument. Gives you a short name
directly from your longname
"""
if dest in RESERVED:
short = RESERVED[dest][0]
if help is None:
help = RESERVED[dest][1]
if default is None:
default = RESERVED[dest][2]
if type is None:
type = RESERVED[dest][3]
kwargs = {}
if action == 'store_true' or action == 'store_false':
type = None
if type != None:
kwargs['type'] = type
if action is not None:
kwargs['action'] = action
if nargs is not None:
kwargs['nargs'] = nargs
if choices is not None:
kwargs['choices'] = choices
if type != None:
kwargs['choices'] = [type(c) for c in choices]
long = '--{name}'.format(name=dest)
found_short = False
for char in _iter_both_cases(dest):
if not dest in RESERVED:
short = '-%s' % char
args = (short, long)
if default is None:
kwargs['required'] = True
kwargs['help'] = help
else:
if help is None:
helptext = 'Default: {default}'.format(default=default)
else:
if help[-1] != '.':
help += '.'
helptext = '{help} Default: {default}'.format(help=help, default=default)
kwargs['help'] = helptext
kwargs['default'] = default
try:
group.add_argument(*args, **kwargs)
found_short = True
break
except argparse.ArgumentError:
pass
if not found_short:
raise ValueError('Could not find short name')
return dest, type
[docs]class ArgumentParser(object):
"MSMBuilder specific wrapper around argparse.ArgumentParser"
def __init__(self, *args, **kwargs):
"""Create an ArgumentParser
Parameters
----------
description: (str, optional)
get_metric: (bool, optional) - Pass true if you want to use the metric parser and get a metric instance returned
"""
self.extra_groups = []
self.metric_parser_list = []
self.print_argparse_bug_warning = False
if 'description' in kwargs:
kwargs['description'] += ('\n' + '-' * 80)
kwargs['formatter_class'] = argparse.RawDescriptionHelpFormatter
if 'get_metric' in kwargs:
self.get_metric = bool(kwargs.pop('get_metric')) # pop gets the value plus removes the entry
else:
self.get_metric = False
if 'get_basic_metric' in kwargs:
self.get_basic_metric = bool(kwargs.pop('get_basic_metric'))
else:
self.get_basic_metric = False
if self.get_metric and self.get_basic_metric:
warnings.warn('You should only pass one of get_metric and get_basic_metric. See arglib.py for details.')
self.get_basic_metric = False
self.parser = argparse.ArgumentParser(*args, **kwargs)
self.parser.add_argument('-q', '--quiet', dest='quiet', help='Pass this flag to run in quiet mode.',
default=False, action='store_true')
if self.get_metric:
self.metric_parser_list = metric_parsers.add_metric_parsers( self, add_layer_metrics=True )
elif self.get_basic_metric:
self.metric_parser_list = metric_parsers.add_metric_parsers( self, add_layer_metrics=False )
self.parser.prog = os.path.split(sys.argv[0])[1]
self.required = self.parser.add_argument_group(title='required arguments')
self.wdefaults = self.parser.add_argument_group(title='arguments with defaults')
self.short_strings = set(['-h'])
self.name_to_type = {}
for v in RESERVED.values():
self.short_strings.add(v[0])
[docs] def add_argument_group(self, title):
self.extra_groups.append(self.parser.add_argument_group(title=title))
[docs] def add_argument(self, dest, help=None, type=None, choices=None, nargs=None, default=None, action=None):
if dest in RESERVED and default is None:
default = RESERVED[dest][2]
if action == 'store_true':
default = False
elif action == 'store_false':
default = True
if (nargs in ['+', '*', '?']) and (self.get_metric):
self.print_argparse_bug_warning = True
if choices:
for choice in choices:
if not isinstance(choice, str):
warnings.warn('arglib bug: choices should all be str')
if default is None:
group = self.required
else:
group = self.wdefaults
if len(self.extra_groups) > 0:
group = self.extra_groups[-1]
name, type = add_argument(group, dest, help, type, choices, nargs, default, action)
self.name_to_type[name] = type
[docs] def add_subparsers(self, *args, **kwargs):
return self.parser.add_subparsers(*args, **kwargs)
[docs] def parse_args(self, args=None, namespace=None, print_banner=True):
if print_banner:
print LicenseString
print CiteString
if self.print_argparse_bug_warning:
print "#" * 80
print "\n"
warnings.warn('Known bug in argparse regarding subparsers and optional arguments with nargs=[+*?] (http://bugs.python.org/issue9571)')
print "\n"
print "#" * 80
namespace = self.parser.parse_args(args=args, namespace=namespace)
if print_banner:
pprint(namespace.__dict__)
if namespace.quiet:
# set the level of the root logger
logging.getLogger().setLevel(logging.WARNING)
if self.get_metric or self.get_basic_metric: # if we want to get the metric, then we have to construct it
metric = metric_parsers.construct_metric(namespace)
return namespace, metric
return namespace
def _typecast(self, namespace):
"""Work around for the argparse bug with respect to defaults and FileType not
playing together nicely -- http://stackoverflow.com/questions/8236954/specifying-default-filenames-with-argparse-but-not-opening-them-on-help"""
for name, type in self.name_to_type.iteritems():
setattr(namespace, name, type(getattr(namespace, name)))
return namespace