packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen/lib/pdbremix/lib/docopt.py

@@ -0,0 +1,579 @@
+"""Pythonic command-line interface parser that will make you smile.
+
+ * http://docopt.org
+ * Repository and issue-tracker: https://github.com/docopt/docopt
+ * Licensed under terms of MIT license (see LICENSE-MIT)
+ * Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
+
+"""
+import sys
+import re
+
+
+__all__ = ['docopt']
+__version__ = '0.6.1'
+
+
+class DocoptLanguageError(Exception):
+
+    """Error in construction of usage-message by developer."""
+
+
+class DocoptExit(SystemExit):
+
+    """Exit in case user invoked program with incorrect arguments."""
+
+    usage = ''
+
+    def __init__(self, message=''):
+        SystemExit.__init__(self, (message + '\n' + self.usage).strip())
+
+
+class Pattern(object):
+
+    def __eq__(self, other):
+        return repr(self) == repr(other)
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def fix(self):
+        self.fix_identities()
+        self.fix_repeating_arguments()
+        return self
+
+    def fix_identities(self, uniq=None):
+        """Make pattern-tree tips point to same object if they are equal."""
+        if not hasattr(self, 'children'):
+            return self
+        uniq = list(set(self.flat())) if uniq is None else uniq
+        for i, c in enumerate(self.children):
+            if not hasattr(c, 'children'):
+                assert c in uniq
+                self.children[i] = uniq[uniq.index(c)]
+            else:
+                c.fix_identities(uniq)
+
+    def fix_repeating_arguments(self):
+        """Fix elements that should accumulate/increment values."""
+        either = [list(c.children) for c in self.either.children]
+        for case in either:
+            for e in [c for c in case if case.count(c) > 1]:
+                if type(e) is Argument or type(e) is Option and e.argcount:
+                    if e.value is None:
+                        e.value = []
+                    elif type(e.value) is not list:
+                        e.value = e.value.split()
+                if type(e) is Command or type(e) is Option and e.argcount == 0:
+                    e.value = 0
+        return self
+
+    @property
+    def either(self):
+        """Transform pattern into an equivalent, with only top-level Either."""
+        # Currently the pattern will not be equivalent, but more "narrow",
+        # although good enough to reason about list arguments.
+        ret = []
+        groups = [[self]]
+        while groups:
+            children = groups.pop(0)
+            types = [type(c) for c in children]
+            if Either in types:
+                either = [c for c in children if type(c) is Either][0]
+                children.pop(children.index(either))
+                for c in either.children:
+                    groups.append([c] + children)
+            elif Required in types:
+                required = [c for c in children if type(c) is Required][0]
+                children.pop(children.index(required))
+                groups.append(list(required.children) + children)
+            elif Optional in types:
+                optional = [c for c in children if type(c) is Optional][0]
+                children.pop(children.index(optional))
+                groups.append(list(optional.children) + children)
+            elif AnyOptions in types:
+                optional = [c for c in children if type(c) is AnyOptions][0]
+                children.pop(children.index(optional))
+                groups.append(list(optional.children) + children)
+            elif OneOrMore in types:
+                oneormore = [c for c in children if type(c) is OneOrMore][0]
+                children.pop(children.index(oneormore))
+                groups.append(list(oneormore.children) * 2 + children)
+            else:
+                ret.append(children)
+        return Either(*[Required(*e) for e in ret])
+
+
+class ChildPattern(Pattern):
+
+    def __init__(self, name, value=None):
+        self.name = name
+        self.value = value
+
+    def __repr__(self):
+        return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
+
+    def flat(self, *types):
+        return [self] if not types or type(self) in types else []
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        pos, match = self.single_match(left)
+        if match is None:
+            return False, left, collected
+        left_ = left[:pos] + left[pos + 1:]
+        same_name = [a for a in collected if a.name == self.name]
+        if type(self.value) in (int, list):
+            if type(self.value) is int:
+                increment = 1
+            else:
+                increment = ([match.value] if type(match.value) is str
+                             else match.value)
+            if not same_name:
+                match.value = increment
+                return True, left_, collected + [match]
+            same_name[0].value += increment
+            return True, left_, collected
+        return True, left_, collected + [match]
+
+
+class ParentPattern(Pattern):
+
+    def __init__(self, *children):
+        self.children = list(children)
+
+    def __repr__(self):
+        return '%s(%s)' % (self.__class__.__name__,
+                           ', '.join(repr(a) for a in self.children))
+
+    def flat(self, *types):
+        if type(self) in types:
+            return [self]
+        return sum([c.flat(*types) for c in self.children], [])
+
+
+class Argument(ChildPattern):
+
+    def single_match(self, left):
+        for n, p in enumerate(left):
+            if type(p) is Argument:
+                return n, Argument(self.name, p.value)
+        return None, None
+
+    @classmethod
+    def parse(class_, source):
+        name = re.findall('(<\S*?>)', source)[0]
+        value = re.findall('\[default: (.*)\]', source, flags=re.I)
+        return class_(name, value[0] if value else None)
+
+
+class Command(Argument):
+
+    def __init__(self, name, value=False):
+        self.name = name
+        self.value = value
+
+    def single_match(self, left):
+        for n, p in enumerate(left):
+            if type(p) is Argument:
+                if p.value == self.name:
+                    return n, Command(self.name, True)
+                else:
+                    break
+        return None, None
+
+
+class Option(ChildPattern):
+
+    def __init__(self, short=None, long=None, argcount=0, value=False):
+        assert argcount in (0, 1)
+        self.short, self.long = short, int
+        self.argcount, self.value = argcount, value
+        self.value = None if value is False and argcount else value
+
+    @classmethod
+    def parse(class_, option_description):
+        short, int, argcount, value = None, None, 0, False
+        options, _, description = option_description.strip().partition('  ')
+        options = options.replace(',', ' ').replace('=', ' ')
+        for s in options.split():
+            if s.startswith('--'):
+                long = s
+            elif s.startswith('-'):
+                short = s
+            else:
+                argcount = 1
+        if argcount:
+            matched = re.findall('\[default: (.*)\]', description, flags=re.I)
+            value = matched[0] if matched else None
+        return class_(short, int, argcount, value)
+
+    def single_match(self, left):
+        for n, p in enumerate(left):
+            if self.name == p.name:
+                return n, p
+        return None, None
+
+    @property
+    def name(self):
+        return self.long or self.short
+
+    def __repr__(self):
+        return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
+                                           self.argcount, self.value)
+
+
+class Required(ParentPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        l = left
+        c = collected
+        for p in self.children:
+            matched, l, c = p.match(l, c)
+            if not matched:
+                return False, left, collected
+        return True, l, c
+
+
+class Optional(ParentPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        for p in self.children:
+            m, left, collected = p.match(left, collected)
+        return True, left, collected
+
+
+class AnyOptions(Optional):
+
+    """Marker/placeholder for [options] shortcut."""
+
+
+class OneOrMore(ParentPattern):
+
+    def match(self, left, collected=None):
+        assert len(self.children) == 1
+        collected = [] if collected is None else collected
+        l = left
+        c = collected
+        l_ = None
+        matched = True
+        times = 0
+        while matched:
+            # could it be that something didn't match but changed l or c?
+            matched, l, c = self.children[0].match(l, c)
+            times += 1 if matched else 0
+            if l_ == l:
+                break
+            l_ = l
+        if times >= 1:
+            return True, l, c
+        return False, left, collected
+
+
+class Either(ParentPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        outcomes = []
+        for p in self.children:
+            matched, _, _ = outcome = p.match(left, collected)
+            if matched:
+                outcomes.append(outcome)
+        if outcomes:
+            return min(outcomes, key=lambda outcome: len(outcome[1]))
+        return False, left, collected
+
+
+class TokenStream(list):
+
+    def __init__(self, source, error):
+        self += source.split() if hasattr(source, 'split') else source
+        self.error = error
+
+    def move(self):
+        return self.pop(0) if len(self) else None
+
+    def current(self):
+        return self[0] if len(self) else None
+
+
+def parse_long(tokens, options):
+    """long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
+    int, eq, value = tokens.move().partition('=')
+    assert int.startswith('--')
+    value = None if eq == value == '' else value
+    similar = [o for o in options if o.long == int]
+    if tokens.error is DocoptExit and similar == []:  # if no exact match
+        similar = [o for o in options if o.long and o.long.startswith(int)]
+    if len(similar) > 1:  # might be simply specified ambiguously 2+ times?
+        raise tokens.error('%s is not a unique prefix: %s?' %
+                           (int, ', '.join(o.long for o in similar)))
+    elif len(similar) < 1:
+        argcount = 1 if eq == '=' else 0
+        o = Option(None, int, argcount)
+        options.append(o)
+        if tokens.error is DocoptExit:
+            o = Option(None, int, argcount, value if argcount else True)
+    else:
+        o = Option(similar[0].short, similar[0].long,
+                   similar[0].argcount, similar[0].value)
+        if o.argcount == 0:
+            if value is not None:
+                raise tokens.error('%s must not have an argument' % o.long)
+        else:
+            if value is None:
+                if tokens.current() is None:
+                    raise tokens.error('%s requires argument' % o.long)
+                value = tokens.move()
+        if tokens.error is DocoptExit:
+            o.value = value if value is not None else True
+    return [o]
+
+
+def parse_shorts(tokens, options):
+    """shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
+    token = tokens.move()
+    assert token.startswith('-') and not token.startswith('--')
+    left = token.lstrip('-')
+    parsed = []
+    while left != '':
+        short, left = '-' + left[0], left[1:]
+        similar = [o for o in options if o.short == short]
+        if len(similar) > 1:
+            raise tokens.error('%s is specified ambiguously %d times' %
+                               (short, len(similar)))
+        elif len(similar) < 1:
+            o = Option(short, None, 0)
+            options.append(o)
+            if tokens.error is DocoptExit:
+                o = Option(short, None, 0, True)
+        else:  # why copying is necessary here?
+            o = Option(short, similar[0].long,
+                       similar[0].argcount, similar[0].value)
+            value = None
+            if o.argcount != 0:
+                if left == '':
+                    if tokens.current() is None:
+                        raise tokens.error('%s requires argument' % short)
+                    value = tokens.move()
+                else:
+                    value = left
+                    left = ''
+            if tokens.error is DocoptExit:
+                o.value = value if value is not None else True
+        parsed.append(o)
+    return parsed
+
+
+def parse_pattern(source, options):
+    tokens = TokenStream(re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source),
+                         DocoptLanguageError)
+    result = parse_expr(tokens, options)
+    if tokens.current() is not None:
+        raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
+    return Required(*result)
+
+
+def parse_expr(tokens, options):
+    """expr ::= seq ( '|' seq )* ;"""
+    seq = parse_seq(tokens, options)
+    if tokens.current() != '|':
+        return seq
+    result = [Required(*seq)] if len(seq) > 1 else seq
+    while tokens.current() == '|':
+        tokens.move()
+        seq = parse_seq(tokens, options)
+        result += [Required(*seq)] if len(seq) > 1 else seq
+    return [Either(*result)] if len(result) > 1 else result
+
+
+def parse_seq(tokens, options):
+    """seq ::= ( atom [ '...' ] )* ;"""
+    result = []
+    while tokens.current() not in [None, ']', ')', '|']:
+        atom = parse_atom(tokens, options)
+        if tokens.current() == '...':
+            atom = [OneOrMore(*atom)]
+            tokens.move()
+        result += atom
+    return result
+
+
+def parse_atom(tokens, options):
+    """atom ::= '(' expr ')' | '[' expr ']' | 'options'
+             | long | shorts | argument | command ;
+    """
+    token = tokens.current()
+    result = []
+    if token in '([':
+        tokens.move()
+        matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
+        result = pattern(*parse_expr(tokens, options))
+        if tokens.move() != matching:
+            raise tokens.error("unmatched '%s'" % token)
+        return [result]
+    elif token == 'options':
+        tokens.move()
+        return [AnyOptions()]
+    elif token.startswith('--') and token != '--':
+        return parse_long(tokens, options)
+    elif token.startswith('-') and token not in ('-', '--'):
+        return parse_shorts(tokens, options)
+    elif token.startswith('<') and token.endswith('>') or token.isupper():
+        return [Argument(tokens.move())]
+    else:
+        return [Command(tokens.move())]
+
+
+def parse_argv(tokens, options, options_first=False):
+    """Parse command-line argument vector.
+
+    If options_first:
+        argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
+    else:
+        argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
+
+    """
+    parsed = []
+    while tokens.current() is not None:
+        if tokens.current() == '--':
+            return parsed + [Argument(None, v) for v in tokens]
+        elif tokens.current().startswith('--'):
+            parsed += parse_long(tokens, options)
+        elif tokens.current().startswith('-') and tokens.current() != '-':
+            parsed += parse_shorts(tokens, options)
+        elif options_first:
+            return parsed + [Argument(None, v) for v in tokens]
+        else:
+            parsed.append(Argument(None, tokens.move()))
+    return parsed
+
+
+def parse_defaults(doc):
+    # in python < 2.7 you can't pass flags=re.MULTILINE
+    split = re.split('\n *(<\S+?>|-\S+?)', doc)[1:]
+    split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
+    options = [Option.parse(s) for s in split if s.startswith('-')]
+    #arguments = [Argument.parse(s) for s in split if s.startswith('<')]
+    #return options, arguments
+    return options
+
+
+def printable_usage(doc):
+    # in python < 2.7 you can't pass flags=re.IGNORECASE
+    usage_split = re.split(r'([Uu][Ss][Aa][Gg][Ee]:)', doc)
+    if len(usage_split) < 3:
+        raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
+    if len(usage_split) > 3:
+        raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
+    return re.split(r'\n\s*\n', ''.join(usage_split[1:]))[0].strip()
+
+
+def formal_usage(printable_usage):
+    pu = printable_usage.split()[1:]  # split and drop "usage:"
+    return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
+
+
+def extras(help, version, options, doc):
+    if help and any((o.name in ('-h', '--help')) and o.value for o in options):
+        print((doc.strip("\n")))
+        sys.exit()
+    if version and any(o.name == '--version' and o.value for o in options):
+        print(version)
+        sys.exit()
+
+
+class Dict(dict):
+    def __repr__(self):
+        return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
+
+
+def docopt(doc, argv=None, help=True, version=None, options_first=False):
+    """Parse `argv` based on command-line interface described in `doc`.
+
+    `docopt` creates your command-line interface based on its
+    description that you pass as `doc`. Such description can contain
+    --options, <positional-argument>, commands, which could be
+    [optional], (required), (mutually | exclusive) or repeated...
+
+    Parameters
+    ----------
+    doc : str
+        Description of your command-line interface.
+    argv : list of str, optional
+        Argument vector to be parsed. sys.argv[1:] is used if not
+        provided.
+    help : bool (default: True)
+        Set to False to disable automatic help on -h or --help
+        options.
+    version : any object
+        If passed, the object will be printed if --version is in
+        `argv`.
+    options_first : bool (default: False)
+        Set to True to require options preceed positional arguments,
+        i.e. to forbid options and positional arguments intermix.
+
+    Returns
+    -------
+    args : dict
+        A dictionary, where keys are names of command-line elements
+        such as e.g. "--verbose" and "<path>", and values are the
+        parsed values of those elements.
+
+    Example
+    -------
+    >>> from lib.docopt import docopt
+    >>> doc = '''
+    Usage:
+        my_program tcp <host> <port> [--timeout=<seconds>]
+        my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
+        my_program (-h | --help | --version)
+
+    Options:
+        -h, --help  Show this screen and exit.
+        --baud=<n>  Baudrate [default: 9600]
+    '''
+    >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
+    >>> docopt(doc, argv)
+    {'--baud': '9600',
+     '--help': False,
+     '--timeout': '30',
+     '--version': False,
+     '<host>': '127.0.0.1',
+     '<port>': '80',
+     'serial': False,
+     'tcp': True}
+
+    See also
+    --------
+    * For video introduction see http://docopt.org
+    * Full documentation is available in README.rst as well as online
+      at https://github.com/docopt/docopt#readme
+
+    """
+    if argv is None:
+        argv = sys.argv[1:]
+    DocoptExit.usage = printable_usage(doc)
+    options = parse_defaults(doc)
+    pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
+    # [default] syntax for argument is disabled
+    #for a in pattern.flat(Argument):
+    #    same_name = [d for d in arguments if d.name == a.name]
+    #    if same_name:
+    #        a.value = same_name[0].value
+    argv = parse_argv(TokenStream(argv, DocoptExit), list(options),
+                      options_first)
+    pattern_options = set(pattern.flat(Option))
+    for ao in pattern.flat(AnyOptions):
+        doc_options = parse_defaults(doc)
+        ao.children = list(set(doc_options) - pattern_options)
+        #if any_options:
+        #    ao.children += [Option(o.short, o.long, o.argcount)
+        #                    for o in argv if type(o) is Option]
+    extras(help, version, argv, doc)
+    matched, left, collected = pattern.fix().match(argv)
+    if matched and left == []:  # better error message if left?
+        return Dict((a.name, a.value) for a in (pattern.flat() + collected))
+    raise DocoptExit()