New version of ipcluster and docs updates.

This branch has a complete rewrite of the ipcluster script.  The script
is now based on Twisted and has support for starting clusters using
PBS, mpirun and on localhost.

The developer docs have been fully updated to reflect our current
dev workflow with lp and bzr.

The changelog has been reformatted some to keep its style consistent.

A new security document has been aded that describes the Foolscap 
security model in depth.

Minor fixed to ipengine and ipcluster.

IPython/external/argparse.py

@@ -0,0 +1,1867 b''
+# -*- coding: utf-8 -*-
+
+# Copyright � 2006 Steven J. Bethard <[e-mail]>.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted under the terms of the 3-clause BSD
+# license. No warranty expressed or implied.
+# For details, see the accompanying file LICENSE.txt.
+
+"""Command-line parsing library
+
+This module is an optparse-inspired command-line parsing library that:
+
+* handles both optional and positional arguments
+* produces highly informative usage messages
+* supports parsers that dispatch to sub-parsers
+
+The following is a simple usage example that sums integers from the
+command-line and writes the result to a file:
+
+    parser = argparse.ArgumentParser(
+        description='sum the integers at the command line')
+    parser.add_argument(
+        'integers', metavar='int', nargs='+', type=int,
+        help='an integer to be summed')
+    parser.add_argument(
+        '--log', default=sys.stdout, type=argparse.FileType('w'),
+        help='the file where the sum should be written')
+    args = parser.parse_args()
+    args.log.write('%s' % sum(args.integers))
+    args.log.close()
+
+The module contains the following public classes:
+
+    ArgumentParser -- The main entry point for command-line parsing. As the
+        example above shows, the add_argument() method is used to populate
+        the parser with actions for optional and positional arguments. Then
+        the parse_args() method is invoked to convert the args at the
+        command-line into an object with attributes.
+
+    ArgumentError -- The exception raised by ArgumentParser objects when
+        there are errors with the parser's actions. Errors raised while
+        parsing the command-line are caught by ArgumentParser and emitted
+        as command-line messages.
+
+    FileType -- A factory for defining types of files to be created. As the
+        example above shows, instances of FileType are typically passed as
+        the type= argument of add_argument() calls.
+
+    Action -- The base class for parser actions. Typically actions are
+        selected by passing strings like 'store_true' or 'append_const' to
+        the action= argument of add_argument(). However, for greater
+        customization of ArgumentParser actions, subclasses of Action may
+        be defined and passed as the action= argument.
+
+    HelpFormatter, RawDescriptionHelpFormatter -- Formatter classes which
+        may be passed as the formatter_class= argument to the
+        ArgumentParser constructor. HelpFormatter is the default, while
+        RawDescriptionHelpFormatter tells the parser not to perform any
+        line-wrapping on description text.
+
+All other classes in this module are considered implementation details.
+(Also note that HelpFormatter and RawDescriptionHelpFormatter are only
+considered public as object names -- the API of the formatter objects is
+still considered an implementation detail.)
+"""
+
+__version__ = '0.8.0'
+
+import os as _os
+import re as _re
+import sys as _sys
+import textwrap as _textwrap
+
+from gettext import gettext as _
+
+SUPPRESS = '==SUPPRESS=='
+
+OPTIONAL = '?'
+ZERO_OR_MORE = '*'
+ONE_OR_MORE = '+'
+PARSER = '==PARSER=='
+
+# =============================
+# Utility functions and classes
+# =============================
+
+class _AttributeHolder(object):
+    """Abstract base class that provides __repr__.
+
+    The __repr__ method returns a string in the format:
+        ClassName(attr=name, attr=name, ...)
+    The attributes are determined either by a class-level attribute,
+    '_kwarg_names', or by inspecting the instance __dict__.
+    """
+    
+    def __repr__(self):
+        type_name = type(self).__name__
+        arg_strings = []
+        for arg in self._get_args():
+            arg_strings.append(repr(arg))
+        for name, value in self._get_kwargs():
+            arg_strings.append('%s=%r' % (name, value))
+        return '%s(%s)' % (type_name, ', '.join(arg_strings))
+
+    def _get_kwargs(self):
+        return sorted(self.__dict__.items())
+
+    def _get_args(self):
+        return []
+
+def _ensure_value(namespace, name, value):
+    if getattr(namespace, name, None) is None:
+        setattr(namespace, name, value)
+    return getattr(namespace, name)
+    
+
+
+# ===============
+# Formatting Help
+# ===============
+
+class HelpFormatter(object):
+
+    def __init__(self,
+                 prog,
+                 indent_increment=2,
+                 max_help_position=24,
+                 width=None):
+
+        # default setting for width
+        if width is None:
+            try:
+                width = int(_os.environ['COLUMNS'])
+            except (KeyError, ValueError):
+                width = 80
+            width -= 2
+        
+        self._prog = prog
+        self._indent_increment = indent_increment
+        self._max_help_position = max_help_position
+        self._width = width
+
+        self._current_indent = 0
+        self._level = 0
+        self._action_max_length = 0
+
+        self._root_section = self._Section(self, None)
+        self._current_section = self._root_section
+
+        self._whitespace_matcher = _re.compile(r'\s+')
+        self._long_break_matcher = _re.compile(r'\n\n\n+')
+
+    # ===============================
+    # Section and indentation methods
+    # ===============================
+
+    def _indent(self):
+        self._current_indent += self._indent_increment
+        self._level += 1
+
+    def _dedent(self):
+        self._current_indent -= self._indent_increment
+        assert self._current_indent >= 0, 'Indent decreased below 0.'
+        self._level -= 1
+
+    class _Section(object):
+        def __init__(self, formatter, parent, heading=None):
+            self.formatter = formatter
+            self.parent = parent
+            self.heading = heading
+            self.items = []
+
+        def format_help(self):
+            # format the indented section
+            if self.parent is not None:
+                self.formatter._indent()
+            join = self.formatter._join_parts
+            for func, args in self.items:
+                func(*args)
+            item_help = join(func(*args) for func, args in self.items)
+            if self.parent is not None:
+                self.formatter._dedent()
+
+            # return nothing if the section was empty            
+            if not item_help:
+                return ''
+
+            # add the heading if the section was non-empty
+            if self.heading is not SUPPRESS and self.heading is not None:
+                current_indent = self.formatter._current_indent
+                heading = '%*s%s:\n' % (current_indent, '', self.heading)
+            else:
+                heading = ''
+
+            # join the section-initial newline, the heading and the help
+            return join(['\n', heading, item_help, '\n'])
+
+    def _add_item(self, func, args):
+        self._current_section.items.append((func, args))
+
+    # ========================
+    # Message building methods
+    # ========================
+
+    def start_section(self, heading):
+        self._indent()
+        section = self._Section(self, self._current_section, heading)
+        self._add_item(section.format_help, [])
+        self._current_section = section
+
+    def end_section(self):
+        self._current_section = self._current_section.parent
+        self._dedent()
+
+    def add_text(self, text):
+        if text is not SUPPRESS and text is not None:
+            self._add_item(self._format_text, [text])
+
+    def add_usage(self, usage, optionals, positionals, prefix=None):
+        if usage is not SUPPRESS:
+            args = usage, optionals, positionals, prefix
+            self._add_item(self._format_usage, args)
+
+    def add_argument(self, action):
+        if action.help is not SUPPRESS:
+
+            # find all invocations            
+            get_invocation = self._format_action_invocation
+            invocations = [get_invocation(action)]
+            for subaction in self._iter_indented_subactions(action):
+                invocations.append(get_invocation(subaction))
+                    
+            # update the maximum item length
+            invocation_length = max(len(s) for s in invocations)
+            action_length = invocation_length + self._current_indent
+            self._action_max_length = max(self._action_max_length,
+                                          action_length)
+
+            # add the item to the list        
+            self._add_item(self._format_action, [action])
+
+    def add_arguments(self, actions):
+        for action in actions:
+            self.add_argument(action)
+
+    # =======================
+    # Help-formatting methods
+    # =======================
+
+    def format_help(self):
+        help = self._root_section.format_help() % dict(prog=self._prog)
+        if help:
+            help = self._long_break_matcher.sub('\n\n', help)
+            help = help.strip('\n') + '\n'
+        return help
+
+    def _join_parts(self, part_strings):
+        return ''.join(part
+                       for part in part_strings
+                       if part and part is not SUPPRESS)
+
+    def _format_usage(self, usage, optionals, positionals, prefix):
+        if prefix is None:
+            prefix = _('usage: ')
+
+        # if no optionals or positionals are available, usage is just prog
+        if usage is None and not optionals and not positionals:
+            usage = '%(prog)s'
+            
+        # if optionals and positionals are available, calculate usage
+        elif usage is None:
+            usage = '%(prog)s' % dict(prog=self._prog)
+                
+            # determine width of "usage: PROG" and width of text
+            prefix_width = len(prefix) + len(usage) + 1
+            prefix_indent = self._current_indent + prefix_width
+            text_width = self._width - self._current_indent
+
+            # put them on one line if they're short enough
+            format = self._format_actions_usage
+            action_usage = format(optionals + positionals)
+            if prefix_width + len(action_usage) + 1 < text_width:
+                usage = '%s %s' % (usage, action_usage)
+            
+            # if they're long, wrap optionals and positionals individually
+            else:
+                optional_usage = format(optionals)
+                positional_usage = format(positionals)
+                indent = ' ' * prefix_indent
+
+                # usage is made of PROG, optionals and positionals
+                parts = [usage, ' ']
+                
+                # options always get added right after PROG
+                if optional_usage:
+                    parts.append(_textwrap.fill(
+                        optional_usage, text_width,
+                        initial_indent=indent,
+                        subsequent_indent=indent).lstrip())
+
+                # if there were options, put arguments on the next line
+                # otherwise, start them right after PROG
+                if positional_usage:
+                    part = _textwrap.fill(
+                        positional_usage, text_width,
+                        initial_indent=indent,
+                        subsequent_indent=indent).lstrip()
+                    if optional_usage:
+                        part = '\n' + indent + part
+                    parts.append(part)
+                usage = ''.join(parts)
+
+        # prefix with 'usage:'
+        return '%s%s\n\n' % (prefix, usage)
+
+    def _format_actions_usage(self, actions):
+        parts = []
+        for action in actions:
+            if action.help is SUPPRESS:
+                continue
+
+            # produce all arg strings        
+            if not action.option_strings:
+                parts.append(self._format_args(action, action.dest))
+
+            # produce the first way to invoke the option in brackets
+            else:
+                option_string = action.option_strings[0]
+
+                # if the Optional doesn't take a value, format is:
+                #    -s or --long
+                if action.nargs == 0:
+                    part = '%s' % option_string
+
+                # if the Optional takes a value, format is:
+                #    -s ARGS or --long ARGS
+                else:
+                    default = action.dest.upper()
+                    args_string = self._format_args(action, default)
+                    part = '%s %s' % (option_string, args_string)
+
+                # make it look optional if it's not required
+                if not action.required:
+                    part = '[%s]' % part
+                parts.append(part)
+
+        return ' '.join(parts)
+
+    def _format_text(self, text):
+        text_width = self._width - self._current_indent
+        indent = ' ' * self._current_indent
+        return self._fill_text(text, text_width, indent) + '\n\n'
+
+    def _format_action(self, action):
+        # determine the required width and the entry label
+        help_position = min(self._action_max_length + 2,
+                            self._max_help_position)
+        help_width = self._width - help_position
+        action_width = help_position - self._current_indent - 2
+        action_header = self._format_action_invocation(action)
+
+        # ho nelp; start on same line and add a final newline
+        if not action.help:
+            tup = self._current_indent, '', action_header
+            action_header = '%*s%s\n' % tup
+            
+        # short action name; start on the same line and pad two spaces
+        elif len(action_header) <= action_width:
+            tup = self._current_indent, '', action_width, action_header
+            action_header = '%*s%-*s  ' % tup
+            indent_first = 0
+
+        # long action name; start on the next line
+        else:
+            tup = self._current_indent, '', action_header
+            action_header = '%*s%s\n' % tup
+            indent_first = help_position
+
+        # collect the pieces of the action help
+        parts = [action_header]
+
+        # if there was help for the action, add lines of help text
+        if action.help:
+            help_text = self._expand_help(action)
+            help_lines = self._split_lines(help_text, help_width)
+            parts.append('%*s%s\n' % (indent_first, '', help_lines[0]))
+            for line in help_lines[1:]:
+                parts.append('%*s%s\n' % (help_position, '', line))
+
+        # or add a newline if the description doesn't end with one
+        elif not action_header.endswith('\n'):
+            parts.append('\n')
+
+        # if there are any sub-actions, add their help as well
+        for subaction in self._iter_indented_subactions(action):
+            parts.append(self._format_action(subaction))
+
+        # return a single string            
+        return self._join_parts(parts)
+
+    def _format_action_invocation(self, action):
+        if not action.option_strings:
+            return self._format_metavar(action, action.dest)
+
+        else:
+            parts = []
+
+            # if the Optional doesn't take a value, format is:
+            #    -s, --long
+            if action.nargs == 0:
+                parts.extend(action.option_strings)
+
+            # if the Optional takes a value, format is:
+            #    -s ARGS, --long ARGS
+            else:
+                default = action.dest.upper()
+                args_string = self._format_args(action, default)
+                for option_string in action.option_strings:
+                    parts.append('%s %s' % (option_string, args_string))
+
+            return ', '.join(parts)
+
+    def _format_metavar(self, action, default_metavar):
+        if action.metavar is not None:
+            name = action.metavar
+        elif action.choices is not None:
+            choice_strs = (str(choice) for choice in action.choices)
+            name = '{%s}' % ','.join(choice_strs)
+        else:
+            name = default_metavar
+        return name
+
+    def _format_args(self, action, default_metavar):
+        name = self._format_metavar(action, default_metavar)
+        if action.nargs is None:
+            result = name
+        elif action.nargs == OPTIONAL:
+            result = '[%s]' % name
+        elif action.nargs == ZERO_OR_MORE:
+            result = '[%s [%s ...]]' % (name, name)
+        elif action.nargs == ONE_OR_MORE:
+            result = '%s [%s ...]' % (name, name)
+        elif action.nargs is PARSER:
+            result = '%s ...' % name
+        else:
+            result = ' '.join([name] * action.nargs)
+        return result
+
+    def _expand_help(self, action):
+        params = dict(vars(action), prog=self._prog)
+        for name, value in params.items():
+            if value is SUPPRESS:
+                del params[name]
+        if params.get('choices') is not None:
+            choices_str = ', '.join(str(c) for c in params['choices'])
+            params['choices'] = choices_str
+        return action.help % params
+
+    def _iter_indented_subactions(self, action):
+        try:
+            get_subactions = action._get_subactions
+        except AttributeError:
+            pass
+        else:
+            self._indent()
+            for subaction in get_subactions():
+                yield subaction
+            self._dedent()
+
+    def _split_lines(self, text, width):
+        text = self._whitespace_matcher.sub(' ', text).strip()
+        return _textwrap.wrap(text, width)
+
+    def _fill_text(self, text, width, indent):
+        text = self._whitespace_matcher.sub(' ', text).strip()
+        return _textwrap.fill(text, width, initial_indent=indent,
+                                           subsequent_indent=indent)
+
+class RawDescriptionHelpFormatter(HelpFormatter):
+    
+    def _fill_text(self, text, width, indent):
+        return ''.join(indent + line for line in text.splitlines(True))
+
+class RawTextHelpFormatter(RawDescriptionHelpFormatter):
+    
+    def _split_lines(self, text, width):
+        return text.splitlines()
+
+# =====================
+# Options and Arguments
+# =====================
+
+class ArgumentError(Exception):
+    """ArgumentError(message, argument)
+
+    Raised whenever there was an error creating or using an argument
+    (optional or positional).
+
+    The string value of this exception is the message, augmented with
+    information about the argument that caused it.
+    """
+    
+    def __init__(self, argument, message):
+        if argument.option_strings:
+            self.argument_name =  '/'.join(argument.option_strings)
+        elif argument.metavar not in (None, SUPPRESS):
+            self.argument_name = argument.metavar
+        elif argument.dest not in (None, SUPPRESS):
+            self.argument_name = argument.dest
+        else:
+            self.argument_name = None
+        self.message = message
+
+    def __str__(self):
+        if self.argument_name is None:
+            format = '%(message)s'
+        else:
+            format = 'argument %(argument_name)s: %(message)s'
+        return format % dict(message=self.message,
+                             argument_name=self.argument_name)
+
+# ==============
+# Action classes
+# ==============
+
+class Action(_AttributeHolder):
+    """Action(*strings, **options)
+
+    Action objects hold the information necessary to convert a
+    set of command-line arguments (possibly including an initial option
+    string) into the desired Python object(s).
+
+    Keyword Arguments:
+
+    option_strings -- A list of command-line option strings which
+        should be associated with this action.
+    
+    dest -- The name of the attribute to hold the created object(s)
+    
+    nargs -- The number of command-line arguments that should be consumed.
+        By default, one argument will be consumed and a single value will
+        be produced.  Other values include:
+            * N (an integer) consumes N arguments (and produces a list)
+            * '?' consumes zero or one arguments
+            * '*' consumes zero or more arguments (and produces a list)
+            * '+' consumes one or more arguments (and produces a list)
+        Note that the difference between the default and nargs=1 is that
+        with the default, a single value will be produced, while with
+        nargs=1, a list containing a single value will be produced.
+
+    const -- The value to be produced if the option is specified and the
+        option uses an action that takes no values.
+
+    default -- The value to be produced if the option is not specified.
+
+    type -- The type which the command-line arguments should be converted
+        to, should be one of 'string', 'int', 'float', 'complex' or a
+        callable object that accepts a single string argument. If None,
+        'string' is assumed.
+        
+    choices -- A container of values that should be allowed. If not None,
+        after a command-line argument has been converted to the appropriate
+        type, an exception will be raised if it is not a member of this
+        collection.
+
+    required -- True if the action must always be specified at the command
+        line. This is only meaningful for optional command-line arguments.
+
+    help -- The help string describing the argument.
+
+    metavar -- The name to be used for the option's argument with the help
+        string. If None, the 'dest' value will be used as the name.
+    """
+
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        self.option_strings = option_strings
+        self.dest = dest
+        self.nargs = nargs
+        self.const = const
+        self.default = default
+        self.type = type
+        self.choices = choices
+        self.required = required
+        self.help = help
+        self.metavar = metavar
+
+    def _get_kwargs(self):
+        names = [
+            'option_strings',
+            'dest',
+            'nargs',
+            'const',
+            'default',
+            'type',
+            'choices',
+            'help',
+            'metavar'
+        ]
+        return [(name, getattr(self, name)) for name in names]
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        raise NotImplementedError(_('.__call__() not defined'))
+
+class _StoreAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        if nargs == 0:
+            raise ValueError('nargs must be > 0')
+        if const is not None and nargs != OPTIONAL:
+            raise ValueError('nargs must be %r to supply const' % OPTIONAL)
+        super(_StoreAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=nargs,
+            const=const,
+            default=default,
+            type=type,
+            choices=choices,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values)
+
+class _StoreConstAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 const,
+                 default=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        super(_StoreConstAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            const=const,
+            default=default,
+            required=required,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, self.const)
+
+class _StoreTrueAction(_StoreConstAction):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=False,
+                 required=False,
+                 help=None):
+        super(_StoreTrueAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            const=True,
+            default=default,
+            required=required,
+            help=help)
+
+class _StoreFalseAction(_StoreConstAction):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=True,
+                 required=False,
+                 help=None):
+        super(_StoreFalseAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            const=False,
+            default=default,
+            required=required,
+            help=help)
+    
+class _AppendAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        if nargs == 0:
+            raise ValueError('nargs must be > 0')
+        if const is not None and nargs != OPTIONAL:
+            raise ValueError('nargs must be %r to supply const' % OPTIONAL)
+        super(_AppendAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=nargs,
+            const=const,
+            default=default,
+            type=type,
+            choices=choices,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        _ensure_value(namespace, self.dest, []).append(values)
+
+class _AppendConstAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 const,
+                 default=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        super(_AppendConstAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            const=const,
+            default=default,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        _ensure_value(namespace, self.dest, []).append(self.const)
+
+class _CountAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=None,
+                 required=False,
+                 help=None):
+        super(_CountAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            default=default,
+            required=required,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        new_count = _ensure_value(namespace, self.dest, 0) + 1
+        setattr(namespace, self.dest, new_count)
+
+class _HelpAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest=SUPPRESS,
+                 default=SUPPRESS,
+                 help=None):
+        super(_HelpAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            default=default,
+            nargs=0,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser.print_help()
+        parser.exit()
+
+class _VersionAction(Action):
+    def __init__(self,
+                 option_strings,
+                 dest=SUPPRESS,
+                 default=SUPPRESS,
+                 help=None):
+        super(_VersionAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            default=default,
+            nargs=0,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser.print_version()
+        parser.exit()
+        
+class _SubParsersAction(Action):
+
+    class _ChoicesPseudoAction(Action):
+        def __init__(self, name, help):
+            sup = super(_SubParsersAction._ChoicesPseudoAction, self)
+            sup.__init__(option_strings=[], dest=name, help=help)
+
+        
+    def __init__(self,
+                 option_strings,
+                 prog,
+                 parser_class,
+                 dest=SUPPRESS,
+                 help=None,
+                 metavar=None):
+        
+        self._prog_prefix = prog
+        self._parser_class = parser_class
+        self._name_parser_map = {}
+        self._choices_actions = []
+
+        super(_SubParsersAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=PARSER,
+            choices=self._name_parser_map,
+            help=help,
+            metavar=metavar)
+
+    def add_parser(self, name, **kwargs):
+        # set prog from the existing prefix
+        if kwargs.get('prog') is None:
+            kwargs['prog'] = '%s %s' % (self._prog_prefix, name)
+
+        # create a pseudo-action to hold the choice help
+        if 'help' in kwargs:
+            help = kwargs.pop('help')
+            choice_action = self._ChoicesPseudoAction(name, help)
+            self._choices_actions.append(choice_action)
+
+        # create the parser and add it to the map
+        parser = self._parser_class(**kwargs)
+        self._name_parser_map[name] = parser
+        return parser
+
+    def _get_subactions(self):
+        return self._choices_actions
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser_name = values[0]
+        arg_strings = values[1:]
+
+        # set the parser name if requested
+        if self.dest is not SUPPRESS:
+            setattr(namespace, self.dest, parser_name)
+
+        # select the parser        
+        try:
+            parser = self._name_parser_map[parser_name]
+        except KeyError:
+            tup = parser_name, ', '.join(self._name_parser_map)
+            msg = _('unknown parser %r (choices: %s)' % tup)
+            raise ArgumentError(self, msg)
+
+        # parse all the remaining options into the namespace
+        parser.parse_args(arg_strings, namespace)
+
+
+# ==============
+# Type classes
+# ==============
+
+class FileType(object):
+    """Factory for creating file object types
+
+    Instances of FileType are typically passed as type= arguments to the
+    ArgumentParser add_argument() method.
+
+    Keyword Arguments:
+    mode -- A string indicating how the file is to be opened. Accepts the
+        same values as the builtin open() function.
+    bufsize -- The file's desired buffer size. Accepts the same values as
+        the builtin open() function.
+    """    
+    def __init__(self, mode='r', bufsize=None):
+        self._mode = mode
+        self._bufsize = bufsize
+    
+    def __call__(self, string):
+        # the special argument "-" means sys.std{in,out}
+        if string == '-':
+            if self._mode == 'r':
+                return _sys.stdin
+            elif self._mode == 'w':
+                return _sys.stdout
+            else:
+                msg = _('argument "-" with mode %r' % self._mode)
+                raise ValueError(msg)
+
+        # all other arguments are used as file names
+        if self._bufsize:
+            return open(string, self._mode, self._bufsize)
+        else:
+            return open(string, self._mode)
+
+
+# ===========================
+# Optional and Positional Parsing
+# ===========================
+
+class Namespace(_AttributeHolder):
+
+    def __init__(self, **kwargs):
+        for name, value in kwargs.iteritems():
+            setattr(self, name, value)
+
+    def __eq__(self, other):
+        return vars(self) == vars(other)
+
+    def __ne__(self, other):
+        return not (self == other)
+
+
+class _ActionsContainer(object):
+    def __init__(self,
+                 description,
+                 prefix_chars,
+                 argument_default,
+                 conflict_handler):
+        super(_ActionsContainer, self).__init__()
+
+        self.description = description
+        self.argument_default = argument_default
+        self.prefix_chars = prefix_chars
+        self.conflict_handler = conflict_handler
+
+        # set up registries
+        self._registries = {}
+
+        # register actions
+        self.register('action', None, _StoreAction)
+        self.register('action', 'store', _StoreAction)
+        self.register('action', 'store_const', _StoreConstAction)
+        self.register('action', 'store_true', _StoreTrueAction)
+        self.register('action', 'store_false', _StoreFalseAction)
+        self.register('action', 'append', _AppendAction)
+        self.register('action', 'append_const', _AppendConstAction)
+        self.register('action', 'count', _CountAction)
+        self.register('action', 'help', _HelpAction)
+        self.register('action', 'version', _VersionAction)
+        self.register('action', 'parsers', _SubParsersAction)
+        
+        # raise an exception if the conflict handler is invalid
+        self._get_handler()
+
+        # action storage
+        self._optional_actions_list = []
+        self._positional_actions_list = []
+        self._positional_actions_full_list = []
+        self._option_strings = {}
+
+        # defaults storage
+        self._defaults = {}
+
+    # ====================
+    # Registration methods
+    # ====================
+
+    def register(self, registry_name, value, object):
+        registry = self._registries.setdefault(registry_name, {})
+        registry[value] = object
+
+    def _registry_get(self, registry_name, value, default=None):
+        return self._registries[registry_name].get(value, default)
+
+    # ==================================
+    # Namespace default settings methods
+    # ==================================
+
+    def set_defaults(self, **kwargs):
+        self._defaults.update(kwargs)
+
+        # if these defaults match any existing arguments, replace
+        # the previous default on the object with the new one
+        for action_list in [self._option_strings.values(),
+                            self._positional_actions_full_list]:
+            for action in action_list:
+                if action.dest in kwargs:
+                    action.default = kwargs[action.dest]
+
+    # =======================
+    # Adding argument actions
+    # =======================
+
+    def add_argument(self, *args, **kwargs):
+        """
+        add_argument(dest, ..., name=value, ...)
+        add_argument(option_string, option_string, ..., name=value, ...)
+        """
+
+        # if no positional args are supplied or only one is supplied and
+        # it doesn't look like an option string, parse a positional
+        # argument
+        chars = self.prefix_chars
+        if not args or len(args) == 1 and args[0][0] not in chars:
+            kwargs = self._get_positional_kwargs(*args, **kwargs)
+
+        # otherwise, we're adding an optional argument
+        else:
+            kwargs = self._get_optional_kwargs(*args, **kwargs)
+
+        # if no default was supplied, use the parser-level default
+        if 'default' not in kwargs:
+            dest = kwargs['dest']
+            if dest in self._defaults:
+                kwargs['default'] = self._defaults[dest]
+            elif self.argument_default is not None:
+                kwargs['default'] = self.argument_default
+            
+        # create the action object, and add it to the parser
+        action_class = self._pop_action_class(kwargs)
+        action = action_class(**kwargs)
+        return self._add_action(action)
+
+    def _add_action(self, action):
+        # resolve any conflicts
+        self._check_conflict(action)
+
+        # add to optional or positional list
+        if action.option_strings:
+            self._optional_actions_list.append(action)
+        else:
+            self._positional_actions_list.append(action)
+            self._positional_actions_full_list.append(action)
+        action.container = self
+
+        # index the action by any option strings it has
+        for option_string in action.option_strings:
+            self._option_strings[option_string] = action
+
+        # return the created action
+        return action
+
+    def _add_container_actions(self, container):
+        for action in container._optional_actions_list:
+            self._add_action(action)
+        for action in container._positional_actions_list:
+            self._add_action(action)
+
+    def _get_positional_kwargs(self, dest, **kwargs):
+        # make sure required is not specified
+        if 'required' in kwargs:
+            msg = _("'required' is an invalid argument for positionals")
+            raise TypeError(msg)
+        
+        # return the keyword arguments with no option strings
+        return dict(kwargs, dest=dest, option_strings=[])
+
+    def _get_optional_kwargs(self, *args, **kwargs):
+        # determine short and long option strings
+        option_strings = []
+        long_option_strings = []
+        for option_string in args:
+            # error on one-or-fewer-character option strings
+            if len(option_string) < 2:
+                msg = _('invalid option string %r: '
+                        'must be at least two characters long')
+                raise ValueError(msg % option_string)
+
+            # error on strings that don't start with an appropriate prefix
+            if not option_string[0] in self.prefix_chars:
+                msg = _('invalid option string %r: '
+                        'must start with a character %r')
+                tup = option_string, self.prefix_chars
+                raise ValueError(msg % tup)
+
+            # error on strings that are all prefix characters
+            if not (set(option_string) - set(self.prefix_chars)):
+                msg = _('invalid option string %r: '
+                        'must contain characters other than %r')
+                tup = option_string, self.prefix_chars
+                raise ValueError(msg % tup)
+
+            # strings starting with two prefix characters are long options
+            option_strings.append(option_string)            
+            if option_string[0] in self.prefix_chars:
+                if option_string[1] in self.prefix_chars:
+                    long_option_strings.append(option_string)
+
+        # infer destination, '--foo-bar' -> 'foo_bar' and '-x' -> 'x'
+        dest = kwargs.pop('dest', None)
+        if dest is None:
+            if long_option_strings:
+                dest_option_string = long_option_strings[0]
+            else:
+                dest_option_string = option_strings[0]
+            dest = dest_option_string.lstrip(self.prefix_chars)
+            dest = dest.replace('-', '_')
+
+        # return the updated keyword arguments
+        return dict(kwargs, dest=dest, option_strings=option_strings)
+
+    def _pop_action_class(self, kwargs, default=None):
+        action = kwargs.pop('action', default)
+        return self._registry_get('action', action, action)
+
+    def _get_handler(self):
+        # determine function from conflict handler string
+        handler_func_name = '_handle_conflict_%s' % self.conflict_handler
+        try:
+            return getattr(self, handler_func_name)
+        except AttributeError:
+            msg = _('invalid conflict_resolution value: %r')
+            raise ValueError(msg % self.conflict_handler)
+
+    def _check_conflict(self, action):
+
+        # find all options that conflict with this option        
+        confl_optionals = []
+        for option_string in action.option_strings:
+            if option_string in self._option_strings:
+                confl_optional = self._option_strings[option_string]
+                confl_optionals.append((option_string, confl_optional))
+
+        # resolve any conflicts
+        if confl_optionals:
+            conflict_handler = self._get_handler()
+            conflict_handler(action, confl_optionals)
+
+    def _handle_conflict_error(self, action, conflicting_actions):
+        message = _('conflicting option string(s): %s')
+        conflict_string = ', '.join(option_string
+                                    for option_string, action
+                                    in conflicting_actions)
+        raise ArgumentError(action, message % conflict_string)
+
+    def _handle_conflict_resolve(self, action, conflicting_actions):
+
+        # remove all conflicting options        
+        for option_string, action in conflicting_actions:
+            
+            # remove the conflicting option
+            action.option_strings.remove(option_string)
+            self._option_strings.pop(option_string, None)
+
+            # if the option now has no option string, remove it from the
+            # container holding it
+            if not action.option_strings:
+                action.container._optional_actions_list.remove(action)
+
+
+class _ArgumentGroup(_ActionsContainer):
+
+    def __init__(self, container, title=None, description=None, **kwargs):
+        # add any missing keyword arguments by checking the container
+        update = kwargs.setdefault
+        update('conflict_handler', container.conflict_handler)
+        update('prefix_chars', container.prefix_chars)
+        update('argument_default', container.argument_default)
+        super_init = super(_ArgumentGroup, self).__init__
+        super_init(description=description, **kwargs)
+        
+        self.title = title
+        self._registries = container._registries
+        self._positional_actions_full_list = container._positional_actions_full_list
+        self._option_strings = container._option_strings
+        self._defaults = container._defaults
+
+
+class ArgumentParser(_AttributeHolder, _ActionsContainer):
+
+    def __init__(self,
+                 prog=None,
+                 usage=None,
+                 description=None,
+                 epilog=None,
+                 version=None,
+                 parents=[],
+                 formatter_class=HelpFormatter,
+                 prefix_chars='-',
+                 argument_default=None,
+                 conflict_handler='error',
+                 add_help=True):
+
+        superinit = super(ArgumentParser, self).__init__
+        superinit(description=description,
+                  prefix_chars=prefix_chars,
+                  argument_default=argument_default,
+                  conflict_handler=conflict_handler)
+
+        # default setting for prog
+        if prog is None:
+            prog = _os.path.basename(_sys.argv[0])
+
+        self.prog = prog
+        self.usage = usage
+        self.epilog = epilog
+        self.version = version
+        self.formatter_class = formatter_class
+        self.add_help = add_help
+
+        self._argument_group_class = _ArgumentGroup
+        self._has_subparsers = False
+        self._argument_groups = []
+
+        # register types
+        def identity(string):
+            return string
+        self.register('type', None, identity)
+
+        # add help and version arguments if necessary
+        # (using explicit default to override global argument_default)
+        if self.add_help:
+            self.add_argument(
+                '-h', '--help', action='help', default=SUPPRESS,
+                help=_('show this help message and exit'))
+        if self.version:
+            self.add_argument(
+                '-v', '--version', action='version', default=SUPPRESS,
+                help=_("show program's version number and exit"))
+
+        # add parent arguments and defaults
+        for parent in parents:
+            self._add_container_actions(parent)
+            try:
+                defaults = parent._defaults
+            except AttributeError:
+                pass
+            else:
+                self._defaults.update(defaults)
+
+        # determines whether an "option" looks like a negative number
+        self._negative_number_matcher = _re.compile(r'^-\d+|-\d*.\d+$')
+                
+
+    # =======================
+    # Pretty __repr__ methods
+    # =======================
+
+    def _get_kwargs(self):
+        names = [
+            'prog',
+            'usage',
+            'description',
+            'version',
+            'formatter_class',
+            'conflict_handler',
+            'add_help',
+        ]
+        return [(name, getattr(self, name)) for name in names]
+
+    # ==================================
+    # Optional/Positional adding methods
+    # ==================================
+
+    def add_argument_group(self, *args, **kwargs):
+        group = self._argument_group_class(self, *args, **kwargs)
+        self._argument_groups.append(group)
+        return group
+
+    def add_subparsers(self, **kwargs):
+        if self._has_subparsers:
+            self.error(_('cannot have multiple subparser arguments'))
+        
+        # add the parser class to the arguments if it's not present
+        kwargs.setdefault('parser_class', type(self))
+
+        # prog defaults to the usage message of this parser, skipping
+        # optional arguments and with no "usage:" prefix
+        if kwargs.get('prog') is None:
+            formatter = self._get_formatter()
+            formatter.add_usage(self.usage, [],
+                                self._get_positional_actions(), '')
+            kwargs['prog'] = formatter.format_help().strip()
+
+        # create the parsers action and add it to the positionals list
+        parsers_class = self._pop_action_class(kwargs, 'parsers')
+        action = parsers_class(option_strings=[], **kwargs)
+        self._positional_actions_list.append(action)
+        self._positional_actions_full_list.append(action)
+        self._has_subparsers = True
+
+        # return the created parsers action
+        return action
+
+    def _add_container_actions(self, container):
+        super(ArgumentParser, self)._add_container_actions(container)
+        try:
+            groups = container._argument_groups
+        except AttributeError:
+            pass
+        else:
+            for group in groups:
+                new_group = self.add_argument_group(
+                    title=group.title,
+                    description=group.description,
+                    conflict_handler=group.conflict_handler)
+                new_group._add_container_actions(group)
+
+    def _get_optional_actions(self):
+        actions = []
+        actions.extend(self._optional_actions_list)
+        for argument_group in self._argument_groups:
+            actions.extend(argument_group._optional_actions_list)
+        return actions
+
+    def _get_positional_actions(self):
+        return list(self._positional_actions_full_list)
+
+
+    # =====================================
+    # Command line argument parsing methods
+    # =====================================
+
+    def parse_args(self, args=None, namespace=None):
+        # args default to the system args
+        if args is None:
+            args = _sys.argv[1:]
+
+        # default Namespace built from parser defaults
+        if namespace is None:
+            namespace = Namespace()
+            
+        # add any action defaults that aren't present
+        optional_actions = self._get_optional_actions()
+        positional_actions = self._get_positional_actions()
+        for action in optional_actions + positional_actions:
+            if action.dest is not SUPPRESS:
+                if not hasattr(namespace, action.dest):
+                    if action.default is not SUPPRESS:
+                        default = action.default
+                        if isinstance(action.default, basestring):
+                            default = self._get_value(action, default)
+                        setattr(namespace, action.dest, default)
+
+        # add any parser defaults that aren't present
+        for dest, value in self._defaults.iteritems():
+            if not hasattr(namespace, dest):
+                setattr(namespace, dest, value)
+            
+        # parse the arguments and exit if there are any errors
+        try:
+            result = self._parse_args(args, namespace)
+        except ArgumentError, err:
+            self.error(str(err))
+
+        # make sure all required optionals are present
+        for action in self._get_optional_actions():
+            if action.required:
+                if getattr(result, action.dest, None) is None:
+                    opt_strs = '/'.join(action.option_strings)
+                    msg = _('option %s is required' % opt_strs)
+                    self.error(msg)
+
+        # return the parsed arguments                    
+        return result
+
+    def _parse_args(self, arg_strings, namespace):            
+
+        # find all option indices, and determine the arg_string_pattern
+        # which has an 'O' if there is an option at an index,
+        # an 'A' if there is an argument, or a '-' if there is a '--'
+        option_string_indices = {}
+        arg_string_pattern_parts = []
+        arg_strings_iter = iter(arg_strings)
+        for i, arg_string in enumerate(arg_strings_iter):
+
+            # all args after -- are non-options
+            if arg_string == '--':
+                arg_string_pattern_parts.append('-')
+                for arg_string in arg_strings_iter:
+                    arg_string_pattern_parts.append('A')
+
+            # otherwise, add the arg to the arg strings
+            # and note the index if it was an option
+            else:
+                option_tuple = self._parse_optional(arg_string)
+                if option_tuple is None:
+                    pattern = 'A'
+                else:
+                    option_string_indices[i] = option_tuple
+                    pattern = 'O'
+                arg_string_pattern_parts.append(pattern)
+
+        # join the pieces together to form the pattern
+        arg_strings_pattern = ''.join(arg_string_pattern_parts)
+
+        # converts arg strings to the appropriate and then takes the action
+        def take_action(action, argument_strings, option_string=None):
+            argument_values = self._get_values(action, argument_strings)
+            # take the action if we didn't receive a SUPPRESS value
+            # (e.g. from a default)            
+            if argument_values is not SUPPRESS:
+                action(self, namespace, argument_values, option_string)
+
+        # function to convert arg_strings into an optional action
+        def consume_optional(start_index):
+            
+            # determine the optional action and parse any explicit
+            # argument out of the option string
+            option_tuple = option_string_indices[start_index]
+            action, option_string, explicit_arg = option_tuple
+
+            # loop because single-dash options can be chained
+            # (e.g. -xyz is the same as -x -y -z if no args are required)
+            match_argument = self._match_argument
+            action_tuples = []
+            while True:
+
+                # if we found no optional action, raise an error
+                if action is None:
+                    self.error(_('no such option: %s') % option_string)
+
+                # if there is an explicit argument, try to match the
+                # optional's string arguments to only this
+                if explicit_arg is not None:
+                    arg_count = match_argument(action, 'A')
+
+                    # if the action is a single-dash option and takes no
+                    # arguments, try to parse more single-dash options out
+                    # of the tail of the option string
+                    chars = self.prefix_chars
+                    if arg_count == 0 and option_string[1] not in chars:
+                        action_tuples.append((action, [], option_string))
+                        parse_optional = self._parse_optional
+                        for char in self.prefix_chars:
+                            option_string = char + explicit_arg
+                            option_tuple = parse_optional(option_string)
+                            if option_tuple[0] is not None:
+                                break
+                        else:
+                            msg = _('ignored explicit argument %r')
+                            raise ArgumentError(action, msg % explicit_arg)
+
+                        # set the action, etc. for the next loop iteration
+                        action, option_string, explicit_arg = option_tuple
+
+                    # if the action expect exactly one argument, we've
+                    # successfully matched the option; exit the loop
+                    elif arg_count == 1:
+                        stop = start_index + 1
+                        args = [explicit_arg]
+                        action_tuples.append((action, args, option_string))
+                        break
+
+                    # error if a double-dash option did not use the
+                    # explicit argument
+                    else:
+                        msg = _('ignored explicit argument %r')
+                        raise ArgumentError(action, msg % explicit_arg)
+                
+                # if there is no explicit argument, try to match the
+                # optional's string arguments with the following strings
+                # if successful, exit the loop
+                else:
+                    start = start_index + 1
+                    selected_patterns = arg_strings_pattern[start:]
+                    arg_count = match_argument(action, selected_patterns)
+                    stop = start + arg_count
+                    args = arg_strings[start:stop]
+                    action_tuples.append((action, args, option_string))
+                    break
+
+            # add the Optional to the list and return the index at which
+            # the Optional's string args stopped
+            assert action_tuples
+            for action, args, option_string in action_tuples:
+                take_action(action, args, option_string)
+            return stop
+
+        # the list of Positionals left to be parsed; this is modified
+        # by consume_positionals()
+        positionals = self._get_positional_actions()
+
+        # function to convert arg_strings into positional actions
+        def consume_positionals(start_index):
+            # match as many Positionals as possible
+            match_partial = self._match_arguments_partial
+            selected_pattern = arg_strings_pattern[start_index:]
+            arg_counts = match_partial(positionals, selected_pattern)
+
+            # slice off the appropriate arg strings for each Positional
+            # and add the Positional and its args to the list
+            for action, arg_count in zip(positionals, arg_counts):
+                args = arg_strings[start_index: start_index + arg_count]
+                start_index += arg_count
+                take_action(action, args)
+
+            # slice off the Positionals that we just parsed and return the
+            # index at which the Positionals' string args stopped
+            positionals[:] = positionals[len(arg_counts):]
+            return start_index
+
+        # consume Positionals and Optionals alternately, until we have
+        # passed the last option string
+        start_index = 0
+        if option_string_indices:
+            max_option_string_index = max(option_string_indices)
+        else:
+            max_option_string_index = -1
+        while start_index <= max_option_string_index:
+            
+            # consume any Positionals preceding the next option
+            next_option_string_index = min(
+                index
+                for index in option_string_indices
+                if index >= start_index)
+            if start_index != next_option_string_index:
+                positionals_end_index = consume_positionals(start_index)
+
+                # only try to parse the next optional if we didn't consume
+                # the option string during the positionals parsing
+                if positionals_end_index > start_index:
+                    start_index = positionals_end_index
+                    continue
+                else:
+                    start_index = positionals_end_index
+
+            # if we consumed all the positionals we could and we're not
+            # at the index of an option string, there were unparseable
+            # arguments
+            if start_index not in option_string_indices:
+                msg = _('extra arguments found: %s')
+                extras = arg_strings[start_index:next_option_string_index]
+                self.error(msg % ' '.join(extras))
+
+            # consume the next optional and any arguments for it
+            start_index = consume_optional(start_index)
+
+        # consume any positionals following the last Optional
+        stop_index = consume_positionals(start_index)
+
+        # if we didn't consume all the argument strings, there were too
+        # many supplied
+        if stop_index != len(arg_strings):
+            extras = arg_strings[stop_index:]
+            self.error(_('extra arguments found: %s') % ' '.join(extras))
+
+        # if we didn't use all the Positional objects, there were too few
+        # arg strings supplied.
+        if positionals:
+            self.error(_('too few arguments'))
+
+        # return the updated namespace
+        return namespace
+
+    def _match_argument(self, action, arg_strings_pattern):
+        # match the pattern for this action to the arg strings
+        nargs_pattern = self._get_nargs_pattern(action)
+        match = _re.match(nargs_pattern, arg_strings_pattern)
+
+        # raise an exception if we weren't able to find a match        
+        if match is None:
+            nargs_errors = {
+                None:_('expected one argument'),
+                OPTIONAL:_('expected at most one argument'),
+                ONE_OR_MORE:_('expected at least one argument')
+            }
+            default = _('expected %s argument(s)') % action.nargs
+            msg = nargs_errors.get(action.nargs, default)
+            raise ArgumentError(action, msg)
+
+        # return the number of arguments matched
+        return len(match.group(1))
+
+    def _match_arguments_partial(self, actions, arg_strings_pattern):
+        # progressively shorten the actions list by slicing off the
+        # final actions until we find a match
+        result = []
+        for i in xrange(len(actions), 0, -1):
+            actions_slice = actions[:i]
+            pattern = ''.join(self._get_nargs_pattern(action)
+                              for action in actions_slice)
+            match = _re.match(pattern, arg_strings_pattern)
+            if match is not None:
+                result.extend(len(string) for string in match.groups())
+                break
+
+        # return the list of arg string counts
+        return result
+    
+    def _parse_optional(self, arg_string):
+        # if it doesn't start with a prefix, it was meant to be positional
+        if not arg_string[0] in self.prefix_chars:
+            return None
+        
+        # if it's just dashes, it was meant to be positional
+        if not arg_string.strip('-'):
+            return None
+
+        # if the option string is present in the parser, return the action
+        if arg_string in self._option_strings:
+            action = self._option_strings[arg_string]
+            return action, arg_string, None
+
+        # search through all possible prefixes of the option string
+        # and all actions in the parser for possible interpretations
+        option_tuples = []
+        prefix_tuples = self._get_option_prefix_tuples(arg_string)
+        for option_string in self._option_strings:
+            for option_prefix, explicit_arg in prefix_tuples:
+                if option_string.startswith(option_prefix):
+                    action = self._option_strings[option_string]
+                    tup = action, option_string, explicit_arg
+                    option_tuples.append(tup)
+                    break
+
+        # if multiple actions match, the option string was ambiguous
+        if len(option_tuples) > 1:
+            options = ', '.join(opt_str for _, opt_str, _ in option_tuples)
+            tup = arg_string, options
+            self.error(_('ambiguous option: %s could match %s') % tup)
+
+        # if exactly one action matched, this segmentation is good,
+        # so return the parsed action
+        elif len(option_tuples) == 1:
+            option_tuple, = option_tuples
+            return option_tuple
+
+        # if it was not found as an option, but it looks like a negative
+        # number, it was meant to be positional
+        if self._negative_number_matcher.match(arg_string):
+            return None
+
+        # it was meant to be an optional but there is no such option
+        # in this parser (though it might be a valid option in a subparser)
+        return None, arg_string, None
+
+    def _get_option_prefix_tuples(self, option_string):
+        result = []
+        
+        # option strings starting with two prefix characters are only
+        # split at the '='
+        chars = self.prefix_chars
+        if option_string[0] in chars and option_string[1] in chars:
+            if '=' in option_string:
+                option_prefix, explicit_arg = option_string.split('=', 1)
+            else:
+                option_prefix = option_string
+                explicit_arg = None
+            tup = option_prefix, explicit_arg
+            result.append(tup)
+
+        # option strings starting with a single prefix character are
+        # split at all indices
+        else:
+            for first_index, char in enumerate(option_string):
+                if char not in self.prefix_chars:
+                    break
+            for i in xrange(len(option_string), first_index, -1):
+                tup = option_string[:i], option_string[i:] or None
+                result.append(tup)
+
+        # return the collected prefix tuples
+        return result                
+
+    def _get_nargs_pattern(self, action):
+        # in all examples below, we have to allow for '--' args
+        # which are represented as '-' in the pattern
+        nargs = action.nargs
+        
+        # the default (None) is assumed to be a single argument
+        if nargs is None:
+            nargs_pattern = '(-*A-*)'
+
+        # allow zero or one arguments
+        elif nargs == OPTIONAL:
+            nargs_pattern = '(-*A?-*)'
+
+        # allow zero or more arguments
+        elif nargs == ZERO_OR_MORE:
+            nargs_pattern = '(-*[A-]*)'
+
+        # allow one or more arguments
+        elif nargs == ONE_OR_MORE:
+            nargs_pattern = '(-*A[A-]*)'
+
+        # allow one argument followed by any number of options or arguments
+        elif nargs is PARSER:
+            nargs_pattern = '(-*A[-AO]*)'
+
+        # all others should be integers            
+        else:
+            nargs_pattern = '(-*%s-*)' % '-*'.join('A' * nargs)
+
+        # if this is an optional action, -- is not allowed        
+        if action.option_strings:
+            nargs_pattern = nargs_pattern.replace('-*', '')
+            nargs_pattern = nargs_pattern.replace('-', '')
+
+        # return the pattern
+        return nargs_pattern
+
+    # ========================
+    # Value conversion methods
+    # ========================
+
+    def _get_values(self, action, arg_strings):
+        # for everything but PARSER args, strip out '--'
+        if action.nargs is not PARSER:
+            arg_strings = [s for s in arg_strings if s != '--']
+        
+        # optional argument produces a default when not present
+        if not arg_strings and action.nargs == OPTIONAL:
+            if action.option_strings:
+                value = action.const
+            else:
+                value = action.default
+            if isinstance(value, basestring):
+                value = self._get_value(action, value)
+                self._check_value(action, value)
+
+        # when nargs='*' on a positional, if there were no command-line
+        # args, use the default if it is anything other than None
+        elif (not arg_strings and action.nargs == ZERO_OR_MORE and
+              not action.option_strings):
+            if action.default is not None:
+                value = action.default
+            else:
+                value = arg_strings
+            self._check_value(action, value)
+        
+        # single argument or optional argument produces a single value
+        elif len(arg_strings) == 1 and action.nargs in [None, OPTIONAL]:
+            arg_string, = arg_strings
+            value = self._get_value(action, arg_string)
+            self._check_value(action, value)
+
+        # PARSER arguments convert all values, but check only the first
+        elif action.nargs is PARSER:
+            value = list(self._get_value(action, v) for v in arg_strings)
+            self._check_value(action, value[0])
+
+        # all other types of nargs produce a list
+        else:
+            value = list(self._get_value(action, v) for v in arg_strings)
+            for v in value:
+                self._check_value(action, v)
+
+        # return the converted value            
+        return value
+
+    def _get_value(self, action, arg_string):
+        type_func = self._registry_get('type', action.type, action.type)
+        if not callable(type_func):
+            msg = _('%r is not callable')
+            raise ArgumentError(action, msg % type_func)
+        
+        # convert the value to the appropriate type
+        try:
+            result = type_func(arg_string)
+
+        # TypeErrors or ValueErrors indicate errors
+        except (TypeError, ValueError):
+            name = getattr(action.type, '__name__', repr(action.type))
+            msg = _('invalid %s value: %r')
+            raise ArgumentError(action, msg % (name, arg_string))
+
+        # return the converted value
+        return result
+
+    def _check_value(self, action, value):
+        # converted value must be one of the choices (if specified)
+        if action.choices is not None and value not in action.choices:
+            tup = value, ', '.join(map(repr, action.choices))
+            msg = _('invalid choice: %r (choose from %s)') % tup
+            raise ArgumentError(action, msg)
+
+        
+
+    # =======================
+    # Help-formatting methods
+    # =======================
+
+    def format_usage(self):
+        formatter = self._get_formatter()
+        formatter.add_usage(self.usage,
+                            self._get_optional_actions(),
+                            self._get_positional_actions())
+        return formatter.format_help()
+
+    def format_help(self):
+        formatter = self._get_formatter()
+
+        # usage
+        formatter.add_usage(self.usage,
+                            self._get_optional_actions(),
+                            self._get_positional_actions())
+
+        # description        
+        formatter.add_text(self.description)
+
+        # positionals
+        formatter.start_section(_('positional arguments'))
+        formatter.add_arguments(self._positional_actions_list)
+        formatter.end_section()
+
+        # optionals
+        formatter.start_section(_('optional arguments'))
+        formatter.add_arguments(self._optional_actions_list)
+        formatter.end_section()
+
+        # user-defined groups
+        for argument_group in self._argument_groups:
+            formatter.start_section(argument_group.title)
+            formatter.add_text(argument_group.description)
+            formatter.add_arguments(argument_group._positional_actions_list)
+            formatter.add_arguments(argument_group._optional_actions_list)
+            formatter.end_section()
+
+        # epilog
+        formatter.add_text(self.epilog)
+
+        # determine help from format above
+        return formatter.format_help()
+
+    def format_version(self):
+        formatter = self._get_formatter()
+        formatter.add_text(self.version)
+        return formatter.format_help()
+
+    def _get_formatter(self):
+        return self.formatter_class(prog=self.prog)
+
+    # =====================
+    # Help-printing methods
+    # =====================
+
+    def print_usage(self, file=None):
+        self._print_message(self.format_usage(), file)
+
+    def print_help(self, file=None):
+        self._print_message(self.format_help(), file)
+
+    def print_version(self, file=None):
+        self._print_message(self.format_version(), file)
+
+    def _print_message(self, message, file=None):
+        if message:
+            if file is None:
+                file = _sys.stderr
+            file.write(message)
+
+
+    # ===============
+    # Exiting methods
+    # ===============
+
+    def exit(self, status=0, message=None):
+        if message:
+            _sys.stderr.write(message)
+        _sys.exit(status)
+
+    def error(self, message):
+        """error(message: string)
+
+        Prints a usage message incorporating the message to stderr and
+        exits.
+        
+        If you override this in a subclass, it should not return -- it
+        should either exit or raise an exception.
+        """
+        self.print_usage(_sys.stderr)
+        self.exit(2, _('%s: error: %s\n') % (self.prog, message))

docs/source/development/config_blueprint.txt

@@ -0,0 +1,33 b''
+=========================================
+Notes on the IPython configuration system
+=========================================
+
+This document has some random notes on the configuration system.
+
+To start, an IPython process needs:
+
+* Configuration files
+* Command line options
+* Additional files (FURL files, extra scripts, etc.)
+
+It feeds these things into the core logic of the process, and as output,
+produces:
+
+* Log files
+* Security files
+
+There are a number of things that complicate this:
+
+* A process may need to be started on a different host that doesn't have
+  any of the config files or additional files.  Those files need to be
+  moved over and put in a staging area.  The process then needs to be told
+  about them.
+* The location of the output files should somehow be set by config files or
+  command line options.
+* Our config files are very hierarchical, but command line options are flat,
+  making it difficult to relate command line options to config files.
+* Some processes (like ipcluster and the daemons) have to manage the input and
+  output files for multiple different subprocesses, each possibly on a
+  different host.  Ahhhh!
+* Our configurations are not singletons.  A given user will likely have
+  many different configurations for different clusters.

docs/source/parallel/parallel_process.txt

@@ -0,0 +1,251 b''
+.. _parallel_process:
+
+===========================================
+Starting the IPython controller and engines
+===========================================
+
+To use IPython for parallel computing, you need to start one instance of
+the controller and one or more instances of the engine. The controller
+and each engine can run on different machines or on the same machine.
+Because of this, there are many different possibilities.
+
+Broadly speaking, there are two ways of going about starting a controller and engines:
+
+* In an automated manner using the :command:`ipcluster` command.
+* In a more manual way using the :command:`ipcontroller` and 
+  :command:`ipengine` commands.
+
+This document describes both of these methods.  We recommend that new users start with the :command:`ipcluster` command as it simplifies many common usage cases.
+
+General considerations
+======================
+
+Before delving into the details about how you can start a controller and engines using the various methods, we outline some of the general issues that come up when starting the controller and engines.  These things come up no matter which method you use to start your IPython cluster.
+
+Let's say that you want to start the controller on ``host0`` and engines on hosts ``host1``-``hostn``.  The following steps are then required:
+
+1. Start the controller on ``host0`` by running :command:`ipcontroller` on
+   ``host0``.
+2. Move the FURL file (:file:`ipcontroller-engine.furl`) created by the 
+   controller from ``host0`` to hosts ``host1``-``hostn``.
+3. Start the engines on hosts ``host1``-``hostn`` by running 
+   :command:`ipengine`.  This command has to be told where the FURL file 
+   (:file:`ipcontroller-engine.furl`) is located.
+
+At this point, the controller and engines will be connected. By default, the
+FURL files created by the controller are put into the
+:file:`~/.ipython/security` directory. If the engines share a filesystem with
+the controller, step 2 can be skipped as the engines will automatically look
+at that location.
+
+The final step required required to actually use the running controller from a
+client is to move the FURL files :file:`ipcontroller-mec.furl` and
+:file:`ipcontroller-tc.furl` from ``host0`` to the host where the clients will
+be run.  If these file are put into the :file:`~/.ipython/security` directory of the client's host, they will be found automatically.  Otherwise, the full path to them has to be passed to the client's constructor.
+
+Using :command:`ipcluster`
+==========================
+
+The :command:`ipcluster` command provides a simple way of starting a controller and engines in the following situations:
+
+1. When the controller and engines are all run on localhost. This is useful
+   for testing or running on a multicore computer.
+2. When engines are started using the :command:`mpirun` command that comes 
+   with most MPI [MPI]_ implementations
+3. When engines are started using the PBS [PBS]_ batch system.
+
+.. note::
+
+    It is also possible for advanced users to add support to
+    :command:`ipcluster` for starting controllers and engines using other
+    methods (like Sun's Grid Engine for example).
+
+.. note::
+
+    Currently :command:`ipcluster` requires that the
+    :file:`~/.ipython/security` directory live on a shared filesystem that is
+    seen by both the controller and engines. If you don't have a shared file
+    system you will need to use :command:`ipcontroller` and
+    :command:`ipengine` directly.
+
+Underneath the hood, :command:`ipcluster` just uses :command:`ipcontroller`
+and :command:`ipengine` to perform the steps described above.
+
+Using :command:`ipcluster` in local mode
+----------------------------------------
+
+To start one controller and 4 engines on localhost, just do::
+
+    $ ipcluster local -n 4
+
+To see other command line options for the local mode, do::
+
+    $ ipcluster local -h
+
+Using :command:`ipcluster` in mpirun mode
+-----------------------------------------
+
+The mpirun mode is useful if you:
+
+1. Have MPI installed.
+2. Your systems are configured to use the :command:`mpirun` command to start 
+   processes.
+
+If these are satisfied, you can start an IPython cluster using::
+
+    $ ipcluster mpirun -n 4
+
+This does the following:
+
+1. Starts the IPython controller on current host.
+2. Uses :command:`mpirun` to start 4 engines.
+
+On newer MPI implementations (such as OpenMPI), this will work even if you don't make any calls to MPI or call :func:`MPI_Init`.  However, older MPI implementations actually require each process to call :func:`MPI_Init` upon starting.  The easiest way of having this done is to install the mpi4py [mpi4py]_ package and then call ipcluster with the ``--mpi`` option::
+
+    $ ipcluster mpirun -n 4 --mpi=mpi4py
+
+Unfortunately, even this won't work for some MPI implementations.  If you are having problems with this, you will likely have to use a custom Python executable that itself calls :func:`MPI_Init` at the appropriate time.  Fortunately, mpi4py comes with such a custom Python executable that is easy to install and use.  However, this custom Python executable approach will not work with :command:`ipcluster` currently.
+
+Additional command line options for this mode can be found by doing::
+
+    $ ipcluster mpirun -h
+
+More details on using MPI with IPython can be found :ref:`here <parallelmpi>`.
+
+
+Using :command:`ipcluster` in PBS mode
+--------------------------------------
+
+The PBS mode uses the Portable Batch System [PBS]_ to start the engines.  To use this mode, you first need to create a PBS script template that will be used to start the engines.  Here is a sample PBS script template:
+
+.. sourcecode:: bash
+
+    #PBS -N ipython
+    #PBS -j oe
+    #PBS -l walltime=00:10:00
+    #PBS -l nodes=${n/4}:ppn=4
+    #PBS -q parallel
+
+    cd $$PBS_O_WORKDIR
+    export PATH=$$HOME/usr/local/bin
+    export PYTHONPATH=$$HOME/usr/local/lib/python2.4/site-packages
+    /usr/local/bin/mpiexec -n ${n} ipengine --logfile=$$PBS_O_WORKDIR/ipengine
+
+There are a few important points about this template:
+
+1. This template will be rendered at runtime using IPython's :mod:`Itpl` 
+   template engine.
+
+2. Instead of putting in the actual number of engines, use the notation
+   ``${n}`` to indicate the number of engines to be started. You can also uses
+   expressions like ``${n/4}`` in the template to indicate the number of 
+   nodes.
+
+3. Because ``$`` is a special character used by the template engine, you must  
+   escape any ``$`` by using ``$$``.  This is important when referring to 
+   environment variables in the template.
+
+4. Any options to :command:`ipengine` should be given in the batch script 
+   template.
+
+5. Depending on the configuration of you system, you may have to set 
+   environment variables in the script template.
+
+Once you have created such a script, save it with a name like :file:`pbs.template`.  Now you are ready to start your job::
+
+    $ ipcluster pbs -n 128 --pbs-script=pbs.template
+
+Additional command line options for this mode can be found by doing::
+
+    $ ipcluster pbs -h
+
+Using the :command:`ipcontroller` and :command:`ipengine` commands
+==================================================================
+
+It is also possible to use the :command:`ipcontroller` and :command:`ipengine` commands to start your controller and engines.  This approach gives you full control over all aspects of the startup process.
+
+Starting the controller and engine on your local machine
+--------------------------------------------------------
+
+To use :command:`ipcontroller` and :command:`ipengine` to start things on your
+local machine, do the following.
+
+First start the controller::
+
+	$ ipcontroller
+	
+Next, start however many instances of the engine you want using (repeatedly) the command::
+
+	$ ipengine
+
+The engines should start and automatically connect to the controller using the FURL files in :file:`~./ipython/security`. You are now ready to use the controller and engines from IPython.
+
+.. warning:: 
+	
+	The order of the above operations is very important.  You *must*
+ 	start the controller before the engines, since the engines connect 
+	to the controller as they get started.
+
+.. note::
+
+    On some platforms (OS X), to put the controller and engine into the
+    background you may need to give these commands in the form ``(ipcontroller
+    &)`` and ``(ipengine &)`` (with the parentheses) for them to work
+    properly.
+
+Starting the controller and engines on different hosts
+------------------------------------------------------
+
+When the controller and engines are running on different hosts, things are
+slightly more complicated, but the underlying ideas are the same:
+
+1. Start the controller on a host using :command:`ipcontroller`.
+2. Copy :file:`ipcontroller-engine.furl` from :file:`~./ipython/security` on the controller's host to the host where the engines will run.
+3. Use :command:`ipengine` on the engine's hosts to start the engines.
+
+The only thing you have to be careful of is to tell :command:`ipengine` where the :file:`ipcontroller-engine.furl` file is located.  There are two ways you can do this:
+
+* Put :file:`ipcontroller-engine.furl` in the :file:`~./ipython/security`
+  directory on the engine's host, where it will be found automatically.
+* Call :command:`ipengine` with the ``--furl-file=full_path_to_the_file``
+  flag.
+
+The ``--furl-file`` flag works like this::
+
+    $ ipengine --furl-file=/path/to/my/ipcontroller-engine.furl
+
+.. note::
+    
+    If the controller's and engine's hosts all have a shared file system  
+    (:file:`~./ipython/security` is the same on all of them), then things
+    will just work!
+
+Make FURL files persistent
+---------------------------
+
+At fist glance it may seem that that managing the FURL files is a bit annoying.  Going back to the house and key analogy, copying the FURL around each time you start the controller is like having to make a new key every time you want to unlock the door and enter your house.  As with your house, you want to be able to create the key (or FURL file) once, and then simply use it at any point in the future.
+
+This is possible.  The only thing you have to do is decide what ports the controller will listen on for the engines and clients.  This is done as follows::
+
+    $ ipcontroller -r --client-port=10101 --engine-port=10102
+
+Then, just copy the furl files over the first time and you are set.  You can start and stop the controller and engines any many times as you want in the future, just make sure to tell the controller to use the *same* ports.
+
+.. note::
+
+    You may ask the question: what ports does the controller listen on if you
+    don't tell is to use specific ones? The default is to use high random port
+    numbers. We do this for two reasons: i) to increase security through
+    obscurity and ii) to multiple controllers on a given host to start and
+    automatically use different ports.
+
+Log files
+---------
+
+All of the components of IPython have log files associated with them.
+These log files can be extremely useful in debugging problems with
+IPython and can be found in the directory :file:`~/.ipython/log`.  Sending
+the log files to us will often help us to debug any problems.
+
+
+.. [PBS] Portable Batch System.  http://www.openpbs.org/

docs/source/parallel/parallel_security.txt

@@ -0,0 +1,363 b''
+.. _parallelsecurity:
+
+===========================
+Security details of IPython
+===========================
+
+IPython's :mod:`IPython.kernel` package exposes the full power of the Python
+interpreter over a TCP/IP network for the purposes of parallel computing. This
+feature brings up the important question of IPython's security model. This
+document gives details about this model and how it is implemented in IPython's
+architecture.
+
+Processs and network topology
+=============================
+
+To enable parallel computing, IPython has a number of different processes that
+run. These processes are discussed at length in the IPython documentation and
+are summarized here:
+
+* The IPython *engine*.  This process is a full blown Python
+  interpreter in which user code is executed.  Multiple
+  engines are started to make parallel computing possible.
+* The IPython *controller*.  This process manages a set of 
+  engines, maintaining a queue for each and presenting
+  an asynchronous interface to the set of engines.
+* The IPython *client*.  This process is typically an
+  interactive Python process that is used to coordinate the
+  engines to get a parallel computation done.
+
+Collectively, these three processes are called the IPython *kernel*.
+
+These three processes communicate over TCP/IP connections with a well defined
+topology. The IPython controller is the only process that listens on TCP/IP
+sockets. Upon starting, an engine connects to a controller and registers
+itself with the controller. These engine/controller TCP/IP connections persist
+for the lifetime of each engine.
+
+The IPython client also connects to the controller using one or more TCP/IP
+connections. These connections persist for the lifetime of the client only.
+
+A given IPython controller and set of engines typically has a relatively short
+lifetime. Typically this lifetime corresponds to the duration of a single
+parallel simulation performed by a single user. Finally, the controller,
+engines and client processes typically execute with the permissions of that
+same user. More specifically, the controller and engines are *not* executed as
+root or with any other superuser permissions.
+
+Application logic
+=================
+
+When running the IPython kernel to perform a parallel computation, a user
+utilizes the IPython client to send Python commands and data through the
+IPython controller to the IPython engines, where those commands are executed
+and the data processed. The design of IPython ensures that the client is the
+only access point for the capabilities of the engines.  That is, the only way of addressing the engines is through a client.
+
+A user can utilize the client to instruct the IPython engines to execute
+arbitrary Python commands. These Python commands can include calls to the
+system shell, access the filesystem, etc., as required by the user's
+application code. From this perspective, when a user runs an IPython engine on
+a host, that engine has the same capabilities and permissions as the user
+themselves (as if they were logged onto the engine's host with a terminal).
+
+Secure network connections
+==========================
+
+Overview
+--------
+
+All TCP/IP connections between the client and controller as well as the
+engines and controller are fully encrypted and authenticated. This section
+describes the details of the encryption and authentication approached used
+within IPython.
+
+IPython uses the Foolscap network protocol [Foolscap]_ for all communications
+between processes. Thus, the details of IPython's security model are directly
+related to those of Foolscap. Thus, much of the following discussion is
+actually just a discussion of the security that is built in to Foolscap.
+
+Encryption
+----------
+
+For encryption purposes, IPython and Foolscap use the well known Secure Socket
+Layer (SSL) protocol [RFC5246]_. We use the implementation of this protocol
+provided by the OpenSSL project through the pyOpenSSL [pyOpenSSL]_ Python
+bindings to OpenSSL.
+
+Authentication
+--------------
+
+IPython clients and engines must also authenticate themselves with the
+controller. This is handled in a capabilities based security model
+[Capability]_. In this model, the controller creates a strong cryptographic
+key or token that represents each set of capability that the controller
+offers. Any party who has this key and presents it to the controller has full
+access to the corresponding capabilities of the controller. This model is
+analogous to using a physical key to gain access to physical items
+(capabilities) behind a locked door.
+
+For a capabilities based authentication system to prevent unauthorized access,
+two things must be ensured:
+
+* The keys must be cryptographically strong.  Otherwise attackers could gain 
+  access by a simple brute force key guessing attack.
+* The actual keys must be distributed only to authorized parties.
+
+The keys in Foolscap are called Foolscap URL's or FURLs. The following section
+gives details about how these FURLs are created in Foolscap. The IPython
+controller creates a number of FURLs for different purposes:
+
+* One FURL that grants IPython engines access to the controller.  Also
+  implicit in this access is permission to execute code sent by an
+  authenticated IPython client.
+* Two or more FURLs that grant IPython clients access to the controller.
+  Implicit in this access is permission to give the controller's engine code 
+  to execute.
+
+Upon starting, the controller creates these different FURLS and writes them
+files in the user-read-only directory :file:`$HOME/.ipython/security`. Thus, only the
+user who starts the controller has access to the FURLs.
+
+For an IPython client or engine to authenticate with a controller, it must
+present the appropriate FURL to the controller upon connecting. If the
+FURL matches what the controller expects for a given capability, access is
+granted. If not, access is denied. The exchange of FURLs is done after
+encrypted communications channels have been established to prevent attackers
+from capturing them.
+
+.. note::
+
+    The FURL is similar to an unsigned private key in SSH.
+
+Details of the Foolscap handshake
+---------------------------------
+
+In this section we detail the precise security handshake that takes place at
+the beginning of any network connection in IPython. For the purposes of this
+discussion, the SERVER is the IPython controller process and the CLIENT is the
+IPython engine or client process.
+
+Upon starting, all IPython processes do the following:
+
+1. Create a public key x509 certificate (ISO/IEC 9594).
+2. Create a hash of the contents of the certificate using the SHA-1 algorithm.
+   The base-32 encoded version of this hash is saved by the process as its 
+   process id (actually in Foolscap, this is the Tub id, but here refer to
+   it as the process id).
+
+Upon starting, the IPython controller also does the following:
+
+1. Save the x509 certificate to disk in a secure location. The CLIENT
+   certificate is never saved to disk.
+2. Create a FURL for each capability that the controller has.  There are
+   separate capabilities the controller offers for clients and engines.  The
+   FURL is created using:  a) the process id of the SERVER, b) the IP 
+   address and port the SERVER is listening on and c) a 160 bit,    
+   cryptographically secure string that represents the capability (the
+   "capability id").
+3. The FURLs are saved to disk in a secure location on the SERVER's host.
+
+For a CLIENT to be able to connect to the SERVER and access a capability of
+that SERVER, the CLIENT must have knowledge of the FURL for that SERVER's
+capability. This typically requires that the file containing the FURL be
+moved from the SERVER's host to the CLIENT's host. This is done by the end
+user who started the SERVER and wishes to have a CLIENT connect to the SERVER.
+
+When a CLIENT connects to the SERVER, the following handshake protocol takes
+place:
+
+1. The CLIENT tells the SERVER what process (or Tub) id it expects the SERVER
+   to have.
+2. If the SERVER has that process id, it notifies the CLIENT that it will now 
+   enter encrypted mode.  If the SERVER has a different id, the SERVER aborts.
+3. Both CLIENT and SERVER initiate the SSL handshake protocol.
+4. Both CLIENT and SERVER request the certificate of their peer and verify
+   that certificate.  If this succeeds, all further communications are 
+   encrypted.
+5. Both CLIENT and SERVER send a hello block containing connection parameters
+   and their process id.
+6. The CLIENT and SERVER check that their peer's stated process id matches the
+   hash of the x509 certificate the peer presented.  If not, the connection is
+   aborted.
+7. The CLIENT verifies that the SERVER's stated id matches the id of the
+   SERVER the CLIENT is intending to connect to.  If not, the connection is 
+   aborted.
+8. The CLIENT and SERVER elect a master who decides on the final connection
+   parameters.
+
+The public/private key pair associated with each process's x509 certificate
+are completely hidden from this handshake protocol. There are however, used
+internally by OpenSSL as part of the SSL handshake protocol. Each process
+keeps their own private key hidden and sends its peer only the public key
+(embedded in the certificate).
+
+Finally, when the CLIENT requests access to a particular SERVER capability,
+the following happens:
+
+1. The CLIENT asks the SERVER for access to a capability by presenting that 
+   capabilities id.
+2. If the SERVER has a capability with that id, access is granted. If not,
+   access is not granted.
+3. Once access has been gained, the CLIENT can use the capability.
+
+Specific security vulnerabilities
+=================================
+
+There are a number of potential security vulnerabilities present in IPython's
+architecture. In this section we discuss those vulnerabilities and detail how
+the security architecture described above prevents them from being exploited.
+
+Unauthorized clients
+--------------------
+
+The IPython client can instruct the IPython engines to execute arbitrary
+Python code with the permissions of the user who started the engines. If an
+attacker were able to connect their own hostile IPython client to the IPython
+controller, they could instruct the engines to execute code.
+
+This attack is prevented by the capabilities based client authentication
+performed after the encrypted channel has been established. The relevant
+authentication information is encoded into the FURL that clients must
+present to gain access to the IPython controller. By limiting the distribution
+of those FURLs, a user can grant access to only authorized persons.
+
+It is highly unlikely that a client FURL could be guessed by an attacker
+in a brute force guessing attack. A given instance of the IPython controller
+only runs for a relatively short amount of time (on the order of hours). Thus
+an attacker would have only a limited amount of time to test a search space of
+size 2**320. Furthermore, even if a controller were to run for a longer amount
+of time, this search space is quite large (larger for instance than that of
+typical username/password pair).
+
+Unauthorized engines
+--------------------
+
+If an attacker were able to connect a hostile engine to a user's controller,
+the user might unknowingly send sensitive code or data to the hostile engine.
+This attacker's engine would then have full access to that code and data.
+
+This type of attack is prevented in the same way as the unauthorized client
+attack, through the usage of the capabilities based authentication scheme.
+
+Unauthorized controllers
+------------------------
+
+It is also possible that an attacker could try to convince a user's IPython
+client or engine to connect to a hostile IPython controller. That controller
+would then have full access to the code and data sent between the IPython
+client and the IPython engines.
+
+Again, this attack is prevented through the FURLs, which ensure that a
+client or engine connects to the correct controller. It is also important to
+note that the FURLs also encode the IP address and port that the
+controller is listening on, so there is little chance of mistakenly connecting
+to a controller running on a different IP address and port.
+
+When starting an engine or client, a user must specify which FURL to use
+for that connection. Thus, in order to introduce a hostile controller, the
+attacker must convince the user to use the FURLs associated with the
+hostile controller. As long as a user is diligent in only using FURLs from
+trusted sources, this attack is not possible.
+
+Other security measures
+=======================
+
+A number of other measures are taken to further limit the security risks
+involved in running the IPython kernel.
+
+First, by default, the IPython controller listens on random port numbers.
+While this can be overridden by the user, in the default configuration, an
+attacker would have to do a port scan to even find a controller to attack.
+When coupled with the relatively short running time of a typical controller
+(on the order of hours), an attacker would have to work extremely hard and
+extremely *fast* to even find a running controller to attack.
+
+Second, much of the time, especially when run on supercomputers or clusters,
+the controller is running behind a firewall. Thus, for engines or client to
+connect to the controller:
+
+* The different processes have to all be behind the firewall.
+
+or:
+
+* The user has to use SSH port forwarding to tunnel the
+  connections through the firewall.
+   
+In either case, an attacker is presented with addition barriers that prevent
+attacking or even probing the system.
+
+Summary
+=======
+
+IPython's architecture has been carefully designed with security in mind. The
+capabilities based authentication model, in conjunction with the encrypted
+TCP/IP channels, address the core potential vulnerabilities in the system,
+while still enabling user's to use the system in open networks.
+
+Other questions
+===============
+
+About keys
+----------
+
+Can you clarify the roles of the certificate and its keys versus the FURL,
+which is also called a key?
+
+The certificate created by IPython processes is a standard public key x509
+certificate, that is used by the SSL handshake protocol to setup encrypted
+channel between the controller and the IPython engine or client. This public
+and private key associated with this certificate are used only by the SSL
+handshake protocol in setting up this encrypted channel.
+
+The FURL serves a completely different and independent purpose from the
+key pair associated with the certificate. When we refer to a FURL as a
+key, we are using the word "key" in the capabilities based security model
+sense. This has nothing to do with "key" in the public/private key sense used
+in the SSL protocol.
+
+With that said the FURL is used as an cryptographic key, to grant
+IPython engines and clients access to particular capabilities that the
+controller offers.
+
+Self signed certificates
+------------------------
+
+Is the controller creating a self-signed certificate? Is this created for per
+instance/session, one-time-setup or each-time the controller is started?
+
+The Foolscap network protocol, which handles the SSL protocol details, creates
+a self-signed x509 certificate using OpenSSL for each IPython process. The
+lifetime of the certificate is handled differently for the IPython controller
+and the engines/client.
+
+For the IPython engines and client, the certificate is only held in memory for
+the lifetime of its process. It is never written to disk.
+
+For the controller, the certificate can be created anew each time the
+controller starts or it can be created once and reused each time the
+controller starts. If at any point, the certificate is deleted, a new one is
+created the next time the controller starts.
+
+SSL private key
+---------------
+
+How the private key (associated with the certificate) is distributed?
+
+In the usual implementation of the SSL protocol, the private key is never
+distributed. We follow this standard always.
+
+SSL versus Foolscap authentication
+----------------------------------
+
+Many SSL connections only perform one sided authentication (the server to the
+client). How is the client authentication in IPython's system related to SSL
+authentication?
+
+We perform a two way SSL handshake in which both parties request and verify
+the certificate of their peer. This mutual authentication is handled by the
+SSL handshake and is separate and independent from the additional
+authentication steps that the CLIENT and SERVER perform after an encrypted
+channel is established.
+
+.. [RFC5246] <http://tools.ietf.org/html/rfc5246>

sandbox/asynparallel.py

@@ -0,0 +1,172 b''
+#!/usr/bin/env python
+"""A parallel tasking tool that uses asynchronous programming. This uses 
+blocking client to get taskid, but returns a Deferred as the result of 
+run(). Users should attach their callbacks on these Deferreds.
+
+Only returning of results is asynchronous. Submitting tasks and getting task
+ids are done synchronously.
+
+Yichun Wei 03/2008
+"""
+
+import inspect
+import itertools
+import numpy as N
+
+from twisted.python import log
+from ipython1.kernel import client
+from ipython1.kernel.client import Task
+
+""" After http://trac.pocoo.org/repos/pocoo/trunk/pocoo/utils/decorators.py
+"""
+class submit_job(object):
+    """ a decorator factory: takes a MultiEngineClient a TaskClient, returns a 
+        decorator, that makes a call to the decorated func as a task in ipython1
+        and submit it to IPython1 controller:
+    """
+    def __init__(self, rc, tc):
+        self.rc = rc
+        self.tc = tc
+
+    def __call__(self, func):
+        return self._decorate(func)
+
+    def _getinfo(self, func):
+        assert inspect.ismethod(func) or inspect.isfunction(func)
+        regargs, varargs, varkwargs, defaults = inspect.getargspec(func)
+        argnames = list(regargs)
+        if varargs:
+            argnames.append(varargs)
+        if varkwargs:
+            argnames.append(varkwargs)
+        counter = itertools.count()
+        fullsign = inspect.formatargspec(
+            regargs, varargs, varkwargs, defaults,
+            formatvalue=lambda value: '=defarg[%i]' % counter.next())[1:-1]
+        shortsign = inspect.formatargspec(
+            regargs, varargs, varkwargs, defaults,
+            formatvalue=lambda value: '')[1:-1]
+        dic = dict(('arg%s' % n, name) for n, name in enumerate(argnames))
+        dic.update(name=func.__name__, argnames=argnames, shortsign=shortsign,
+            fullsign = fullsign, defarg = func.func_defaults or ())
+        return dic
+
+    def _decorate(self, func):
+        """
+        Takes a function and a remote controller and returns a function
+        decorated that is going to submit the job with the controller. 
+        The decorated function is obtained by evaluating a lambda 
+        function with the correct signature.
+
+        the TaskController setupNS doesn't cope with functions, but we
+        can use RemoteController to push functions/modules into engines.
+
+        Changes:
+        200803. In new ipython1, we use push_function for functions.
+        """
+        rc, tc = self.rc, self.tc
+        infodict = self._getinfo(func)
+        if 'rc' in infodict['argnames']:
+            raise NameError, "You cannot use rc as argument names!"
+
+        # we assume the engines' namepace has been prepared.
+        # ns[func.__name__] is already the decorated closure function.
+        # we need to change it back to the original function:
+        ns = {}
+        ns[func.__name__] = func
+
+        # push func and all its environment/prerequesites to engines
+        rc.push_function(ns, block=True) # note it is nonblock by default, not know if it causes problems
+
+        def do_submit_func(*args, **kwds):
+            jobns = {} 
+
+            # Initialize job namespace with args that have default args 
+            # now we support calls that uses default args
+            for n in infodict['fullsign'].split(','):
+                try:
+                    vname, var = n.split('=')
+                    vname, var = vname.strip(), var.strip()
+                except: # no defarg, one of vname, var is None
+                    pass
+                else:
+                    jobns.setdefault(vname, eval(var, infodict))
+
+            # push args and kwds, overwritting default args if needed.
+            nokwds = dict((n,v) for n,v in zip(infodict['argnames'], args)) # truncated
+            jobns.update(nokwds)
+            jobns.update(kwds)
+
+            task = Task('a_very_long_and_rare_name = %(name)s(%(shortsign)s)' % infodict, 
+                pull=['a_very_long_and_rare_name'], push=jobns,)
+            jobid = tc.run(task)
+            # res is a deferred, one can attach callbacks on it
+            res = tc.task_controller.get_task_result(jobid, block=True)
+            res.addCallback(lambda x: x.ns['a_very_long_and_rare_name'])
+            res.addErrback(log.err)
+            return res 
+
+        do_submit_func.rc = rc
+        do_submit_func.tc = tc
+        return do_submit_func
+
+
+def parallelized(rc, tc, initstrlist=[]):
+    """ rc - remote controller
+        tc - taks controller
+        strlist - a list of str that's being executed on engines.
+    """
+    for cmd in initstrlist:
+        rc.execute(cmd, block=True)
+    return submit_job(rc, tc)
+
+
+from twisted.internet import defer
+from numpy import array, nan
+
+def pmap(func, parr, **kwds):
+    """Run func on every element of parr (array), using the elements 
+    as the only one parameter (so you can usually use a dict that 
+    wraps many parameters). -> a result array of Deferreds with the 
+    same shape. func.tc will be used as the taskclient.
+
+    **kwds are passed on to func, not changed.
+    """
+    assert func.tc
+    tc = func.tc
+
+    def run(p, **kwds):
+        if p:
+            return func(p, **kwds)
+        else:
+            return defer.succeed(nan) 
+
+    reslist = [run(p, **kwds).addErrback(log.err) for p in parr.flat]
+    resarr = array(reslist)
+    resarr.shape = parr.shape
+    return resarr
+
+
+if __name__=='__main__':
+
+    rc = client.MultiEngineClient(client.default_address)
+    tc = client.TaskClient(client.default_task_address)
+
+    # if commenting out the decorator you get a local running version 
+    # instantly
+    @parallelized(rc, tc)
+    def f(a, b=1):
+        #from time import sleep 
+        #sleep(1)
+        print "a,b=", a,b
+        return a+b
+
+    def showres(x):
+        print 'ans:',x
+
+    res = f(11,5)
+    res.addCallback(showres)
+
+    # this is not necessary in Twisted 8.0
+    from twisted.internet import reactor
+    reactor.run()

sandbox/minitraits.py

@@ -0,0 +1,119 b''
+import types
+
+class AttributeBase(object):
+    
+    def __get__(self, inst, cls=None):
+        if inst is None:
+            return self
+        try:
+            return inst._attributes[self.name]
+        except KeyError:
+            raise AttributeError("object has no attribute %r" % self.name)
+    
+    def __set__(self, inst, value):
+        actualValue = self.validate(inst, self.name, value)
+        inst._attributes[self.name] = actualValue
+    
+    def validate(self, inst, name, value):
+        raise NotImplementedError("validate must be implemented by a subclass")
+
+class NameFinder(type):
+    
+    def __new__(cls, name, bases, classdict):
+        attributeList = []
+        for k,v in classdict.iteritems():
+            if isinstance(v, AttributeBase):
+                v.name = k
+                attributeList.append(k)
+        classdict['_attributeList'] = attributeList
+        return type.__new__(cls, name, bases, classdict)
+
+class HasAttributes(object):
+    __metaclass__ = NameFinder
+    
+    def __init__(self):
+        self._attributes = {}
+    
+    def getAttributeNames(self):
+        return self._attributeList
+    
+    def getAttributesOfType(self, t, default=None):
+        result = {}
+        for a in self._attributeList:
+            if self.__class__.__dict__[a].__class__ == t:
+                try:
+                    value = getattr(self, a)
+                except AttributeError:
+                    value = None
+                result[a] = value
+        return result
+
+class TypedAttribute(AttributeBase):
+    
+    def validate(self, inst, name, value):
+        if type(value) != self._type:
+            raise TypeError("attribute %s must be of type %s" % (name, self._type))
+        else:
+            return value
+
+# class Option(TypedAttribute):
+#     
+#     _type = types.IntType
+# 
+# class Param(TypedAttribute):
+#     
+#     _type = types.FloatType
+# 
+# class String(TypedAttribute):
+#     
+#     _type = types.StringType
+        
+class TypedSequenceAttribute(AttributeBase):
+    
+    def validate(self, inst, name, value):
+        if type(value) != types.TupleType and type(value) != types.ListType:
+            raise TypeError("attribute %s must be a list or tuple" % (name))
+        else:
+            for item in value:
+                if type(item) != self._subtype:
+                    raise TypeError("attribute %s must be a list or tuple of items with type %s" % (name, self._subtype))
+            return value
+
+# class Instance(AttributeBase):
+#     
+#     def __init__(self, cls):
+#         self.cls = cls
+#     
+#     def validate(self, inst, name, value):
+#         if not isinstance(value, self.cls):
+#             raise TypeError("attribute %s must be an instance of class %s" % (name, self.cls))
+#         else:
+#             return value
+        
+
+# class OptVec(TypedSequenceAttribute):
+#     
+#     _subtype = types.IntType
+# 
+# class PrmVec(TypedSequenceAttribute):
+#     
+#     _subtype = types.FloatType
+# 
+# class StrVec(TypedSequenceAttribute):
+#     
+#     _subtype = types.StringType
+# 
+# 
+# class Bar(HasAttributes):
+#     
+#     a = Option()
+# 
+# class Foo(HasAttributes):
+#     
+#     a = Option()
+#     b = Param()
+#     c = String()
+#     d = OptVec()
+#     e = PrmVec()
+#     f = StrVec()
+#     h = Instance(Bar)
  No newline at end of file

IPython/kernel/config/__init__.py

@@ -1,123 +1,124 b''
 # encoding: utf-8
 
 """Default kernel configuration."""
 
 __docformat__ = "restructuredtext en"
 
 #-------------------------------------------------------------------------------
 #  Copyright (C) 2008  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #-------------------------------------------------------------------------------
 
 #-------------------------------------------------------------------------------
 # Imports
 #-------------------------------------------------------------------------------
 
 from os.path import join as pjoin
 
 from IPython.external.configobj import ConfigObj
 from IPython.config.api import ConfigObjManager
 from IPython.genutils import get_ipython_dir, get_security_dir
 
 default_kernel_config = ConfigObj()
 
 security_dir = get_security_dir()
 
 #-------------------------------------------------------------------------------
 # Engine Configuration
 #-------------------------------------------------------------------------------
 
 engine_config = dict(
     logfile = '',    # Empty means log to stdout
     furl_file = pjoin(security_dir, 'ipcontroller-engine.furl')
 )
 
 #-------------------------------------------------------------------------------
 # MPI Configuration
 #-------------------------------------------------------------------------------
 
 mpi_config = dict(
     mpi4py = """from mpi4py import MPI as mpi
 mpi.size = mpi.COMM_WORLD.Get_size()
 mpi.rank = mpi.COMM_WORLD.Get_rank()
 """,
     pytrilinos = """from PyTrilinos import Epetra
 class SimpleStruct:
     pass
 mpi = SimpleStruct()
 mpi.rank = 0
 mpi.size = 0
 """,
     default = ''
 )
 
 #-------------------------------------------------------------------------------
 # Controller Configuration
 #-------------------------------------------------------------------------------
 
 controller_config = dict(
 
     logfile = '',    # Empty means log to stdout
     import_statement = '',
+    reuse_furls = False, # If False, old furl files are deleted
 
     engine_tub = dict(
         ip = '',         # Empty string means all interfaces
         port = 0,        # 0 means pick a port for me
         location = '',    # Empty string means try to set automatically
         secure = True,
         cert_file = pjoin(security_dir, 'ipcontroller-engine.pem'),
     ),
     engine_fc_interface = 'IPython.kernel.enginefc.IFCControllerBase',
     engine_furl_file = pjoin(security_dir, 'ipcontroller-engine.furl'),
     
     controller_interfaces = dict(
         # multiengine = dict(
         #     controller_interface = 'IPython.kernel.multiengine.IMultiEngine',
         #     fc_interface = 'IPython.kernel.multienginefc.IFCMultiEngine',
         #     furl_file = 'ipcontroller-mec.furl'
         # ),
         task = dict(
             controller_interface = 'IPython.kernel.task.ITaskController',
             fc_interface = 'IPython.kernel.taskfc.IFCTaskController',
             furl_file = pjoin(security_dir, 'ipcontroller-tc.furl')
         ),
         multiengine = dict(
             controller_interface = 'IPython.kernel.multiengine.IMultiEngine',
             fc_interface = 'IPython.kernel.multienginefc.IFCSynchronousMultiEngine',
             furl_file = pjoin(security_dir, 'ipcontroller-mec.furl')
         )
     ),
 
     client_tub = dict(
         ip = '',         # Empty string means all interfaces
         port = 0,        # 0 means pick a port for me
         location = '',    # Empty string means try to set automatically
         secure = True,
         cert_file = pjoin(security_dir, 'ipcontroller-client.pem')
     )
 )
 
 #-------------------------------------------------------------------------------
 # Client Configuration
 #-------------------------------------------------------------------------------
 
 client_config = dict(
     client_interfaces = dict(
         task = dict(
             furl_file = pjoin(security_dir, 'ipcontroller-tc.furl')
         ),
         multiengine = dict(
             furl_file = pjoin(security_dir, 'ipcontroller-mec.furl')
         )
     )
 )
 
 default_kernel_config['engine'] = engine_config
 default_kernel_config['mpi'] = mpi_config
 default_kernel_config['controller'] = controller_config
 default_kernel_config['client'] = client_config
 
 
 config_manager = ConfigObjManager(default_kernel_config, 'IPython.kernel.ini')
  No newline at end of file

IPython/kernel/engineconnector.py

@@ -1,87 +1,92 b''
 # encoding: utf-8
 
 """A class that manages the engines connection to the controller."""
 
 __docformat__ = "restructuredtext en"
 
 #-------------------------------------------------------------------------------
 #  Copyright (C) 2008  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #-------------------------------------------------------------------------------
 
 #-------------------------------------------------------------------------------
 # Imports
 #-------------------------------------------------------------------------------
 
 import os
 import cPickle as pickle
 
-from twisted.python import log
+from twisted.python import log, failure
+from twisted.internet import defer
 
 from IPython.kernel.fcutil import find_furl
 from IPython.kernel.enginefc import IFCEngine
 
 #-------------------------------------------------------------------------------
 # The ClientConnector class
 #-------------------------------------------------------------------------------
 
 class EngineConnector(object):
     """Manage an engines connection to a controller.
     
     This class takes a foolscap `Tub` and provides a `connect_to_controller` 
     method that will use the `Tub` to connect to a controller and register
     the engine with the controller.
     """
     
     def __init__(self, tub):
         self.tub = tub
         
     def connect_to_controller(self, engine_service, furl_or_file):
         """
         Make a connection to a controller specified by a furl.
         
         This method takes an `IEngineBase` instance and a foolcap URL and uses
         the `tub` attribute to make a connection to the controller.  The 
         foolscap URL contains all the information needed to connect to the 
         controller, including the ip and port as well as any encryption and 
         authentication information needed for the connection.
         
         After getting a reference to the controller, this method calls the 
         `register_engine` method of the controller to actually register the 
         engine.
         
         :Parameters:
             engine_service : IEngineBase
                 An instance of an `IEngineBase` implementer
             furl_or_file : str
                 A furl or a filename containing a furl
         """
         if not self.tub.running:
             self.tub.startService()
         self.engine_service = engine_service
         self.engine_reference = IFCEngine(self.engine_service)
-        self.furl = find_furl(furl_or_file)
+        try:
+            self.furl = find_furl(furl_or_file)
+        except ValueError:
+            return defer.fail(failure.Failure())
+            # return defer.fail(failure.Failure(ValueError('not a valid furl or furl file: %r' % furl_or_file)))
         d = self.tub.getReference(self.furl)
         d.addCallbacks(self._register, self._log_failure)
         return d
     
     def _log_failure(self, reason):
-        log.err('engine registration failed:')
+        log.err('EngineConnector: engine registration failed:')
         log.err(reason)
         return reason
 
     def _register(self, rr):
         self.remote_ref = rr
         # Now register myself with the controller
         desired_id = self.engine_service.id
         d = self.remote_ref.callRemote('register_engine', self.engine_reference, 
             desired_id, os.getpid(), pickle.dumps(self.engine_service.properties,2))
         return d.addCallbacks(self._reference_sent, self._log_failure)
 
     def _reference_sent(self, registration_dict):
         self.engine_service.id = registration_dict['id']
         log.msg("engine registration succeeded, got id: %r" % self.engine_service.id)
         return self.engine_service.id
 

IPython/kernel/scripts/ipcluster.py

@@ -1,347 +1,486 b''
 #!/usr/bin/env python
 # encoding: utf-8
 
-"""Start an IPython cluster conveniently, either locally or remotely.
+"""Start an IPython cluster = (controller + engines)."""
 
-Basic usage
------------
-
-For local operation, the simplest mode of usage is:
-
-  %prog -n N
-
-where N is the number of engines you want started.
-
-For remote operation, you must call it with a cluster description file:
-
-  %prog -f clusterfile.py
-
-The cluster file is a normal Python script which gets run via execfile().  You
-can have arbitrary logic in it, but all that matters is that at the end of the
-execution, it declares the variables 'controller', 'engines', and optionally
-'sshx'.  See the accompanying examples for details on what these variables must
-contain.
-
-
-Notes
------
-
-WARNING: this code is still UNFINISHED and EXPERIMENTAL!  It is incomplete,
-some listed options are not really implemented, and all of its interfaces are
-subject to change.
-
-When operating over SSH for a remote cluster, this program relies on the
-existence of a particular script called 'sshx'.  This script must live in the
-target systems where you'll be running your controller and engines, and is
-needed to configure your PATH and PYTHONPATH variables for further execution of
-python code at the other end of an SSH connection.  The script can be as simple
-as:
-
-#!/bin/sh
-. $HOME/.bashrc
-"$@"
-
-which is the default one provided by IPython.  You can modify this or provide
-your own.  Since it's quite likely that for different clusters you may need
-this script to configure things differently or that it may live in different
-locations, its full path can be set in the same file where you define the
-cluster setup.  IPython's order of evaluation for this variable is the
-following:
-
-  a) Internal default: 'sshx'.  This only works if it is in the default system
-  path which SSH sets up in non-interactive mode.
-
-  b) Environment variable: if $IPYTHON_SSHX is defined, this overrides the
-  internal default.
-
-  c) Variable 'sshx' in the cluster configuration file: finally, this will
-  override the previous two values.
- 
-This code is Unix-only, with precious little hope of any of this ever working
-under Windows, since we need SSH from the ground up, we background processes,
-etc.  Ports of this functionality to Windows are welcome.
-
-
-Call summary
-------------
-
-    %prog [options]
-"""
-
-__docformat__ = "restructuredtext en"
-
-#-------------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
 #  Copyright (C) 2008  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
-#-------------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
 
-#-------------------------------------------------------------------------------
-# Stdlib imports
-#-------------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+# Imports
+#-----------------------------------------------------------------------------
 
 import os
-import signal
+import re
 import sys
-import time
+import signal
+pjoin = os.path.join
 
-from optparse import OptionParser
-from subprocess import Popen,call
+from twisted.internet import reactor, defer
+from twisted.internet.protocol import ProcessProtocol
+from twisted.python import failure, log
+from twisted.internet.error import ProcessDone, ProcessTerminated
+from twisted.internet.utils import getProcessOutput
 
-#---------------------------------------------------------------------------
-# IPython imports
-#---------------------------------------------------------------------------
-from IPython.tools import utils
-from IPython.genutils import get_ipython_dir
+from IPython.external import argparse
+from IPython.external import Itpl
+from IPython.kernel.twistedutil import gatherBoth
+from IPython.kernel.util import printer
+from IPython.genutils import get_ipython_dir, num_cpus
 
-#---------------------------------------------------------------------------
-# Normal code begins
-#---------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+# General process handling code
+#-----------------------------------------------------------------------------
 
-def parse_args():
-    """Parse command line and return opts,args."""
+def find_exe(cmd):
+    try:
+        import win32api
+    except ImportError:
+        raise ImportError('you need to have pywin32 installed for this to work')
+    else:
+        (path, offest) = win32api.SearchPath(os.environ['PATH'],cmd)
+        return path
 
-    parser = OptionParser(usage=__doc__)
-    newopt = parser.add_option  # shorthand
+class ProcessStateError(Exception):
+    pass
 
-    newopt("--controller-port", type="int", dest="controllerport",
-           help="the TCP port the controller is listening on")
+class UnknownStatus(Exception):
+    pass
 
-    newopt("--controller-ip", type="string", dest="controllerip",
-           help="the TCP ip address of the controller")
+class LauncherProcessProtocol(ProcessProtocol):
+    """
+    A ProcessProtocol to go with the ProcessLauncher.
+    """
+    def __init__(self, process_launcher):
+        self.process_launcher = process_launcher
+    
+    def connectionMade(self):
+        self.process_launcher.fire_start_deferred(self.transport.pid)
+    
+    def processEnded(self, status):
+        value = status.value
+        if isinstance(value, ProcessDone):
+            self.process_launcher.fire_stop_deferred(0)
+        elif isinstance(value, ProcessTerminated):
+            self.process_launcher.fire_stop_deferred(
+                {'exit_code':value.exitCode,
+                 'signal':value.signal,
+                 'status':value.status
+                }
+            )
+        else:
+            raise UnknownStatus("unknown exit status, this is probably a bug in Twisted")
 
-    newopt("-n", "--num", type="int", dest="n",default=2,
-           help="the number of engines to start")
+    def outReceived(self, data):
+        log.msg(data)
 
-    newopt("--engine-port", type="int", dest="engineport",
-           help="the TCP port the controller will listen on for engine "
-           "connections")
-    
-    newopt("--engine-ip", type="string", dest="engineip",
-           help="the TCP ip address the controller will listen on "
-           "for engine connections")
+    def errReceived(self, data):
+        log.err(data)
 
-    newopt("--mpi", type="string", dest="mpi",
-           help="use mpi with package:  for instance --mpi=mpi4py")
+class ProcessLauncher(object):
+    """
+    Start and stop an external process in an asynchronous manner.
+    
+    Currently this uses deferreds to notify other parties of process state
+    changes.  This is an awkward design and should be moved to using
+    a formal NotificationCenter.
+    """
+    def __init__(self, cmd_and_args):
+        self.cmd = cmd_and_args[0]
+        self.args = cmd_and_args
+        self._reset()
+    
+    def _reset(self):
+        self.process_protocol = None
+        self.pid = None
+        self.start_deferred = None
+        self.stop_deferreds = []
+        self.state = 'before' # before, running, or after
+    
+    @property
+    def running(self):
+        if self.state == 'running':
+            return True
+        else:
+            return False
+    
+    def fire_start_deferred(self, pid):
+        self.pid = pid
+        self.state = 'running'
+        log.msg('Process %r has started with pid=%i' % (self.args, pid))
+        self.start_deferred.callback(pid)
+    
+    def start(self):
+        if self.state == 'before':
+            self.process_protocol = LauncherProcessProtocol(self)
+            self.start_deferred = defer.Deferred()
+            self.process_transport = reactor.spawnProcess(
+                self.process_protocol,
+                self.cmd,
+                self.args,
+                env=os.environ
+            )
+            return self.start_deferred
+        else:
+            s = 'the process has already been started and has state: %r' % \
+                self.state
+            return defer.fail(ProcessStateError(s))
+    
+    def get_stop_deferred(self):
+        if self.state == 'running' or self.state == 'before':
+            d = defer.Deferred()
+            self.stop_deferreds.append(d)
+            return d
+        else:
+            s = 'this process is already complete'
+            return defer.fail(ProcessStateError(s))
+    
+    def fire_stop_deferred(self, exit_code):
+        log.msg('Process %r has stopped with %r' % (self.args, exit_code))
+        self.state = 'after'
+        for d in self.stop_deferreds:
+            d.callback(exit_code)
+    
+    def signal(self, sig):
+        """
+        Send a signal to the process.
+        
+        The argument sig can be ('KILL','INT', etc.) or any signal number.
+        """
+        if self.state == 'running':
+            self.process_transport.signalProcess(sig)
     
-    newopt("-l", "--logfile", type="string", dest="logfile",
-           help="log file name")
+    # def __del__(self):
+    #     self.signal('KILL')
+    
+    def interrupt_then_kill(self, delay=1.0):
+        self.signal('INT')
+        reactor.callLater(delay, self.signal, 'KILL')
+
 
-    newopt('-f','--cluster-file',dest='clusterfile',
-           help='file describing a remote cluster')
+#-----------------------------------------------------------------------------
+# Code for launching controller and engines
+#-----------------------------------------------------------------------------
 
-    return parser.parse_args()
 
-def numAlive(controller,engines):
-    """Return the number of processes still alive."""
-    retcodes = [controller.poll()] + \
-               [e.poll() for e in engines]
-    return retcodes.count(None)
+class ControllerLauncher(ProcessLauncher):
+    
+    def __init__(self, extra_args=None):
+        if sys.platform == 'win32':
+            args = [find_exe('ipcontroller.bat')]
+        else:
+            args = ['ipcontroller']
+        self.extra_args = extra_args
+        if extra_args is not None:
+            args.extend(extra_args)
+        
+        ProcessLauncher.__init__(self, args)
 
-stop = lambda pid: os.kill(pid,signal.SIGINT)
-kill = lambda pid: os.kill(pid,signal.SIGTERM)
 
-def cleanup(clean,controller,engines):
-    """Stop the controller and engines with the given cleanup method."""
+class EngineLauncher(ProcessLauncher):
     
-    for e in engines:
-        if e.poll() is None:
-            print 'Stopping engine, pid',e.pid
-            clean(e.pid)
-    if controller.poll() is None:
-        print 'Stopping controller, pid',controller.pid
-        clean(controller.pid)
-
-
-def ensureDir(path):
-    """Ensure a directory exists or raise an exception."""
-    if not os.path.isdir(path):
-        os.makedirs(path)
-
-
-def startMsg(control_host,control_port=10105):
-    """Print a startup message"""
-    print
-    print 'Your cluster is up and running.'
-    print
-    print 'For interactive use, you can make a MultiEngineClient with:'
-    print
-    print 'from IPython.kernel import client'
-    print "mec = client.MultiEngineClient()"
-    print
-    print 'You can then cleanly stop the cluster from IPython using:'
-    print
-    print 'mec.kill(controller=True)'
-    print
+    def __init__(self, extra_args=None):
+        if sys.platform == 'win32':
+            args = [find_exe('ipengine.bat')]
+        else:
+            args = ['ipengine']
+        self.extra_args = extra_args
+        if extra_args is not None:
+            args.extend(extra_args)
+        
+        ProcessLauncher.__init__(self, args)
 
+
+class LocalEngineSet(object):
     
-def clusterLocal(opt,arg):
-    """Start a cluster on the local machine."""
+    def __init__(self, extra_args=None):
+        self.extra_args = extra_args
+        self.launchers = []
     
-    # Store all logs inside the ipython directory
-    ipdir = get_ipython_dir()
-    pjoin = os.path.join
-
-    logfile = opt.logfile
-    if logfile is None:
-        logdir_base = pjoin(ipdir,'log')
-        ensureDir(logdir_base)
-        logfile = pjoin(logdir_base,'ipcluster-')
-
-    print 'Starting controller:',
-    controller = Popen(['ipcontroller','--logfile',logfile,'-x','-y'])
-    print 'Controller PID:',controller.pid
-
-    print 'Starting engines:   ',
-    time.sleep(5)
-
-    englogfile = '%s%s-' % (logfile,controller.pid)
-    mpi = opt.mpi
-    if mpi: # start with mpi - killing the engines with sigterm will not work if you do this
-        engines = [Popen(['mpirun', '-np', str(opt.n), 'ipengine', '--mpi', 
-            mpi, '--logfile',englogfile])]
-        # engines = [Popen(['mpirun', '-np', str(opt.n), 'ipengine', '--mpi', mpi])]
-    else: # do what we would normally do
-        engines = [ Popen(['ipengine','--logfile',englogfile])
-                    for i in range(opt.n) ]
-    eids = [e.pid for e in engines]
-    print 'Engines PIDs:  ',eids
-    print 'Log files: %s*' % englogfile
+    def start(self, n):
+        dlist = []
+        for i in range(n):
+            el = EngineLauncher(extra_args=self.extra_args)
+            d = el.start()
+            self.launchers.append(el)
+            dlist.append(d)
+        dfinal = gatherBoth(dlist, consumeErrors=True)
+        dfinal.addCallback(self._handle_start)
+        return dfinal
     
-    proc_ids = eids + [controller.pid]
-    procs = engines + [controller]
-
-    grpid = os.getpgrp()
-    try:
-        startMsg('127.0.0.1')
-        print 'You can also hit Ctrl-C to stop it, or use from the cmd line:'
-        print
-        print 'kill -INT',grpid
-        print
-        try:
-            while True:
-                time.sleep(5)
-        except:
-            pass
-    finally:
-        print 'Stopping cluster.  Cleaning up...'
-        cleanup(stop,controller,engines)
-        for i in range(4):
-            time.sleep(i+2)
-            nZombies = numAlive(controller,engines)
-            if  nZombies== 0:
-                print 'OK: All processes cleaned up.'
-                break
-            print 'Trying again, %d processes did not stop...' % nZombies
-            cleanup(kill,controller,engines)
-            if numAlive(controller,engines) == 0:
-                print 'OK: All processes cleaned up.'
-                break
-        else:
-            print '*'*75
-            print 'ERROR: could not kill some processes, try to do it',
-            print 'manually.'
-            zombies = []
-            if controller.returncode is None:
-                print 'Controller is alive: pid =',controller.pid
-                zombies.append(controller.pid)
-            liveEngines = [ e for e in engines if e.returncode is None ]
-            for e in liveEngines:
-                print 'Engine is alive:     pid =',e.pid
-                zombies.append(e.pid)
-            print
-            print 'Zombie summary:',' '.join(map(str,zombies))
-
-def clusterRemote(opt,arg):
-    """Start a remote cluster over SSH"""
-
-    # B. Granger, 9/3/08
-    # The launching of a remote cluster using SSH and a clusterfile
-    # is broken.  Because it won't be fixed before the 0.9 release, 
-    # we are removing it.  For now, we just print a message to the 
-    # user and abort.
+    def _handle_start(self, r):
+        log.msg('Engines started with pids: %r' % r)
+        return r
     
-    print """The launching of a remote IPython cluster using SSL
-and a clusterfile has been removed in this release.  
-It has been broken for a while and we are in the process 
-of building a new process management system that will be 
-used to provide a more robust way of starting an IPython
-cluster.
-
-For now remote clusters have to be launched using ipcontroller
-and ipengine separately.
-    """
-    sys.exit(1)
-
-    # Load the remote cluster configuration
-    clConfig = {}
-    execfile(opt.clusterfile,clConfig)
-    contConfig = clConfig['controller']
-    engConfig = clConfig['engines']
-    # Determine where to find sshx:
-    sshx = clConfig.get('sshx',os.environ.get('IPYTHON_SSHX','sshx'))
+    def _handle_stop(self, r):
+        log.msg('Engines received signal: %r' % r)
+        return r
+    
+    def signal(self, sig):
+        dlist = []
+        for el in self.launchers:
+            d = el.get_stop_deferred()
+            dlist.append(d)
+            el.signal(sig)
+        dfinal = gatherBoth(dlist, consumeErrors=True)
+        dfinal.addCallback(self._handle_stop)
+        return dfinal
+    
+    def interrupt_then_kill(self, delay=1.0):
+        dlist = []
+        for el in self.launchers:
+            d = el.get_stop_deferred()
+            dlist.append(d)
+            el.interrupt_then_kill(delay)
+        dfinal = gatherBoth(dlist, consumeErrors=True)
+        dfinal.addCallback(self._handle_stop)
+        return dfinal
+
+
+class BatchEngineSet(object):
     
-    # Store all logs inside the ipython directory
-    ipdir = get_ipython_dir()
-    pjoin = os.path.join
-
-    logfile = opt.logfile
-    if logfile is None:
-        logdir_base = pjoin(ipdir,'log')
-        ensureDir(logdir_base)
-        logfile = pjoin(logdir_base,'ipcluster')
-
-    # Append this script's PID to the logfile name always
-    logfile = '%s-%s' % (logfile,os.getpid())
+    # Subclasses must fill these in.  See PBSEngineSet
+    submit_command = ''
+    delete_command = ''
+    job_id_regexp = ''
     
-    print 'Starting controller:'
-    # Controller data:
-    xsys = os.system
-
-    contHost = contConfig['host']
-    contLog = '%s-con-%s-' % (logfile,contHost)
-    cmd = "ssh %s '%s' 'ipcontroller --logfile %s' &" % \
-          (contHost,sshx,contLog)
-    #print 'cmd:<%s>' % cmd  # dbg
-    xsys(cmd)
-    time.sleep(2)
-
-    print 'Starting engines:   '
-    for engineHost,engineData in engConfig.iteritems():
-        if isinstance(engineData,int):
-            numEngines = engineData
+    def __init__(self, template_file, **kwargs):
+        self.template_file = template_file
+        self.context = {}
+        self.context.update(kwargs)
+        self.batch_file = self.template_file+'-run'
+
+    def parse_job_id(self, output):
+        m = re.match(self.job_id_regexp, output)
+        if m is not None:
+            job_id = m.group()
         else:
-            raise NotImplementedError('port configuration not finished for engines')
-
-        print 'Sarting %d engines on %s' % (numEngines,engineHost)
-        engLog = '%s-eng-%s-' % (logfile,engineHost)
-        for i in range(numEngines):
-            cmd = "ssh %s '%s' 'ipengine --controller-ip %s --logfile %s' &" % \
-                      (engineHost,sshx,contHost,engLog)
-            #print 'cmd:<%s>' % cmd  # dbg
-            xsys(cmd)
-        # Wait after each host a little bit
-        time.sleep(1)
-            
-    startMsg(contConfig['host'])
+            raise Exception("job id couldn't be determined: %s" % output)
+        self.job_id = job_id
+        log.msg('Job started with job id: %r' % job_id)
+        return job_id
+    
+    def write_batch_script(self, n):
+        self.context['n'] = n
+        template = open(self.template_file, 'r').read()
+        log.msg('Using template for batch script: %s' % self.template_file)
+        script_as_string = Itpl.itplns(template, self.context)
+        log.msg('Writing instantiated batch script: %s' % self.batch_file)
+        f = open(self.batch_file,'w')
+        f.write(script_as_string)
+        f.close()
+
+    def handle_error(self, f):
+        f.printTraceback()
+        f.raiseException()
+    
+    def start(self, n):
+        self.write_batch_script(n)
+        d = getProcessOutput(self.submit_command,
+            [self.batch_file],env=os.environ)
+        d.addCallback(self.parse_job_id)
+        d.addErrback(self.handle_error)
+        return d
         
-def main():
-    """Main driver for the two big options: local or remote cluster."""
+    def kill(self):
+        d = getProcessOutput(self.delete_command,
+            [self.job_id],env=os.environ)
+        return d
+
+class PBSEngineSet(BatchEngineSet):
     
-    if sys.platform=='win32':
-        print """ipcluster does not work on Microsoft Windows.  Please start
-your IPython cluster using the ipcontroller and ipengine scripts."""
-        sys.exit(1)
+    submit_command = 'qsub'
+    delete_command = 'qdel'
+    job_id_regexp = '\d+'
     
-    opt,arg = parse_args()
+    def __init__(self, template_file, **kwargs):
+        BatchEngineSet.__init__(self, template_file, **kwargs)
+
+
+#-----------------------------------------------------------------------------
+# Main functions for the different types of clusters
+#-----------------------------------------------------------------------------
+
+# TODO:
+# The logic in these codes should be moved into classes like LocalCluster
+# MpirunCluster, PBSCluster, etc.  This would remove alot of the duplications.
+# The main functions should then just parse the command line arguments, create
+# the appropriate class and call a 'start' method.
+
+def main_local(args):
+    cont_args = []
+    cont_args.append('--logfile=%s' % pjoin(args.logdir,'ipcontroller'))
+    if args.x:
+        cont_args.append('-x')
+    if args.y:
+        cont_args.append('-y')
+    cl = ControllerLauncher(extra_args=cont_args)
+    dstart = cl.start()
+    def start_engines(cont_pid):
+        engine_args = []
+        engine_args.append('--logfile=%s' % \
+            pjoin(args.logdir,'ipengine%s-' % cont_pid))
+        eset = LocalEngineSet(extra_args=engine_args)
+        def shutdown(signum, frame):
+            log.msg('Stopping local cluster')
+            # We are still playing with the times here, but these seem
+            # to be reliable in allowing everything to exit cleanly.
+            eset.interrupt_then_kill(0.5)
+            cl.interrupt_then_kill(0.5)
+            reactor.callLater(1.0, reactor.stop)
+        signal.signal(signal.SIGINT,shutdown)
+        d = eset.start(args.n)
+        return d
+    def delay_start(cont_pid):
+        # This is needed because the controller doesn't start listening
+        # right when it starts and the controller needs to write
+        # furl files for the engine to pick up
+        reactor.callLater(1.0, start_engines, cont_pid)
+    dstart.addCallback(delay_start)
+    dstart.addErrback(lambda f: f.raiseException())
+
+def main_mpirun(args):
+    cont_args = []
+    cont_args.append('--logfile=%s' % pjoin(args.logdir,'ipcontroller'))
+    if args.x:
+        cont_args.append('-x')
+    if args.y:
+        cont_args.append('-y')
+    cl = ControllerLauncher(extra_args=cont_args)
+    dstart = cl.start()
+    def start_engines(cont_pid):
+        raw_args = ['mpirun']
+        raw_args.extend(['-n',str(args.n)])
+        raw_args.append('ipengine')
+        raw_args.append('-l')
+        raw_args.append(pjoin(args.logdir,'ipengine%s-' % cont_pid))
+        if args.mpi:
+            raw_args.append('--mpi=%s' % args.mpi)
+        eset = ProcessLauncher(raw_args)
+        def shutdown(signum, frame):
+            log.msg('Stopping local cluster')
+            # We are still playing with the times here, but these seem
+            # to be reliable in allowing everything to exit cleanly.
+            eset.interrupt_then_kill(1.0)
+            cl.interrupt_then_kill(1.0)
+            reactor.callLater(2.0, reactor.stop)
+        signal.signal(signal.SIGINT,shutdown)
+        d = eset.start()
+        return d
+    def delay_start(cont_pid):
+        # This is needed because the controller doesn't start listening
+        # right when it starts and the controller needs to write
+        # furl files for the engine to pick up
+        reactor.callLater(1.0, start_engines, cont_pid)
+    dstart.addCallback(delay_start)
+    dstart.addErrback(lambda f: f.raiseException())
+
+def main_pbs(args):
+    cont_args = []
+    cont_args.append('--logfile=%s' % pjoin(args.logdir,'ipcontroller'))
+    if args.x:
+	cont_args.append('-x')
+    if args.y:
+	cont_args.append('-y')
+    cl = ControllerLauncher(extra_args=cont_args)
+    dstart = cl.start()
+    def start_engines(r):
+        pbs_set =  PBSEngineSet(args.pbsscript)
+        def shutdown(signum, frame):
+            log.msg('Stopping pbs cluster')
+            d = pbs_set.kill()
+            d.addBoth(lambda _: cl.interrupt_then_kill(1.0))
+            d.addBoth(lambda _: reactor.callLater(2.0, reactor.stop))
+        signal.signal(signal.SIGINT,shutdown)
+        d = pbs_set.start(args.n)
+        return d
+    dstart.addCallback(start_engines)
+    dstart.addErrback(lambda f: f.raiseException())
+
+
+def get_args():
+    base_parser = argparse.ArgumentParser(add_help=False)
+    base_parser.add_argument(
+        '-x',
+        action='store_true',
+        dest='x',
+        help='turn off client security'
+    )
+    base_parser.add_argument(
+        '-y',
+        action='store_true',
+        dest='y',
+        help='turn off engine security'
+    )
+    base_parser.add_argument(
+        "--logdir", 
+        type=str,
+        dest="logdir",
+        help="directory to put log files (default=$IPYTHONDIR/log)",
+        default=pjoin(get_ipython_dir(),'log')
+    )
+    base_parser.add_argument(
+        "-n",
+        "--num", 
+        type=int,
+        dest="n",
+        default=2,
+        help="the number of engines to start"
+    )
+    
+    parser = argparse.ArgumentParser(
+        description='IPython cluster startup.  This starts a controller and\
+        engines using various approaches.  THIS IS A TECHNOLOGY PREVIEW AND\
+        THE API WILL CHANGE SIGNIFICANTLY BEFORE THE FINAL RELEASE.'
+    )
+    subparsers = parser.add_subparsers(
+        help='available cluster types.  For help, do "ipcluster TYPE --help"')
+    
+    parser_local = subparsers.add_parser(
+        'local',
+        help='run a local cluster',
+        parents=[base_parser]
+    )
+    parser_local.set_defaults(func=main_local)
+    
+    parser_mpirun = subparsers.add_parser(
+        'mpirun',
+        help='run a cluster using mpirun',
+        parents=[base_parser]
+    )
+    parser_mpirun.add_argument(
+        "--mpi",
+        type=str,
+        dest="mpi", # Don't put a default here to allow no MPI support
+        help="how to call MPI_Init (default=mpi4py)"
+    )
+    parser_mpirun.set_defaults(func=main_mpirun)
+    
+    parser_pbs = subparsers.add_parser(
+        'pbs', 
+        help='run a pbs cluster',
+        parents=[base_parser]
+    )
+    parser_pbs.add_argument(
+        '--pbs-script',
+        type=str, 
+        dest='pbsscript',
+        help='PBS script template',
+        default='pbs.template'
+    )
+    parser_pbs.set_defaults(func=main_pbs)
+    args = parser.parse_args()
+    return args
 
-    clusterfile = opt.clusterfile
-    if clusterfile:
-        clusterRemote(opt,arg)
-    else:
-        clusterLocal(opt,arg)
-        
-            
-if __name__=='__main__':
+def main():
+    args = get_args()
+    reactor.callWhenRunning(args.func, args)
+    log.startLogging(sys.stdout)
+    reactor.run()
+
+if __name__ == '__main__':
     main()

IPython/kernel/scripts/ipcontroller.py

@@ -1,366 +1,388 b''
 #!/usr/bin/env python
 # encoding: utf-8
 
 """The IPython controller."""
 
 __docformat__ = "restructuredtext en"
 
 #-------------------------------------------------------------------------------
 #  Copyright (C) 2008  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #-------------------------------------------------------------------------------
 
 #-------------------------------------------------------------------------------
 # Imports
 #-------------------------------------------------------------------------------
 
 # Python looks for an empty string at the beginning of sys.path to enable
 # importing from the cwd.
 import sys
 sys.path.insert(0, '')
 
 import sys, time, os
 from optparse import OptionParser
 
 from twisted.application import internet, service
 from twisted.internet import reactor, error, defer
 from twisted.python import log
 
 from IPython.kernel.fcutil import Tub, UnauthenticatedTub, have_crypto
 
 # from IPython.tools import growl
 # growl.start("IPython1 Controller")
 
 from IPython.kernel.error import SecurityError
 from IPython.kernel import controllerservice
 from IPython.kernel.fcutil import check_furl_file_security
 
 from IPython.kernel.config import config_manager as kernel_config_manager
 from IPython.config.cutils import import_item
 
 
 #-------------------------------------------------------------------------------
 # Code
 #-------------------------------------------------------------------------------
 
 def make_tub(ip, port, secure, cert_file):
     """
     Create a listening tub given an ip, port, and cert_file location.
     
     :Parameters:
         ip : str
             The ip address that the tub should listen on.  Empty means all
         port : int
             The port that the tub should listen on.  A value of 0 means
             pick a random port
         secure: boolean
             Will the connection be secure (in the foolscap sense)
         cert_file:
             A filename of a file to be used for theSSL certificate
     """
     if secure:
         if have_crypto:
             tub = Tub(certFile=cert_file)
         else:
-            raise SecurityError("OpenSSL is not available, so we can't run in secure mode, aborting")
+            raise SecurityError("""
+OpenSSL/pyOpenSSL is not available, so we can't run in secure mode.
+Try running without security using 'ipcontroller -xy'.
+""")
     else:
         tub = UnauthenticatedTub()
     
     # Set the strport based on the ip and port and start listening
     if ip == '':
         strport = "tcp:%i" % port
     else:
         strport = "tcp:%i:interface=%s" % (port, ip)
     listener = tub.listenOn(strport)
     
     return tub, listener
 
 def make_client_service(controller_service, config):
     """
     Create a service that will listen for clients.
     
     This service is simply a `foolscap.Tub` instance that has a set of Referenceables
     registered with it.
     """
 
     # Now create the foolscap tub
     ip = config['controller']['client_tub']['ip']
     port = config['controller']['client_tub'].as_int('port')
     location = config['controller']['client_tub']['location']
     secure = config['controller']['client_tub']['secure']
     cert_file = config['controller']['client_tub']['cert_file']
     client_tub, client_listener = make_tub(ip, port, secure, cert_file)
     
     # Set the location in the trivial case of localhost
     if ip == 'localhost' or ip == '127.0.0.1':
         location = "127.0.0.1"
     
     if not secure:
         log.msg("WARNING: you are running the controller with no client security")
     
     def set_location_and_register():
         """Set the location for the tub and return a deferred."""
 
         def register(empty, ref, furl_file):
             client_tub.registerReference(ref, furlFile=furl_file)
         
         if location == '':
             d = client_tub.setLocationAutomatically()
         else:
             d = defer.maybeDeferred(client_tub.setLocation, "%s:%i" % (location, client_listener.getPortnum()))
             
         for ciname, ci in config['controller']['controller_interfaces'].iteritems():
             log.msg("Adapting Controller to interface: %s" % ciname)
             furl_file = ci['furl_file']
             log.msg("Saving furl for interface [%s] to file: %s" % (ciname, furl_file))
             check_furl_file_security(furl_file, secure)
             adapted_controller = import_item(ci['controller_interface'])(controller_service)
             d.addCallback(register, import_item(ci['fc_interface'])(adapted_controller), 
                 furl_file=ci['furl_file'])
     
     reactor.callWhenRunning(set_location_and_register)
     return client_tub
 
 
 def make_engine_service(controller_service, config):
     """
     Create a service that will listen for engines.
     
     This service is simply a `foolscap.Tub` instance that has a set of Referenceables
     registered with it.
     """
 
     # Now create the foolscap tub
     ip = config['controller']['engine_tub']['ip']
     port = config['controller']['engine_tub'].as_int('port')
     location = config['controller']['engine_tub']['location']
     secure = config['controller']['engine_tub']['secure']
     cert_file = config['controller']['engine_tub']['cert_file']
     engine_tub, engine_listener = make_tub(ip, port, secure, cert_file)
     
     # Set the location in the trivial case of localhost
     if ip == 'localhost' or ip == '127.0.0.1':
         location = "127.0.0.1"
     
     if not secure:
         log.msg("WARNING: you are running the controller with no engine security")
     
     def set_location_and_register():
         """Set the location for the tub and return a deferred."""
 
         def register(empty, ref, furl_file):
             engine_tub.registerReference(ref, furlFile=furl_file)
         
         if location == '':
             d = engine_tub.setLocationAutomatically()
         else:
             d = defer.maybeDeferred(engine_tub.setLocation, "%s:%i" % (location, engine_listener.getPortnum()))
     
         furl_file = config['controller']['engine_furl_file']
         engine_fc_interface = import_item(config['controller']['engine_fc_interface'])
         log.msg("Saving furl for the engine to file: %s" % furl_file)
         check_furl_file_security(furl_file, secure)
         fc_controller = engine_fc_interface(controller_service)
         d.addCallback(register, fc_controller, furl_file=furl_file)
     
     reactor.callWhenRunning(set_location_and_register)
     return engine_tub
     
 def start_controller():
     """
     Start the controller by creating the service hierarchy and starting the reactor.
     
     This method does the following:
     
         * It starts the controller logging
         * In execute an import statement for the controller
         * It creates 2 `foolscap.Tub` instances for the client and the engines
           and registers `foolscap.Referenceables` with the tubs to expose the
           controller to engines and clients.
     """
     config = kernel_config_manager.get_config_obj()
     
     # Start logging
     logfile = config['controller']['logfile']
     if logfile:
         logfile = logfile + str(os.getpid()) + '.log'
         try:
             openLogFile = open(logfile, 'w')
         except:
             openLogFile = sys.stdout
     else:
         openLogFile = sys.stdout
     log.startLogging(openLogFile)
     
     # Execute any user defined import statements
     cis = config['controller']['import_statement']
     if cis:
         try:
             exec cis in globals(), locals()
         except:
             log.msg("Error running import_statement: %s" % cis)
     
+    # Delete old furl files unless the reuse_furls is set
+    reuse = config['controller']['reuse_furls']
+    if not reuse:
+        paths = (config['controller']['engine_furl_file'],
+            config['controller']['controller_interfaces']['task']['furl_file'],
+            config['controller']['controller_interfaces']['multiengine']['furl_file']
+        )
+        for p in paths:
+            if os.path.isfile(p):
+                os.remove(p)
+    
     # Create the service hierarchy
     main_service = service.MultiService()
     # The controller service
     controller_service = controllerservice.ControllerService()
     controller_service.setServiceParent(main_service)
     # The client tub and all its refereceables
     client_service = make_client_service(controller_service, config)
     client_service.setServiceParent(main_service)
     # The engine tub
     engine_service = make_engine_service(controller_service, config)
     engine_service.setServiceParent(main_service)
     # Start the controller service and set things running
     main_service.startService()
     reactor.run()
 
 def init_config():
     """
     Initialize the configuration using default and command line options.
     """
     
     parser = OptionParser()
     
     # Client related options
     parser.add_option(
         "--client-ip", 
         type="string",
         dest="client_ip",
         help="the IP address or hostname the controller will listen on for client connections"
     )
     parser.add_option(
         "--client-port", 
         type="int", 
         dest="client_port",
         help="the port the controller will listen on for client connections"
     )    
     parser.add_option(
         '--client-location',
         type="string",
         dest="client_location",
         help="hostname or ip for clients to connect to"
     )
     parser.add_option(
         "-x",
         action="store_false",
         dest="client_secure",
         help="turn off all client security"
     )
     parser.add_option(
         '--client-cert-file',
         type="string",
         dest="client_cert_file",
         help="file to store the client SSL certificate"
     )
     parser.add_option(
         '--task-furl-file',
         type="string",
         dest="task_furl_file",
         help="file to store the FURL for task clients to connect with"
     )
     parser.add_option(
         '--multiengine-furl-file',
         type="string",
         dest="multiengine_furl_file",
         help="file to store the FURL for multiengine clients to connect with"
     )
     # Engine related options
     parser.add_option(
         "--engine-ip", 
         type="string",
         dest="engine_ip",
         help="the IP address or hostname the controller will listen on for engine connections"
     )
     parser.add_option(
         "--engine-port", 
         type="int", 
         dest="engine_port",
         help="the port the controller will listen on for engine connections"
     )    
     parser.add_option(
         '--engine-location',
         type="string",
         dest="engine_location",
         help="hostname or ip for engines to connect to"
     )
     parser.add_option(
         "-y",
         action="store_false",
         dest="engine_secure",
         help="turn off all engine security"
     )
     parser.add_option(
         '--engine-cert-file',
         type="string",
         dest="engine_cert_file",
         help="file to store the engine SSL certificate"
     )
     parser.add_option(
         '--engine-furl-file',
         type="string",
         dest="engine_furl_file",
         help="file to store the FURL for engines to connect with"
     )
     parser.add_option(
         "-l", "--logfile",
         type="string",
         dest="logfile",
         help="log file name (default is stdout)"
     )
     parser.add_option(
         "--ipythondir",
         type="string",
         dest="ipythondir",
         help="look for config files and profiles in this directory"
     )
+    parser.add_option(
+        "-r",
+        action="store_true",
+        dest="reuse_furls",
+        help="try to reuse all furl files"
+    )
     
     (options, args) = parser.parse_args()
     
     kernel_config_manager.update_config_obj_from_default_file(options.ipythondir)
     config = kernel_config_manager.get_config_obj()
     
     # Update with command line options
     if options.client_ip is not None:
         config['controller']['client_tub']['ip'] = options.client_ip
     if options.client_port is not None:
         config['controller']['client_tub']['port'] = options.client_port
     if options.client_location is not None:
         config['controller']['client_tub']['location'] = options.client_location
     if options.client_secure is not None:
         config['controller']['client_tub']['secure'] = options.client_secure
     if options.client_cert_file is not None:
         config['controller']['client_tub']['cert_file'] = options.client_cert_file
     if options.task_furl_file is not None:
         config['controller']['controller_interfaces']['task']['furl_file'] = options.task_furl_file
     if options.multiengine_furl_file is not None:
         config['controller']['controller_interfaces']['multiengine']['furl_file'] = options.multiengine_furl_file
     if options.engine_ip is not None:
         config['controller']['engine_tub']['ip'] = options.engine_ip
     if options.engine_port is not None:
         config['controller']['engine_tub']['port'] = options.engine_port
     if options.engine_location is not None:
         config['controller']['engine_tub']['location'] = options.engine_location
     if options.engine_secure is not None:
         config['controller']['engine_tub']['secure'] = options.engine_secure
     if options.engine_cert_file is not None:
         config['controller']['engine_tub']['cert_file'] = options.engine_cert_file
     if options.engine_furl_file is not None:
         config['controller']['engine_furl_file'] = options.engine_furl_file
+    if options.reuse_furls is not None:
+            config['controller']['reuse_furls'] = options.reuse_furls
 
     if options.logfile is not None:
         config['controller']['logfile'] = options.logfile
     
     kernel_config_manager.update_config_obj(config)
 
 def main():
     """
     After creating the configuration information, start the controller.
     """
     init_config()
     start_controller()
     
 if __name__ == "__main__":
     main()

IPython/kernel/scripts/ipengine.py

@@ -1,172 +1,176 b''
 #!/usr/bin/env python
 # encoding: utf-8
 
 """Start the IPython Engine."""
 
 __docformat__ = "restructuredtext en"
 
 #-------------------------------------------------------------------------------
 #  Copyright (C) 2008  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #-------------------------------------------------------------------------------
 
 #-------------------------------------------------------------------------------
 # Imports
 #-------------------------------------------------------------------------------
 
 # Python looks for an empty string at the beginning of sys.path to enable
 # importing from the cwd.
 import sys
 sys.path.insert(0, '')
 
 import sys, os
 from optparse import OptionParser
 
 from twisted.application import service
 from twisted.internet import reactor
 from twisted.python import log
 
 from IPython.kernel.fcutil import Tub, UnauthenticatedTub
 
 from IPython.kernel.core.config import config_manager as core_config_manager
 from IPython.config.cutils import import_item
 from IPython.kernel.engineservice import EngineService
 from IPython.kernel.config import config_manager as kernel_config_manager
 from IPython.kernel.engineconnector import EngineConnector
 
 
 #-------------------------------------------------------------------------------
 # Code
 #-------------------------------------------------------------------------------
 
 def start_engine():
     """
     Start the engine, by creating it and starting the Twisted reactor.
     
     This method does:
     
         * If it exists, runs the `mpi_import_statement` to call `MPI_Init`
         * Starts the engine logging
         * Creates an IPython shell and wraps it in an `EngineService`
         * Creates a `foolscap.Tub` to use in connecting to a controller.
         * Uses the tub and the `EngineService` along with a Foolscap URL
           (or FURL) to connect to the controller and register the engine
           with the controller
     """
     kernel_config = kernel_config_manager.get_config_obj()
     core_config = core_config_manager.get_config_obj()
     
 
     # Execute the mpi import statement that needs to call MPI_Init
     global mpi
     mpikey = kernel_config['mpi']['default']
     mpi_import_statement = kernel_config['mpi'].get(mpikey, None)
     if mpi_import_statement is not None:
         try:
             exec mpi_import_statement in globals()
         except:
             mpi = None
     else:
         mpi = None
     
     # Start logging
     logfile = kernel_config['engine']['logfile']
     if logfile:
         logfile = logfile + str(os.getpid()) + '.log'
         try:
             openLogFile = open(logfile, 'w')
         except:
             openLogFile = sys.stdout
     else:
         openLogFile = sys.stdout
     log.startLogging(openLogFile)
     
     # Create the underlying shell class and EngineService
     shell_class = import_item(core_config['shell']['shell_class'])
     engine_service = EngineService(shell_class, mpi=mpi)
     shell_import_statement = core_config['shell']['import_statement']
     if shell_import_statement:
         try:
             engine_service.execute(shell_import_statement)
         except:
             log.msg("Error running import_statement: %s" % shell_import_statement)
     
     # Create the service hierarchy
     main_service = service.MultiService()
     engine_service.setServiceParent(main_service)
     tub_service = Tub()
     tub_service.setServiceParent(main_service)
     # This needs to be called before the connection is initiated
     main_service.startService()
     
     # This initiates the connection to the controller and calls
     # register_engine to tell the controller we are ready to do work
     engine_connector = EngineConnector(tub_service)
     furl_file = kernel_config['engine']['furl_file']
     log.msg("Using furl file: %s" % furl_file)
     d = engine_connector.connect_to_controller(engine_service, furl_file)
-    d.addErrback(lambda _: reactor.stop())
+    def handle_error(f):
+        log.err(f)
+        if reactor.running:
+            reactor.stop()
+    d.addErrback(handle_error)
     
     reactor.run()
 
 
 def init_config():
     """
     Initialize the configuration using default and command line options.
     """
     
     parser = OptionParser()
     
     parser.add_option(
         "--furl-file",
         type="string", 
         dest="furl_file",
         help="The filename containing the FURL of the controller"
     )
     parser.add_option(
         "--mpi",
         type="string",
         dest="mpi",
         help="How to enable MPI (mpi4py, pytrilinos, or empty string to disable)"
     )
     parser.add_option(
         "-l",
         "--logfile",
         type="string",
         dest="logfile",
         help="log file name (default is stdout)"
     )
     parser.add_option(
         "--ipythondir",
         type="string",
         dest="ipythondir",
         help="look for config files and profiles in this directory"
     )
     
     (options, args) = parser.parse_args()
     
     kernel_config_manager.update_config_obj_from_default_file(options.ipythondir)
     core_config_manager.update_config_obj_from_default_file(options.ipythondir)
     
     kernel_config = kernel_config_manager.get_config_obj()
     # Now override with command line options
     if options.furl_file is not None:
         kernel_config['engine']['furl_file'] = options.furl_file
     if options.logfile is not None:
         kernel_config['engine']['logfile'] = options.logfile
     if options.mpi is not None:
         kernel_config['mpi']['default'] = options.mpi
 
 
 def main():
     """
     After creating the configuration information, start the engine.
     """
     init_config()
     start_engine()
 
 
 if __name__ == "__main__":
     main()

MANIFEST.in

@@ -1,33 +1,32 b''
-include README_Windows.txt
-include win32_manual_post_install.py
 include ipython.py
 include setupbase.py
+include setupegg.py
 
 graft scripts
 
 graft setupext
 
 graft IPython/UserConfig
 
 graft IPython/kernel
 graft IPython/config
 graft IPython/testing
 graft IPython/tools
 
 recursive-include IPython/Extensions igrid_help*
 
 graft docs
 exclude docs/\#*
 exclude docs/man/*.1
 
 # docs subdirs we want to skip
 prune docs/attic
 prune docs/build
 
 global-exclude *~
 global-exclude *.flc
 global-exclude *.pyc
 global-exclude .dircopy.log
 global-exclude .svn
 global-exclude .bzr
 global-exclude .hgignore

docs/source/changes.txt

@@ -1,360 +1,393 b''
 .. _changes:
 
 ==========
 What's new
 ==========
 
 .. contents::
 ..
     1  Release 0.9.1
     2  Release 0.9
       2.1  New features
       2.2  Bug fixes
       2.3  Backwards incompatible changes
       2.4  Changes merged in from IPython1
         2.4.1  New features
         2.4.2  Bug fixes
         2.4.3  Backwards incompatible changes
     3  Release 0.8.4
     4  Release 0.8.3
     5  Release 0.8.2
     6  Older releases
 ..
 
-Release DEV
+Release dev
 ===========
 
+New features
+------------
+
+* The wonderful TextMate editor can now be used with %edit on OS X.  Thanks
+  to Matt Foster for this patch.
+
+* Fully refactored :command:`ipcluster` command line program for starting
+  IPython clusters.  This new version is a complete rewrite and 1) is fully
+  cross platform (we now use Twisted's process management), 2) has much
+  improved performance, 3) uses subcommands for different types of clusters, 
+  4) uses argparse for parsing command line options, 5) has better support
+  for starting clusters using :command:`mpirun`, 6) has experimental support
+  for starting engines using PBS.  However, this new version of ipcluster
+  should be considered a technology preview.  We plan on changing the API
+  in significant ways before it is final.
+
+* The :mod:`argparse` module has been added to :mod:`IPython.external`.
+
+* Fully description of the security model added to the docs.
+
 * cd completer: show bookmarks if no other completions are available.
 
-* Remove ipy_leo.py. "easy_install ipython-extension" to get it.
-  (done to decouple it from ipython release cycle)
-  
 * sh profile: easy way to give 'title' to prompt: assign to variable
   '_prompt_title'. It looks like this::
       
         [~]|1> _prompt_title = 'sudo!'
         sudo![~]|2>
-        
+
+* %edit: If you do '%edit pasted_block', pasted_block
+  variable gets updated with new data (so repeated 
+  editing makes sense)
+
+Bug fixes
+---------
+
+* The ipengine and ipcontroller scripts now handle missing furl files
+  more gracefully by giving better error messages.
+
 * %rehashx: Aliases no longer contain dots. python3.0 binary
   will create alias python30. Fixes:
   #259716 "commands with dots in them don't work"
-  
+
 * %cpaste: %cpaste -r repeats the last pasted block.
   The block is assigned to pasted_block even if code
   raises exception.
 
-* %edit: If you do '%edit pasted_block', pasted_block
-  variable gets updated with new data (so repeated 
-  editing makes sense)
+Backwards incompatible changes
+------------------------------
+
+* The controller now has a ``-r`` flag that needs to be used if you want to
+  reuse existing furl files.  Otherwise they are deleted (the default).
+
+* Remove ipy_leo.py. "easy_install ipython-extension" to get it.
+  (done to decouple it from ipython release cycle)
+
 
 
 Release 0.9.1
 =============
 
 This release was quickly made to restore compatibility with Python 2.4, which
 version 0.9 accidentally broke.  No new features were introduced, other than
 some additional testing support for internal use.
 
 
 Release 0.9
 ===========
 
 New features
 ------------
 
-* All furl files and security certificates are now put in a read-only directory
-  named ~./ipython/security.
+* All furl files and security certificates are now put in a read-only
+  directory named ~./ipython/security.
 
 * A single function :func:`get_ipython_dir`, in :mod:`IPython.genutils` that
   determines the user's IPython directory in a robust manner.
 
-* Laurent's WX application has been given a top-level script called ipython-wx,
-  and it has received numerous fixes.  We expect this code to be
+* Laurent's WX application has been given a top-level script called
+  ipython-wx, and it has received numerous fixes. We expect this code to be
   architecturally better integrated with Gael's WX 'ipython widget' over the
   next few releases.
 
 * The Editor synchronization work by Vivian De Smedt has been merged in.  This
   code adds a number of new editor hooks to synchronize with editors under
   Windows.
 
 * A new, still experimental but highly functional, WX shell by Gael Varoquaux.
   This work was sponsored by Enthought, and while it's still very new, it is
   based on a more cleanly organized arhictecture of the various IPython
-  components.  We will continue to develop this over the next few releases as a
+  components. We will continue to develop this over the next few releases as a
   model for GUI components that use IPython.
 
 * Another GUI frontend, Cocoa based (Cocoa is the OSX native GUI framework),
   authored by Barry Wark.  Currently the WX and the Cocoa ones have slightly
   different internal organizations, but the whole team is working on finding
   what the right abstraction points are for a unified codebase.
 
 * As part of the frontend work, Barry Wark also implemented an experimental
   event notification system that various ipython components can use.  In the
   next release the implications and use patterns of this system regarding the
   various GUI options will be worked out.
 
 * IPython finally has a full test system, that can test docstrings with
   IPython-specific functionality.  There are still a few pieces missing for it
   to be widely accessible to all users (so they can run the test suite at any
   time and report problems), but it now works for the developers.  We are
   working hard on continuing to improve it, as this was probably IPython's
   major Achilles heel (the lack of proper test coverage made it effectively
   impossible to do large-scale refactoring).  The full test suite can now
   be run using the :command:`iptest` command line program.
 
 * The notion of a task has been completely reworked.  An `ITask` interface has
   been created.  This interface defines the methods that tasks need to
   implement.  These methods are now responsible for things like submitting
   tasks and processing results.  There are two basic task types:
   :class:`IPython.kernel.task.StringTask` (this is the old `Task` object, but
   renamed) and the new :class:`IPython.kernel.task.MapTask`, which is based on
   a function.
 
 * A new interface, :class:`IPython.kernel.mapper.IMapper` has been defined to
   standardize the idea of a `map` method.  This interface has a single `map`
   method that has the same syntax as the built-in `map`.  We have also defined
   a `mapper` factory interface that creates objects that implement
   :class:`IPython.kernel.mapper.IMapper` for different controllers.  Both the
   multiengine and task controller now have mapping capabilties.
 
 * The parallel function capabilities have been reworks.  The major changes are
   that i) there is now an `@parallel` magic that creates parallel functions,
   ii) the syntax for mulitple variable follows that of `map`, iii) both the
   multiengine and task controller now have a parallel function implementation.
 
 * All of the parallel computing capabilities from `ipython1-dev` have been
   merged into IPython proper.  This resulted in the following new subpackages:
   :mod:`IPython.kernel`, :mod:`IPython.kernel.core`, :mod:`IPython.config`,
   :mod:`IPython.tools` and :mod:`IPython.testing`.
 
 * As part of merging in the `ipython1-dev` stuff, the `setup.py` script and
   friends have been completely refactored.  Now we are checking for
   dependencies using the approach that matplotlib uses.
 
-* The documentation has been completely reorganized to accept the documentation
-  from `ipython1-dev`.
+* The documentation has been completely reorganized to accept the 
+  documentation from `ipython1-dev`.
 
 * We have switched to using Foolscap for all of our network protocols in
   :mod:`IPython.kernel`.  This gives us secure connections that are both
   encrypted and authenticated.
 
 * We have a brand new `COPYING.txt` files that describes the IPython license
-  and copyright.  The biggest change is that we are putting "The IPython
-  Development Team" as the copyright holder.  We give more details about
-  exactly what this means in this file.  All developer should read this and use
+  and copyright. The biggest change is that we are putting "The IPython
+  Development Team" as the copyright holder. We give more details about
+  exactly what this means in this file. All developer should read this and use
   the new banner in all IPython source code files.
 
 * sh profile: ./foo runs foo as system command, no need to do !./foo anymore
 
 * String lists now support ``sort(field, nums = True)`` method (to easily sort
   system command output). Try it with ``a = !ls -l ; a.sort(1, nums=1)``.
 
 * '%cpaste foo' now assigns the pasted block as string list, instead of string
 
 * The ipcluster script now run by default with no security.  This is done
   because the main usage of the script is for starting things on localhost.
   Eventually when ipcluster is able to start things on other hosts, we will put
   security back.
 
 * 'cd --foo' searches directory history for string foo, and jumps to that dir.
   Last part of dir name is checked first. If no matches for that are found,
   look at the whole path.
 
   
 Bug fixes
 ---------
 
 * The Windows installer has been fixed.  Now all IPython scripts have ``.bat``
   versions created.  Also, the Start Menu shortcuts have been updated.
 
 * The colors escapes in the multiengine client are now turned off on win32 as
   they don't print correctly.
 
 * The :mod:`IPython.kernel.scripts.ipengine` script was exec'ing
   mpi_import_statement incorrectly, which was leading the engine to crash when
   mpi was enabled.
 
 * A few subpackages had missing ``__init__.py`` files.
 
 * The documentation is only created if Sphinx is found.  Previously, the
   ``setup.py`` script would fail if it was missing.
 
 * Greedy ``cd`` completion has been disabled again (it was enabled in 0.8.4) as
   it caused problems on certain platforms.
           
 
 Backwards incompatible changes
 ------------------------------
 
 * The ``clusterfile`` options of the :command:`ipcluster` command has been
   removed as it was not working and it will be replaced soon by something much
   more robust.
 
 * The :mod:`IPython.kernel` configuration now properly find the user's
   IPython directory.
 
 * In ipapi, the :func:`make_user_ns` function has been replaced with
   :func:`make_user_namespaces`, to support dict subclasses in namespace
   creation.
 
 * :class:`IPython.kernel.client.Task` has been renamed
   :class:`IPython.kernel.client.StringTask` to make way for new task types.
 
 * The keyword argument `style` has been renamed `dist` in `scatter`, `gather`
   and `map`.
 
 * Renamed the values that the rename `dist` keyword argument can have from
   `'basic'` to `'b'`.
 
 * IPython has a larger set of dependencies if you want all of its capabilities.
   See the `setup.py` script for details.
 
 * The constructors for :class:`IPython.kernel.client.MultiEngineClient` and 
   :class:`IPython.kernel.client.TaskClient` no longer take the (ip,port) tuple.
   Instead they take the filename of a file that contains the FURL for that
   client.  If the FURL file is in your IPYTHONDIR, it will be found automatically
   and the constructor can be left empty.
 
 * The asynchronous clients in :mod:`IPython.kernel.asyncclient` are now created 
   using the factory functions :func:`get_multiengine_client` and 
   :func:`get_task_client`.  These return a `Deferred` to the actual client.
 
 * The command line options to `ipcontroller` and `ipengine` have changed to
   reflect the new Foolscap network protocol and the FURL files.  Please see the
   help for these scripts for details.
 
 * The configuration files for the kernel have changed because of the Foolscap
   stuff.  If you were using custom config files before, you should delete them
   and regenerate new ones.
 
 Changes merged in from IPython1
 -------------------------------
 
 New features
 ............
 
 * Much improved ``setup.py`` and ``setupegg.py`` scripts.  Because Twisted and
   zope.interface are now easy installable, we can declare them as dependencies
   in our setupegg.py script.
 
 * IPython is now compatible with Twisted 2.5.0 and 8.x.
 
 * Added a new example of how to use :mod:`ipython1.kernel.asynclient`.
 
 * Initial draft of a process daemon in :mod:`ipython1.daemon`.  This has not
   been merged into IPython and is still in `ipython1-dev`.
   
 * The ``TaskController`` now has methods for getting the queue status.
 
 * The ``TaskResult`` objects not have information about how long the task
   took to run.
   
 * We are attaching additional attributes to exceptions ``(_ipython_*)`` that 
   we use to carry additional info around.
   
 * New top-level module :mod:`asyncclient` that has asynchronous versions (that
   return deferreds) of the client classes.  This is designed to users who want
   to run their own Twisted reactor.
   
 * All the clients in :mod:`client` are now based on Twisted.  This is done by 
   running the Twisted reactor in a separate thread and using the
   :func:`blockingCallFromThread` function that is in recent versions of Twisted.
 
 * Functions can now be pushed/pulled to/from engines using
   :meth:`MultiEngineClient.push_function` and
   :meth:`MultiEngineClient.pull_function`.
 
 * Gather/scatter are now implemented in the client to reduce the work load
   of the controller and improve performance.
 
 * Complete rewrite of the IPython docuementation.  All of the documentation
   from the IPython website has been moved into docs/source as restructured
   text documents.  PDF and HTML documentation are being generated using 
   Sphinx.
 
 * New developer oriented documentation: development guidelines and roadmap. 
 
 * Traditional ``ChangeLog`` has been changed to a more useful ``changes.txt``
   file that is organized by release and is meant to provide something more
   relevant for users.
 
 Bug fixes
 .........
 
 * Created a proper ``MANIFEST.in`` file to create source distributions.
 
 * Fixed a bug in the ``MultiEngine`` interface.  Previously, multi-engine 
   actions were being collected with a :class:`DeferredList` with 
   ``fireononeerrback=1``.  This meant that methods were returning 
   before all engines had given their results.  This was causing extremely odd 
   bugs in certain cases. To fix this problem, we have 1) set 
   ``fireononeerrback=0`` to make sure all results (or exceptions) are in 
   before returning and 2) introduced a :exc:`CompositeError` exception 
   that wraps all of the engine exceptions.  This is a huge change as it means 
   that users will have to catch :exc:`CompositeError` rather than the actual
   exception.
 
 Backwards incompatible changes
 ..............................
 
 * All names have been renamed to conform to the lowercase_with_underscore
   convention.  This will require users to change references to all names like
   ``queueStatus`` to ``queue_status``.
 
 * Previously, methods like :meth:`MultiEngineClient.push` and
   :meth:`MultiEngineClient.push` used ``*args`` and ``**kwargs``.  This was
   becoming a problem as we weren't able to introduce new keyword arguments into
   the API.  Now these methods simple take a dict or sequence.  This has also
   allowed us to get rid of the ``*All`` methods like :meth:`pushAll` and
   :meth:`pullAll`.  These things are now handled with the ``targets`` keyword
   argument that defaults to ``'all'``.
 
 * The :attr:`MultiEngineClient.magicTargets` has been renamed to
   :attr:`MultiEngineClient.targets`. 
 
 * All methods in the MultiEngine interface now accept the optional keyword
   argument ``block``.
 
 * Renamed :class:`RemoteController` to :class:`MultiEngineClient` and 
   :class:`TaskController` to :class:`TaskClient`.
 
 * Renamed the top-level module from :mod:`api` to :mod:`client`.
 
 * Most methods in the multiengine interface now raise a :exc:`CompositeError`
   exception that wraps the user's exceptions, rather than just raising the raw
   user's exception.
 
 * Changed the ``setupNS`` and ``resultNames`` in the ``Task`` class to ``push`` 
   and ``pull``.
 
   
 Release 0.8.4
 =============
 
 This was a quick release to fix an unfortunate bug that slipped into the 0.8.3
 release.  The ``--twisted`` option was disabled, as it turned out to be broken
 across several platforms.
 
 
 Release 0.8.3
 =============
   
 * pydb is now disabled by default (due to %run -d problems). You can enable
   it by passing -pydb command line argument to IPython. Note that setting
   it in config file won't work.
 
   
 Release 0.8.2
 =============
 
 * %pushd/%popd behave differently; now "pushd /foo" pushes CURRENT directory 
   and jumps to /foo. The current behaviour is closer to the documented 
   behaviour, and should not trip anyone.
 
   
 Older releases
 ==============
 
 Changes in earlier releases of IPython are described in the older file
 ``ChangeLog``.  Please refer to this document for details.
 

docs/source/config/index.txt

@@ -1,10 +1,10 b''
 ===============================
 Configuration and customization
 ===============================
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
    initial_config.txt
    customization.txt
    new_config.txt

docs/source/development/development.txt

@@ -1,446 +1,310 b''
 .. _development:
 
 ==============================
 IPython development guidelines
 ==============================
 
 
 Overview
 ========
 
-IPython is the next generation of IPython.  It is named such for two reasons:
-
-- Eventually, IPython will become IPython version 1.0.
-- This new code base needs to be able to co-exist with the existing IPython until
-  it is a full replacement for it.  Thus we needed a different name.  We couldn't
-  use ``ipython`` (lowercase) as some files systems are case insensitive.
-
-There are two, no three, main goals of the IPython effort:
-
-1. Clean up the existing codebase and write lots of tests.
-2. Separate the core functionality of IPython from the terminal to enable IPython
-   to be used from within a variety of GUI applications.
-3. Implement a system for interactive parallel computing.
-
-While the third goal may seem a bit unrelated to the main focus of IPython, it
-turns out that the technologies required for this goal are nearly identical
-with those required for goal two. This is the main reason the interactive
-parallel computing capabilities are being put into IPython proper. Currently
-the third of these goals is furthest along.
-
-This document describes IPython from the perspective of developers.  
-
-
-Project organization
-====================
-
-Subpackages
------------
-
-IPython is organized into semi self-contained subpackages.  Each of the
-subpackages will have its own:
-
-- **Dependencies**.  One of the most important things to keep in mind in
-  partitioning code amongst subpackages, is that they should be used to cleanly
-  encapsulate dependencies.
-  
-- **Tests**.  Each subpackage shoud have its own ``tests`` subdirectory that
-  contains all of the tests for that package.  For information about writing
-  tests for IPython, see the `Testing System`_ section of this document.
-  
-- **Configuration**.  Each subpackage should have its own ``config``
-  subdirectory that contains the configuration information for the components
-  of the subpackage.  For information about how the IPython configuration
-  system works, see the `Configuration System`_ section of this document.
-  
-- **Scripts**.  Each subpackage should have its own ``scripts`` subdirectory
-  that contains all of the command line scripts associated with the subpackage.
-
-Installation and dependencies
------------------------------
-   
-IPython will not use `setuptools`_ for installation. Instead, we will use
-standard ``setup.py`` scripts that use `distutils`_. While there are a number a
-extremely nice features that `setuptools`_ has (like namespace packages), the
-current implementation of `setuptools`_ has performance problems, particularly
-on shared file systems. In particular, when Python packages are installed on
-NSF file systems, import times become much too long (up towards 10 seconds).
-
-Because IPython is being used extensively in the context of high performance
-computing, where performance is critical but shared file systems are common, we
-feel these performance hits are not acceptable. Thus, until the performance
-problems associated with `setuptools`_ are addressed, we will stick with plain
-`distutils`_. We are hopeful that these problems will be addressed and that we
-will eventually begin using `setuptools`_. Because of this, we are trying to
-organize IPython in a way that will make the eventual transition to
-`setuptools`_ as painless as possible.
-
-Because we will be using `distutils`_, there will be no method for
-automatically installing dependencies.  Instead, we are following the approach
-of `Matplotlib`_ which can be summarized as follows:
-
-- Distinguish between required and optional dependencies.  However, the required
-  dependencies for IPython should be only the Python standard library.
-  
-- Upon installation check to see which optional dependencies are present and
-  tell the user which parts of IPython need which optional dependencies.
-
-It is absolutely critical that each subpackage of IPython has a clearly
-specified set of dependencies and that dependencies are not carelessly
-inherited from other IPython subpackages. Furthermore, tests that have certain
-dependencies should not fail if those dependencies are not present. Instead
-they should be skipped and print a message.
-
-.. _setuptools: http://peak.telecommunity.com/DevCenter/setuptools
-.. _distutils: http://docs.python.org/lib/module-distutils.html
-.. _Matplotlib: http://matplotlib.sourceforge.net/
-
-Specific subpackages
---------------------
-
-``core``
-    This is the core functionality of IPython that is independent of the
-    terminal, network and GUIs.  Most of the code that is in the current
-    IPython trunk will be refactored, cleaned up and moved here.
-
-``kernel``
-    The enables the IPython core to be expose to a the network.  This is
-    also where all of the parallel computing capabilities are to be found.
-    
-``config``
-    The configuration package used by IPython.
+This document describes IPython from the perspective of developers. Most
+importantly, it gives information for people who want to contribute to the
+development of IPython. So if you want to help out, read on!
+
+How to contribute to IPython
+============================
+
+IPython development is done using Bazaar [Bazaar]_ and Launchpad [Launchpad]_.
+This makes it easy for people to contribute to the development of IPython.
+Here is a sketch of how to get going.
 
-``frontends``
-    The various frontends for IPython.  A frontend is the end-user application
-    that exposes the capabilities of IPython to the user.  The most basic
-    frontend will simply be a terminal based application that looks just like
-    today 's IPython.  Other frontends will likely be more powerful and based
-    on GUI toolkits.
+Install Bazaar and create a Launchpad account
+---------------------------------------------
 
-``notebook``
-    An application that allows users to work with IPython notebooks.
+First make sure you have installed Bazaar (see their `website
+<http://bazaar-vcs.org/>`_). To see that Bazaar is installed and knows about
+you, try the following::
 
-``tools``
-    This is where general utilities go.
+    $ bzr whoami
+    Joe Coder <[e-mail]>
 
+This should display your name and email. Next, you will want to create an
+account on the `Launchpad website <http://www.launchpad.net>`_ and setup your
+ssh keys. For more information of setting up your ssh keys, see `this link
+<https://help.launchpad.net/YourAccount/CreatingAnSSHKeyPair>`_.
 
-Version control
-===============
+Get the main IPython branch from Launchpad
+------------------------------------------
 
-In the past, IPython development has been done using `Subversion`__.  Recently,
-we made the transition to using `Bazaar`__ and `Launchpad`__.  This makes it
-much easier for people to contribute code to IPython.  Here is a sketch of how
-to use Bazaar for IPython development.  First, you should install Bazaar.
-After you have done that, make sure that it is working by getting the latest
-main branch of IPython::
+Now, you can get a copy of the main IPython development branch (we call this
+the "trunk")::
 
     $ bzr branch lp:ipython
 
-Now you can create a new branch for you to do your work in::
+Create a working branch
+-----------------------
+
+When working on IPython, you won't actually make edits directly to the
+:file:`lp:ipython` branch. Instead, you will create a separate branch for your
+changes. For now, let's assume you want to do your work in a branch named
+"ipython-mybranch". Create this branch by doing::
 
     $ bzr branch ipython ipython-mybranch
 
-The typical work cycle in this branch will be to make changes in
-``ipython-mybranch`` and then commit those changes using the commit command::
+When you actually create a branch, you will want to give it a name that
+reflects the nature of the work that you will be doing in it, like
+"install-docs-update".
+
+Make edits in your working branch
+---------------------------------
+
+Now you are ready to actually make edits in your :file:`ipython-mybranch`
+branch. Before doing this, it is helpful to install this branch so you can
+test your changes as you work. This is easiest if you have setuptools
+installed. Then, just do::
+
+    $ cd ipython-mybranch
+    $ python setupegg.py develop
+
+Now, make some changes. After a while, you will want to commit your changes.
+This let's Bazaar know that you like the changes you have made and gives you
+an opportunity to keep a nice record of what you have done. This looks like
+this::
 
     $ ...do work in ipython-mybranch...
-    $ bzr ci -m "the commit message goes here"
+    $ bzr commit -m "the commit message goes here"
 
 Please note that since we now don't use an old-style linear ChangeLog (that
 tends to cause problems with distributed version control systems), you should
 ensure that your log messages are reasonably detailed.  Use a docstring-like
 approach in the commit messages (including the second line being left
 *blank*)::
 
   Single line summary of  changes being committed.
 
-  - more details when warranted ...
-  - including crediting outside contributors if they sent the
+  * more details when warranted ...
+  * including crediting outside contributors if they sent the
     code/bug/idea!
 
-If we couple this with a policy of making single commits for each reasonably
-atomic change, the bzr log should give an excellent view of the project, and
-the `--short` log option becomes a nice summary.
+As you work, you will repeat this edit/commit cycle many times. If you work on
+your branch for a long time, you will also want to get the latest changes from
+the :file:`lp:ipython` branch. This can be done with the following sequence of
+commands::
 
-While working with this branch, it is a good idea to merge in changes that have
-been made upstream in the parent branch.  This can be done by doing::
-
-    $ bzr pull
+    $ ls
+    ipython
+    ipython-mybranch
     
-If this command shows that the branches have diverged, then you should do a
-merge instead::
+    $ cd ipython
+    $ bzr pull
+    $ cd ../ipython-mybranch
+    $ bzr merge ../ipython
+    $ bzr commit -m "Merging changes from trunk"
 
-    $ bzr merge lp:ipython
+Along the way, you should also run the IPython test suite.  You can do this using the :command:`iptest` command::
 
-If you want others to be able to see your branch, you can create an account
-with launchpad and push the branch to your own workspace::
+    $ cd
+    $ iptest
 
-    $ bzr push bzr+ssh://<me>@bazaar.launchpad.net/~<me>/+junk/ipython-mybranch
+The :command:`iptest` command will also pick up and run any tests you have written.
 
-Finally, once the work in your branch is done, you can merge your changes back
-into the `ipython` branch by using merge::
+Post your branch and request a code review
+------------------------------------------
 
-    $ cd ipython
-    $ merge ../ipython-mybranch
-    [resolve any conflicts]
-    $ bzr ci -m "Fixing that bug"
-    $ bzr push
+Once you are done with your edits, you should post your branch on Launchpad so
+that other IPython developers can review the changes and help you merge your
+changes into the main development branch. To post your branch on Launchpad,
+do::
+
+    $ cd ipython-mybranch
+    $ bzr push lp:~yourusername/ipython/ipython-mybranch
+
+Then, go to the `IPython Launchpad site <www.launchpad.net/ipython>`_, and you
+should see your branch under the "Code" tab. If you click on your branch, you
+can provide a short description of the branch as well as mark its status. Most
+importantly, you should click the link that reads "Propose for merging into
+another branch". What does this do?
 
-But this will require you to have write permissions to the `ipython` branch.
-It you don't you can tell one of the IPython devs about your branch and they
-can do the merge for you.
+This let's the other IPython developers know that your branch is ready to be
+reviewed and merged into the main development branch. During this review
+process, other developers will give you feedback and help you get your code
+ready to be merged. What types of things will we be looking for:
 
-More information about Bazaar workflows can be found `here`__.
+* All code is documented.
+* All code has tests.
+* The entire IPython test suite passes.
 
-.. __: http://subversion.tigris.org/
-.. __: http://bazaar-vcs.org/
-.. __: http://www.launchpad.net/ipython
-.. __: http://doc.bazaar-vcs.org/bzr.dev/en/user-guide/index.html
+Once your changes have been reviewed and approved, someone will merge them
+into the main development branch.
 
 Documentation
 =============
 
 Standalone documentation
 ------------------------
 
 All standalone documentation should be written in plain text (``.txt``) files
-using `reStructuredText`_ for markup and formatting. All such documentation
-should be placed in the top level directory ``docs`` of the IPython source
-tree. Or, when appropriate, a suitably named subdirectory should be used. The
-documentation in this location will serve as the main source for IPython
-documentation and all existing documentation should be converted to this
-format.
+using reStructuredText [reStructuredText]_ for markup and formatting. All such
+documentation should be placed in directory :file:`docs/source` of the IPython
+source tree. The documentation in this location will serve as the main source
+for IPython documentation and all existing documentation should be converted
+to this format.
 
-In the future, the text files in the ``docs`` directory will be used to
-generate all forms of documentation for IPython. This include documentation on
-the IPython website as well as *pdf* documentation.
+To build the final documentation, we use Sphinx [Sphinx]_.  Once you have Sphinx installed, you can build the html docs yourself by doing::
 
-.. _reStructuredText: http://docutils.sourceforge.net/rst.html
+    $ cd ipython-mybranch/docs
+    $ make html
 
 Docstring format
 ----------------
 
-Good docstrings are very important. All new code will use `Epydoc`_ for
-generating API docs, so we will follow the `Epydoc`_ conventions. More
-specifically, we will use `reStructuredText`_ for markup and formatting, since
-it is understood by a wide variety of tools. This means that if in the future
-we have any reason to change from `Epydoc`_ to something else, we'll have fewer
-transition pains.
-
-Details about using `reStructuredText`_ for docstrings can be found `here
+Good docstrings are very important. All new code should have docstrings that
+are formatted using reStructuredText for markup and formatting, since it is
+understood by a wide variety of tools. Details about using reStructuredText
+for docstrings can be found `here
 <http://epydoc.sourceforge.net/manual-othermarkup.html>`_.
 
-.. _Epydoc: http://epydoc.sourceforge.net/
-
 Additional PEPs of interest regarding documentation of code:
 
-- `Docstring Conventions <http://www.python.org/peps/pep-0257.html>`_
-- `Docstring Processing System Framework <http://www.python.org/peps/pep-0256.html>`_
-- `Docutils Design Specification <http://www.python.org/peps/pep-0258.html>`_
+* `Docstring Conventions <http://www.python.org/peps/pep-0257.html>`_
+* `Docstring Processing System Framework <http://www.python.org/peps/pep-0256.html>`_
+* `Docutils Design Specification <http://www.python.org/peps/pep-0258.html>`_
 
 
 Coding conventions
 ==================
 
 General
 -------
 
 In general, we'll try to follow the standard Python style conventions as
 described here:
 
-- `Style Guide for Python Code  <http://www.python.org/peps/pep-0008.html>`_  
+* `Style Guide for Python Code  <http://www.python.org/peps/pep-0008.html>`_  
 
 
 Other comments:
 
-- In a large file, top level classes and functions should be 
+* In a large file, top level classes and functions should be 
   separated by 2-3 lines to make it easier to separate them visually.
-- Use 4 spaces for indentation.
-- Keep the ordering of methods the same in classes that have the same 
-  methods.  This is particularly true for classes that implement 
-  similar interfaces and for interfaces that are similar.
+* Use 4 spaces for indentation.
+* Keep the ordering of methods the same in classes that have the same 
+  methods.  This is particularly true for classes that implement an interface.
 
 Naming conventions
 ------------------
 
 In terms of naming conventions, we'll follow the guidelines from the `Style
 Guide for Python Code`_.
 
 For all new IPython code (and much existing code is being refactored), we'll use:
 
-- All ``lowercase`` module names.
+* All ``lowercase`` module names.
 
-- ``CamelCase`` for class names.
+* ``CamelCase`` for class names.
 
-- ``lowercase_with_underscores`` for methods, functions, variables and
+* ``lowercase_with_underscores`` for methods, functions, variables and
   attributes.
 
-This may be confusing as most of the existing IPython codebase uses a different
-convention (``lowerCamelCase`` for methods and attributes).  Slowly, we will
-move IPython over to the new convention, providing shadow names for backward
-compatibility in public interfaces.
-
-There are, however, some important exceptions to these rules.  In some cases,
+There are, however, some important exceptions to these rules. In some cases,
 IPython code will interface with packages (Twisted, Wx, Qt) that use other
-conventions.  At some level this makes it impossible to adhere to our own
-standards at all times.  In particular, when subclassing classes that use other
-naming conventions, you must follow their naming conventions.  To deal with
+conventions. At some level this makes it impossible to adhere to our own
+standards at all times. In particular, when subclassing classes that use other
+naming conventions, you must follow their naming conventions. To deal with
 cases like this, we propose the following policy:
 
-- If you are subclassing a class that uses different conventions, use its
+* If you are subclassing a class that uses different conventions, use its
   naming conventions throughout your subclass.  Thus, if you are creating a
   Twisted Protocol class, used Twisted's
   ``namingSchemeForMethodsAndAttributes.``
 
-- All IPython's official interfaces should use our conventions.  In some cases
+* All IPython's official interfaces should use our conventions.  In some cases
   this will mean that you need to provide shadow names (first implement
   ``fooBar`` and then ``foo_bar = fooBar``).  We want to avoid this at all
   costs, but it will probably be necessary at times.  But, please use this
   sparingly!
 
 Implementation-specific *private* methods will use
-``_single_underscore_prefix``.  Names with a leading double underscore will
+``_single_underscore_prefix``. Names with a leading double underscore will
 *only* be used in special cases, as they makes subclassing difficult (such
 names are not easily seen by child classes).
 
 Occasionally some run-in lowercase names are used, but mostly for very short
 names or where we are implementing methods very similar to existing ones in a
 base class (like ``runlines()`` where ``runsource()`` and ``runcode()`` had
 established precedent).
 
 The old IPython codebase has a big mix of classes and modules prefixed with an
 explicit ``IP``. In Python this is mostly unnecessary, redundant and frowned
 upon, as namespaces offer cleaner prefixing. The only case where this approach
 is justified is for classes which are expected to be imported into external
 namespaces and a very generic name (like Shell) is too likely to clash with
 something else. We'll need to revisit this issue as we clean up and refactor
 the code, but in general we should remove as many unnecessary ``IP``/``ip``
 prefixes as possible. However, if a prefix seems absolutely necessary the more
 specific ``IPY`` or ``ipy`` are preferred.
 
 .. _devel_testing:
 
 Testing system
 ==============
 
-It is extremely important that all code contributed to IPython has tests. Tests
-should be written as unittests, doctests or as entities that the `Nose`_
-testing package will find. Regardless of how the tests are written, we will use
-`Nose`_ for discovering and running the tests. `Nose`_ will be required to run
-the IPython test suite, but will not be required to simply use IPython.
+It is extremely important that all code contributed to IPython has tests.
+Tests should be written as unittests, doctests or as entities that the Nose
+[Nose]_ testing package will find. Regardless of how the tests are written, we
+will use Nose for discovering and running the tests. Nose will be required to
+run the IPython test suite, but will not be required to simply use IPython.
 
-.. _Nose: http://code.google.com/p/python-nose/
+Tests of Twisted using code need to follow two additional guidelines:
 
-Tests of `Twisted`__ using code should be written by subclassing the
-``TestCase`` class that comes with ``twisted.trial.unittest``. When this is
-done, `Nose`_ will be able to run the tests and the twisted reactor will be
-handled correctly.
+1. Twisted using tests should be written by subclassing the :class:`TestCase`
+   class that comes with :mod:`twisted.trial.unittest`. 
 
-.. __: http://www.twistedmatrix.com
+2. All :class:`Deferred` instances that are created in the test must be
+   properly chained and the final one *must* be the return value of the test
+   method.
 
-Each subpackage in IPython should have its own ``tests`` directory that
+When these two things are done, Nose will be able to run the tests and the
+twisted reactor will be handled correctly.
+
+Each subpackage in IPython should have its own :file:`tests` directory that
 contains all of the tests for that subpackage. This allows each subpackage to
 be self-contained. If a subpackage has any dependencies beyond the Python
 standard library, the tests for that subpackage should be skipped if the
 dependencies are not found. This is very important so users don't get tests
 failing simply because they don't have dependencies.
 
-We also need to look into use Noses ability to tag tests to allow a more
-modular approach of running tests.
+To run the IPython test suite, use the :command:`iptest` command that is installed with IPython::
 
-.. _devel_config:
+    $ iptest
 
-Configuration system
-====================
-
-IPython uses `.ini`_ files for configuration purposes. This represents a huge
-improvement over the configuration system used in IPython. IPython works with
-these files using the `ConfigObj`_ package, which IPython includes as
-``ipython1/external/configobj.py``.
-
-Currently, we are using raw `ConfigObj`_ objects themselves. Each subpackage of
-IPython should contain a ``config`` subdirectory that contains all of the
-configuration information for the subpackage. To see how configuration
-information is defined (along with defaults) see at the examples in
-``ipython1/kernel/config`` and ``ipython1/core/config``. Likewise, to see how
-the configuration information is used, see examples in
-``ipython1/kernel/scripts/ipengine.py``.
-
-Eventually, we will add a new layer on top of the raw `ConfigObj`_ objects. We
-are calling this new layer, ``tconfig``, as it will use a `Traits`_-like
-validation model.  We won't actually use `Traits`_, but will implement
-something similar in pure Python.  But, even in this new system, we will still
-use `ConfigObj`_ and `.ini`_ files underneath the hood. Talk to Fernando if you
-are interested in working on this part of IPython. The current prototype of
-``tconfig`` is located in the IPython sandbox.
-
-.. _.ini: http://docs.python.org/lib/module-ConfigParser.html
-.. _ConfigObj: http://www.voidspace.org.uk/python/configobj.html
-.. _Traits: http://code.enthought.com/traits/
-
-
-Installation and testing scenarios
-==================================
-
-This section outlines the various scenarios that we need to test before we
-release an IPython version.  These scenarios represent different ways of
-installing IPython and its dependencies.
-
-Installation scenarios under Linux and OS X
--------------------------------------------
-
-    1.  Install from tarball using ``python setup.py install``.
-        a.  With only readline+nose dependencies installed.
-        b.  With all dependencies installed (readline, zope.interface, Twisted,
-        foolscap, Sphinx, nose, pyOpenSSL).
-	    
-    2.  Install using easy_install.
-
-        a.  With only readline+nose dependencies installed.
-            i.  Default dependencies: ``easy_install ipython-0.9.beta3-py2.5.egg``
-            ii. Optional dependency sets: ``easy_install -f ipython-0.9.beta3-py2.5.egg IPython[kernel,doc,test,security]``
-
-        b.  With all dependencies already installed.
-	
-
-Installation scenarios under Win32
-----------------------------------
-
-	1.  Install everything from .exe installers
-	2.  easy_install?
-
-
-Tests to run for these scenarios
---------------------------------
-
-    1.  Run the full test suite.
-    2.  Start a controller and engines and try a few things by hand.
-        a.  Using ipcluster.
-        b.  Using ipcontroller/ipengine by hand.
-
-    3.  Run a few of the parallel examples.
-    4.  Try the kernel with and without security with and without PyOpenSSL
-        installed.
-    5.  Beat on the IPython terminal a bunch.
-    6.  Make sure that furl files are being put in proper locations.
+This command runs Nose with the proper options and extensions.
 
+.. _devel_config:
 
 Release checklist
 =================
 
 Most of the release process is automated by the :file:`release` script in the
 :file:`tools` directory.  This is just a handy reminder for the release manager.
 
 #. Run the release script, which makes the tar.gz, eggs and Win32 .exe
    installer.  It posts them to the site and registers the release with PyPI.
 
-#. Updating the website with announcements and links to the updated changes.txt
-   in html form.  Remember to put a short note both on the news page of the site
-   and on launcphad.
+#. Updating the website with announcements and links to the updated
+   changes.txt in html form. Remember to put a short note both on the news
+   page of the site and on Launcphad.
 
 #. Drafting a short release announcement with i) highlights and ii) a link to
    the html changes.txt.
 
 #. Make sure that the released version of the docs is live on the site.
 
 #. Celebrate!
+
+.. [Bazaar] Bazaar. http://bazaar-vcs.org/
+.. [Launchpad] Launchpad. http://www.launchpad.net/ipython
+.. [reStructuredText] reStructuredText.  http://docutils.sourceforge.net/rst.html
+.. [Sphinx] Sphinx. http://sphinx.pocoo.org/
+.. [Nose] Nose: a discovery based unittest extension. http://code.google.com/p/python-nose/

docs/source/development/index.txt

@@ -1,10 +1,11 b''
 ==================
 Development
 ==================
 
 .. toctree::
    :maxdepth: 2
 
    development.txt
    roadmap.txt
    notification_blueprint.txt
+   config_blueprint.txt

docs/source/development/notification_blueprint.txt

@@ -1,49 +1,83 b''
 .. _notification:
 
 ==========================================
 IPython.kernel.core.notification blueprint
 ==========================================
 
 Overview
 ========
-The :mod:`IPython.kernel.core.notification` module will provide a simple implementation of a notification center and support for the observer pattern within the :mod:`IPython.kernel.core`. The main intended use case is to provide notification of Interpreter events to an observing frontend during the execution of a single block of code.
+
+The :mod:`IPython.kernel.core.notification` module will provide a simple
+implementation of a notification center and support for the observer pattern
+within the :mod:`IPython.kernel.core`. The main intended use case is to
+provide notification of Interpreter events to an observing frontend during the
+execution of a single block of code.
 
 Functional Requirements
 =======================
+
 The notification center must:
-    * Provide synchronous notification of events to all registered observers.
-    * Provide typed or labeled notification types
-    * Allow observers to register callbacks for individual or all notification types
-    * Allow observers to register callbacks for events from individual or all notifying objects
-    * Notification to the observer consists of the notification type, notifying object and user-supplied extra information [implementation: as keyword parameters to the registered callback]
-    * Perform as O(1) in the case of no registered observers.
-    * Permit out-of-process or cross-network extension.
+
+* Provide synchronous notification of events to all registered observers.
+
+* Provide typed or labeled notification types.
+
+* Allow observers to register callbacks for individual or all notification
+  types.
+
+* Allow observers to register callbacks for events from individual or all
+  notifying objects.
+
+* Notification to the observer consists of the notification type, notifying
+  object and user-supplied extra information [implementation: as keyword
+  parameters to the registered callback].
+
+* Perform as O(1) in the case of no registered observers.
+
+* Permit out-of-process or cross-network extension.
     
 What's not included
-==============================================================
+===================
+
 As written, the :mod:`IPython.kernel.core.notificaiton` module does not:
-    * Provide out-of-process or network notifications [these should be handled by a separate, Twisted aware module in :mod:`IPython.kernel`].
-    * Provide zope.interface-style interfaces for the notification system [these should also be provided by the :mod:`IPython.kernel` module]
+
+* Provide out-of-process or network notifications (these should be handled by
+  a separate, Twisted aware module in :mod:`IPython.kernel`).
+
+* Provide zope.interface-style interfaces for the notification system (these
+  should also be provided by the :mod:`IPython.kernel` module).
     
 Use Cases
 =========
+
 The following use cases describe the main intended uses of the notificaiton module and illustrate the main success scenario for each use case:
 
     1. Dwight Schroot is writing a frontend for the IPython project. His frontend is stuck in the stone age and must communicate synchronously with an IPython.kernel.core.Interpreter instance. Because code is executed in blocks by the Interpreter, Dwight's UI freezes every time he executes a long block of code. To keep track of the progress of his long running block, Dwight adds the following code to his frontend's set-up code::
 
         from IPython.kernel.core.notification import NotificationCenter
         center = NotificationCenter.sharedNotificationCenter
         center.registerObserver(self, type=IPython.kernel.core.Interpreter.STDOUT_NOTIFICATION_TYPE, notifying_object=self.interpreter, callback=self.stdout_notification)
     
     and elsewhere in his front end::
 
         def stdout_notification(self, type, notifying_object, out_string=None):
             self.writeStdOut(out_string)
     
-    If everything works, the Interpreter will (according to its published API) fire a notification via the :data:`IPython.kernel.core.notification.sharedCenter` of type :const:`STD_OUT_NOTIFICATION_TYPE` before writing anything to stdout [it's up to the Intereter implementation to figure out when to do this]. The notificaiton center will then call the registered callbacks for that event type (in this case, Dwight's frontend's stdout_notification method). Again, according to its API, the Interpreter provides an additional keyword argument when firing the notificaiton of out_string, a copy of the string it will write to stdout.
+If everything works, the Interpreter will (according to its published API)
+fire a notification via the
+:data:`IPython.kernel.core.notification.sharedCenter` of type
+:const:`STD_OUT_NOTIFICATION_TYPE` before writing anything to stdout [it's up
+to the Intereter implementation to figure out when to do this]. The
+notificaiton center will then call the registered callbacks for that event
+type (in this case, Dwight's frontend's stdout_notification method). Again,
+according to its API, the Interpreter provides an additional keyword argument
+when firing the notificaiton of out_string, a copy of the string it will write
+to stdout.
 
-    Like magic, Dwight's frontend is able to provide output, even during long-running calculations. Now if Jim could just convince Dwight to use Twisted...
+Like magic, Dwight's frontend is able to provide output, even during
+long-running calculations. Now if Jim could just convince Dwight to use
+Twisted...
 
     2. Boss Hog is writing a frontend for the IPython project. Because Boss Hog is stuck in the stone age, his frontend will be written in a new Fortran-like dialect of python and will run only from the command line. Because he doesn't need any fancy notification system and is used to worrying about every cycle on his rat-wheel powered mini, Boss Hog is adamant that the new notification system not produce any performance penalty. As they say in Hazard county, there's no such thing as a free lunch. If he wanted zero overhead, he should have kept using IPython 0.8. Instead, those tricky Duke boys slide in a suped-up bridge-out jumpin' awkwardly confederate-lovin' notification module that imparts only a constant (and small) performance penalty when the Interpreter (or any other object) fires an event for which there are no registered observers. Of course, the same notificaiton-enabled Interpreter can then be used in frontends that require notifications, thus saving the IPython project from a nasty civil war.
     
     3. Barry is wrting a frontend for the IPython project. Because Barry's front end is the *new hotness*, it uses an asynchronous event model to communicate with a Twisted :mod:`~IPython.kernel.engineservice` that communicates with the IPython :class:`~IPython.kernel.core.interpreter.Interpreter`. Using the :mod:`IPython.kernel.notification` module, an asynchronous wrapper on the :mod:`IPython.kernel.core.notification` module, Barry's frontend can register for notifications from the interpreter that are delivered asynchronously. Even if Barry's frontend is running on a separate process or even host from the Interpreter, the notifications are delivered, as if by dark and twisted magic. Just like Dwight's frontend, Barry's frontend can now recieve notifications of e.g. writing to stdout/stderr, opening/closing an external file, an exception in the executing code, etc.
  No newline at end of file

docs/source/development/roadmap.txt

@@ -1,107 +1,81 b''
 .. _roadmap:
 
 ===================
 Development roadmap
 ===================
 
-.. contents::
-
 IPython is an ambitious project that is still under heavy development.  However, we want IPython to become useful to as many people as possible, as quickly as possible.  To help us accomplish this, we are laying out a roadmap of where we are headed and what needs to happen to get there.  Hopefully, this will help the IPython developers figure out the best things to work on for each upcoming release.
 
-Speaking of releases, we are going to begin releasing a new version of IPython every four weeks.  We are hoping that a regular release schedule, along with a clear roadmap of where we are headed will propel the project forward.
-
-Where are we headed
-===================
-
-Our goal with IPython is simple: to provide a *powerful*, *robust* and *easy to use* framework for parallel computing.  While there are other secondary goals you will hear us talking about at various times, this is the primary goal of IPython that frames the roadmap.
-
-Steps along the way
-===================
-
-Here we describe the various things that we need to work on to accomplish this goal.
-
-Setting up for regular release schedule
----------------------------------------
-
-We would like to begin to release IPython regularly (probably a 4 week release cycle).  To get ready for this, we need to revisit the development guidelines and put in information about releasing IPython.  
+Work targeted to particular releases
+====================================
 
-Process startup and management
-------------------------------
+Release 0.10
+------------
 
-IPython is implemented using a distributed set of processes that communicate using TCP/IP network channels.  Currently, users have to start each of the various processes separately using command line scripts.  This is both difficult and error prone.  Furthermore, there are a number of things that often need to be managed once the processes have been started, such as the sending of signals and the shutting down and cleaning up of processes.
+* Initial refactor of :command:`ipcluster`.
 
-We need to build a system that makes it trivial for users to start and manage IPython processes.  This system should have the following properties:
+* Better TextMate integration.
 
-* It should possible to do everything through an extremely simple API that users
-  can call from their own Python script.  No shell commands should be needed.
-  
-* This simple API should be configured using standard .ini files.
+* Merge in the daemon branch.
 
-* The system should make it possible to start processes using a number of different
-  approaches:  SSH, PBS/Torque, Xgrid, Windows Server, mpirun, etc.
-  
-* The controller and engine processes should each have a daemon for monitoring, 
-  signaling and clean up.
-  
-* The system should be secure.
+Release 0.11
+------------
 
-* The system should work under all the major operating systems, including
-  Windows.
+* Refactor the configuration system and command line options for
+  :command:`ipengine` and :command:`ipcontroller`. This will include the
+  creation of cluster directories that encapsulate all the configuration
+  files, log files and security related files for a particular cluster.
 
-Initial work has begun on the daemon infrastructure, and some of the needed logic is contained in the ipcluster script.
+* Refactor :command:`ipcluster` to support the new configuration system.
 
-Ease of use/high-level approaches to parallelism
-------------------------------------------------
+* Refactor the daemon stuff to support the new configuration system.
 
-While our current API for clients is well designed, we can still do a lot better in designing a user-facing API that is super simple.  The main goal here is that it should take *almost no extra code* for users to get their code running in parallel.  For this to be possible, we need to tie into Python's standard idioms that enable efficient coding.  The biggest ones we are looking at are using context managers (i.e., Python 2.5's ``with`` statement) and decorators.  Initial work on this front has begun, but more work is needed.
+* Merge back in the core of the notebook.
 
-We also need to think about new models for expressing parallelism.  This is fun work as most of the foundation has already been established.
+Release 0.12
+------------
 
-Security
---------
+* Fully integrate process startup with the daemons for full process 
+  management.
 
-Currently, IPython has no built in security or security model.  Because we would like IPython to be usable on public computer systems and over wide area networks, we need to come up with a robust solution for security.  Here are some of the specific things that need to be included:
+* Make the capabilites of :command:`ipcluster` available from simple Python 
+  classes.
 
-* User authentication between all processes (engines, controller and clients).
+Major areas of work
+===================
 
-* Optional TSL/SSL based encryption of all communication channels.
+Refactoring the main IPython core
+---------------------------------
 
-* A good way of picking network ports so multiple users on the same system can
-  run their own controller and engines without interfering with those of others.
-  
-* A clear model for security that enables users to evaluate the security risks
-  associated with using IPython in various manners.
+Process management for :mod:`IPython.kernel`
+--------------------------------------------
 
-For the implementation of this, we plan on using Twisted's support for SSL and authentication.  One things that we really should look at is the `Foolscap`_ network protocol, which provides many of these things out of the box.
+Configuration system
+--------------------
 
-.. _Foolscap: http://foolscap.lothar.com/trac
+Performance problems
+--------------------
 
-The security work needs to be done in conjunction with other network protocol stuff.
+Currently, we have a number of performance issues that are waiting to bite users:
 
-As of the 0.9 release of IPython, we are using Foolscap and we have implemented
-a full security model.
+* The controller stores a large amount of state in Python dictionaries. Under
+  heavy usage, these dicts with get very large, causing memory usage problems.
+  We need to develop more scalable solutions to this problem, such as using a
+  sqlite database to store this state. This will also help the controller to
+  be more fault tolerant.
 
-Latent performance issues
--------------------------
+* We currently don't have a good way of handling large objects in the
+  controller. The biggest problem is that because we don't have any way of
+  streaming objects, we get lots of temporary copies in the low-level buffers.
+  We need to implement a better serialization approach and true streaming
+  support.
 
-Currently, we have a number of performance issues that are waiting to bite users:
+* The controller currently unpickles and repickles objects. We need to use the
+  [push|pull]_serialized methods instead.
 
-	* The controller store a large amount of state in Python dictionaries.  Under heavy
-	  usage, these dicts with get very large, causing memory usage problems.  We need to 
-	  develop more scalable solutions to this problem, such as using a sqlite database
-	  to store this state.  This will also help the controller to be more fault tolerant.
-	* Currently, the client to controller connections are done through XML-RPC using 
-	  HTTP 1.0.  This is very inefficient as XML-RPC is a very verbose protocol and 
-	  each request must be handled with a new connection.  We need to move these network
-	  connections over to PB or Foolscap.  Done!
-	* We currently don't have a good way of handling large objects in the controller.
-	  The biggest problem is that because we don't have any way of streaming objects,
-	  we get lots of temporary copies in the low-level buffers.  We need to implement
-	  a better serialization approach and true streaming support.
-	* The controller currently unpickles and repickles objects.  We need to use the 
-	  [push|pull]_serialized methods instead.
-	* Currently the controller is a bottleneck.  We need the ability to scale the 
-	  controller by aggregating multiple controllers into one effective controller.
+* Currently the controller is a bottleneck. The best approach for this is to
+  separate the controller itself into multiple processes, one for the core
+  controller and one each for the controller interfaces.
 
 
 

docs/source/index.txt

@@ -1,32 +1,30 b''
 =====================
 IPython Documentation
 =====================
 
 .. htmlonly::
 
    :Release: |release|
    :Date: |today|
 
    Contents:
 
 .. toctree::
    :maxdepth: 2
 
    overview.txt
    install/index.txt
    interactive/index.txt
    parallel/index.txt
    config/index.txt
    changes.txt
    development/index.txt
    faq.txt
    history.txt
    license_and_copyright.txt
    credits.txt
 
-
 .. htmlonly::
-
-  * :ref:`genindex`
-  * :ref:`modindex`
-  * :ref:`search`
+   * :ref:`genindex`
+   * :ref:`modindex`
+   * :ref:`search`

docs/source/install/install.txt

@@ -1,191 +1,217 b''
 Overview
 ========
 
 This document describes the steps required to install IPython.  IPython is organized into a number of subpackages, each of which has its own dependencies.  All of the subpackages come with IPython, so you don't need to download and install them separately.  However, to use a given subpackage, you will need to install all of its dependencies.  
 
 
 Please let us know if you have problems installing IPython or any of its
 dependencies. IPython requires Python version 2.4 or greater.  We have not tested
 IPython with the upcoming 2.6 or 3.0 versions.
 
 .. warning::
 
 	IPython will not work with Python 2.3 or below.
 
 Some of the installation approaches use the :mod:`setuptools` package and its :command:`easy_install` command line program.  In many scenarios, this provides the most simple method of installing IPython and its dependencies.  It is not required though.  More information about :mod:`setuptools` can be found on its website.
 
 More general information about installing Python packages can be found in Python's documentation at http://www.python.org/doc/.
 
+Quickstart
+==========
+
+If you have :mod:`setuptools` installed and you are on OS X or Linux (not Windows), the following will download and install IPython *and* the main optional dependencies::
+
+    $ easy_install ipython[kernel,security,test]
+
+This will get Twisted, zope.interface and Foolscap, which are needed for IPython's parallel computing features as well as the nose package, which will enable you to run IPython's test suite.  To run IPython's test suite, use the :command:`iptest` command::
+
+    $ iptest
+
+Read on for more specific details and instructions for Windows.
+
 Installing IPython itself
 =========================
 
 Given a properly built Python, the basic interactive IPython shell will work with no external dependencies.  However, some Python distributions (particularly on Windows and OS X), don't come with a working :mod:`readline` module.  The IPython shell will work without :mod:`readline`, but will lack many features that users depend on, such as tab completion and command line editing.  See below for details of how to make sure you have a working :mod:`readline`.
 
 Installation using easy_install
 -------------------------------
 
 If you have :mod:`setuptools` installed, the easiest way of getting IPython is to simple use :command:`easy_install`::
 
-	$ easy_install IPython
+	$ easy_install ipython
 
 That's it.
 
 Installation from source
 ------------------------
 
 If you don't want to use :command:`easy_install`, or don't have it installed, just grab the latest stable build of IPython from `here <http://ipython.scipy.org/dist/>`_.  Then do the following::
 
 	$ tar -xzf ipython.tar.gz
 	$ cd ipython
 	$ python setup.py install
 
 If you are installing to a location (like ``/usr/local``) that requires higher permissions, you may need to run the last command with :command:`sudo`.
 
 Windows
 -------
 
 There are a few caveats for Windows users.  The main issue is that a basic ``python setup.py install`` approach won't create ``.bat`` file or Start Menu shortcuts, which most users want.  To get an installation with these, there are two choices:
 
 1.  Install using :command:`easy_install`.
 
 2.  Install using our binary ``.exe`` Windows installer, which can be found at `here <http://ipython.scipy.org/dist/>`_
 
 3.  Install from source, but using :mod:`setuptools` (``python setupegg.py install``).
 
 Installing the development version
 ----------------------------------
 
 It is also possible to install the development version of IPython from our `Bazaar <http://bazaar-vcs.org/>`_ source code
 repository.  To do this you will need to have Bazaar installed on your system.  Then just do::
 
 	$ bzr branch lp:ipython
 	$ cd ipython
 	$ python setup.py install
 
 Again, this last step on Windows won't create ``.bat`` files or Start Menu shortcuts, so you will have to use one of the other approaches listed above.
 
 Some users want to be able to follow the development branch as it changes.  If you have :mod:`setuptools` installed, this is easy. Simply replace the last step by::
 
 	$ python setupegg.py develop
 
 This creates links in the right places and installs the command line script to the appropriate places.  Then, if you want to update your IPython at any time, just do::
 
 	$ bzr pull
 
 Basic optional dependencies
 ===========================
 
 There are a number of basic optional dependencies that most users will want to get.  These are:
 
 * readline (for command line editing, tab completion, etc.)
 * nose (to run the IPython test suite)
 * pexpect (to use things like irunner)
 
 If you are comfortable installing these things yourself, have at it, otherwise read on for more details.
 
 readline
 --------
 
 In principle, all Python distributions should come with a working :mod:`readline` module.  But, reality is not quite that simple.  There are two common situations where you won't have a working :mod:`readline` module:
 
 * If you are using the built-in Python on Mac OS X.
 
 * If you are running Windows, which doesn't have a :mod:`readline` module.
 
 On OS X, the built-in Python doesn't not have :mod:`readline` because of license issues.  Starting with OS X 10.5 (Leopard), Apple's built-in Python has a BSD-licensed not-quite-compatible readline replacement. As of IPython 0.9, many of the issues related to the differences between readline and libedit have been resolved.  For many users, libedit may be sufficient.
 
 Most users on OS X will want to get the full :mod:`readline` module.  To get a working :mod:`readline` module, just do (with :mod:`setuptools` installed)::
 
 	$ easy_install readline
 
 .. note:
 
     Other Python distributions on OS X (such as fink, MacPorts and the 
     official python.org binaries) already have readline installed so 
     you don't have to do this step.
 
 If needed, the readline egg can be build and installed from source (see the wiki page at http://ipython.scipy.org/moin/InstallationOSXLeopard).
 
-On Windows, you will need the PyReadline module.  PyReadline is a separate, Windows only implementation of readline that uses native Windows calls through :mod:`ctypes`.  The easiest way of installing PyReadline is you use the binary installer available `here <http://ipython.scipy.org/dist/>`_.  The :mod:`ctypes` module, which comes with Python 2.5 and greater, is required by PyReadline.  It is available for Python 2.4 at http://python.net/crew/theller/ctypes.
+On Windows, you will need the PyReadline module. PyReadline is a separate,
+Windows only implementation of readline that uses native Windows calls through
+:mod:`ctypes`. The easiest way of installing PyReadline is you use the binary
+installer available `here <http://ipython.scipy.org/dist/>`_. The
+:mod:`ctypes` module, which comes with Python 2.5 and greater, is required by
+PyReadline. It is available for Python 2.4 at
+http://python.net/crew/theller/ctypes.
 
 nose
 ----
 
 To run the IPython test suite you will need the :mod:`nose` package.  Nose provides a great way of sniffing out and running all of the IPython tests.  The simplest way of getting nose, is to use :command:`easy_install`::
 
 	$ easy_install nose
 
 Another way of getting this is to do::
 
-    $ easy_install IPython[test]
+    $ easy_install ipython[test]
 
 For more installation options, see the `nose website <http://somethingaboutorange.com/mrl/projects/nose/>`_.  Once you have nose installed, you can run IPython's test suite using the iptest command::
 
 	$ iptest
 
 
 pexpect
 -------
 
 The `pexpect <http://www.noah.org/wiki/Pexpect>`_ package is used in IPython's :command:`irunner` script.  On Unix platforms (including OS X), just do::
 
 	$ easy_install pexpect
 
 Windows users are out of luck as pexpect does not run there.
 
 Dependencies for IPython.kernel (parallel computing)
 ====================================================
 
 The IPython kernel provides a nice architecture for parallel computing.  The main focus of this architecture is on interactive parallel computing.  These features require a number of additional packages:
 
 * zope.interface (yep, we use interfaces)
 * Twisted (asynchronous networking framework)
 * Foolscap (a nice, secure network protocol)
 * pyOpenSSL (security for network connections)
 
 On a Unix style platform (including OS X), if you want to use :mod:`setuptools`, you can just do::
 
-    $ easy_install IPython[kernel]    # the first three
-    $ easy_install IPython[security]  # pyOpenSSL
+    $ easy_install ipython[kernel]    # the first three
+    $ easy_install ipython[security]  # pyOpenSSL
 
 zope.interface and Twisted
 --------------------------
 
-On Unix style platforms (including OS X), the simplest way of getting the these is to use :command:`easy_install`::
+Twisted [Twisted]_ and zope.interface [ZopeInterface]_ are used for networking related things. On Unix
+style platforms (including OS X), the simplest way of getting the these is to
+use :command:`easy_install`::
 
 	$ easy_install zope.interface
 	$ easy_install Twisted
 
 Of course, you can also download the source tarballs from the `Twisted website <twistedmatrix.org>`_ and the `zope.interface page at PyPI <http://pypi.python.org/pypi/zope.interface>`_ and do the usual ``python setup.py install`` if you prefer.
 
 Windows is a bit different.  For zope.interface and Twisted, simply get the latest binary ``.exe`` installer from the Twisted website.  This installer includes both zope.interface and Twisted and should just work.
 
 Foolscap
 --------
 
-Foolscap uses Twisted to provide a very nice secure RPC protocol that we use to implement our parallel computing features.
+Foolscap [Foolscap]_ uses Twisted to provide a very nice secure RPC protocol that we use to implement our parallel computing features.
 
 On all platforms a simple::
 
     $ easy_install foolscap
 
 should work.  You can also download the source tarballs from the `Foolscap website <http://foolscap.lothar.com/trac>`_ and do ``python setup.py install`` if you prefer.
 
 pyOpenSSL
 ---------
 
-IPython requires an older version of pyOpenSSL (0.6 rather than the current 0.7).  There are a couple of options for getting this:
+IPython requires an older version of pyOpenSSL [pyOpenSSL]_ (0.6 rather than the current 0.7).  There are a couple of options for getting this:
 
 1.  Most Linux distributions have packages for pyOpenSSL.
 2.  The built-in Python 2.5 on OS X 10.5 already has it installed.
 3.  There are source tarballs on the pyOpenSSL website.  On Unix-like
     platforms, these can be built using ``python seutp.py install``.
 4.  There is also a binary ``.exe`` Windows installer on the `pyOpenSSL website <http://pyopenssl.sourceforge.net/>`_.
 
 Dependencies for IPython.frontend (the IPython GUI)
 ===================================================
 
 wxPython
 --------
 
-Starting with IPython 0.9, IPython has a new IPython.frontend package that has a nice wxPython based IPython GUI.  As you would expect, this GUI requires wxPython.  Most Linux distributions have wxPython packages available and the built-in Python on OS X comes with wxPython preinstalled.  For Windows, a binary installer is available on the `wxPython website <http://www.wxpython.org/>`_. 
  No newline at end of file
+Starting with IPython 0.9, IPython has a new IPython.frontend package that has a nice wxPython based IPython GUI.  As you would expect, this GUI requires wxPython.  Most Linux distributions have wxPython packages available and the built-in Python on OS X comes with wxPython preinstalled.  For Windows, a binary installer is available on the `wxPython website <http://www.wxpython.org/>`_.
+
+.. [Twisted] Twisted matrix.  http://twistedmatrix.org
+.. [ZopeInterface] http://pypi.python.org/pypi/zope.interface
+.. [Foolscap] Foolscap network protocol.  http://foolscap.lothar.com/trac
+.. [pyOpenSSL] pyOpenSSL.  http://pyopenssl.sourceforge.net
  No newline at end of file

docs/source/interactive/index.txt

@@ -1,11 +1,11 b''
 ==================================
 Using IPython for interactive work
 ==================================
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
    tutorial.txt
    reference.txt
    shell.txt
    extension_api.txt

docs/source/interactive/reference.txt

@@ -1,3200 +1,3194 b''
-.. IPython documentation master file, created by sphinx-quickstart.py on Mon Mar 24 17:01:34 2008.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root 'toctree' directive.
-
 =================
 IPython reference
 =================
 
-.. contents::
-
 .. _command_line_options:
 
 Command-line usage
 ==================
 
 You start IPython with the command::
 
     $ ipython [options] files
 
 If invoked with no options, it executes all the files listed in sequence
 and drops you into the interpreter while still acknowledging any options
 you may have set in your ipythonrc file. This behavior is different from
 standard Python, which when called as python -i will only execute one
 file and ignore your configuration setup.
 
 Please note that some of the configuration options are not available at
 the command line, simply because they are not practical here. Look into
 your ipythonrc configuration file for details on those. This file
 typically installed in the $HOME/.ipython directory. For Windows users,
 $HOME resolves to C:\\Documents and Settings\\YourUserName in most
 instances. In the rest of this text, we will refer to this directory as
 IPYTHONDIR.
 
 .. _Threading options:
 
 
 Special Threading Options
 -------------------------
 
 The following special options are ONLY valid at the beginning of the
 command line, and not later. This is because they control the initial-
 ization of ipython itself, before the normal option-handling mechanism
 is active.
 
     -gthread, -qthread, -q4thread, -wthread, -pylab: 
 	Only one of these can be given, and it can only be given as
 	the first option passed to IPython (it will have no effect in
 	any other position).  They provide threading support for the
 	GTK, Qt (versions 3 and 4) and WXPython toolkits, and for the
 	matplotlib library.
 
 	With any of the first four options, IPython starts running a
 	separate thread for the graphical toolkit's operation, so that
 	you can open and control graphical elements from within an
 	IPython command line, without blocking. All four provide
 	essentially the same functionality, respectively for GTK, Qt3,
 	Qt4 and WXWidgets (via their Python interfaces).
 
 	Note that with -wthread, you can additionally use the
 	-wxversion option to request a specific version of wx to be
 	used.  This requires that you have the wxversion Python module
 	installed, which is part of recent wxPython distributions.
 
 	If -pylab is given, IPython loads special support for the mat
 	plotlib library (http://matplotlib.sourceforge.net), allowing
 	interactive usage of any of its backends as defined in the
 	user's ~/.matplotlib/matplotlibrc file. It automatically
 	activates GTK, Qt or WX threading for IPyhton if the choice of
 	matplotlib backend requires it. It also modifies the %run
 	command to correctly execute (without blocking) any
 	matplotlib-based script which calls show() at the end.
 
     -tk
 	The -g/q/q4/wthread options, and -pylab (if matplotlib is
 	configured to use GTK, Qt3, Qt4 or WX), will normally block Tk
 	graphical interfaces. This means that when either GTK, Qt or WX
 	threading is active, any attempt to open a Tk GUI will result in a
 	dead window, and possibly cause the Python interpreter to crash.
 	An extra option, -tk, is available to address this issue. It can
 	only be given as a second option after any of the above (-gthread,
 	-wthread or -pylab).
 
 	If -tk is given, IPython will try to coordinate Tk threading
 	with GTK, Qt or WX. This is however potentially unreliable, and
 	you will have to test on your platform and Python configuration to
 	determine whether it works for you. Debian users have reported
 	success, apparently due to the fact that Debian builds all of Tcl,
 	Tk, Tkinter and Python with pthreads support. Under other Linux
 	environments (such as Fedora Core 2/3), this option has caused
 	random crashes and lockups of the Python interpreter. Under other
 	operating systems (Mac OSX and Windows), you'll need to try it to
 	find out, since currently no user reports are available.
     
 	There is unfortunately no way for IPython to determine at run time
 	whether -tk will work reliably or not, so you will need to do some
 	experiments before relying on it for regular work.
 
 
 
 Regular Options
 ---------------
 
 After the above threading options have been given, regular options can
 follow in any order. All options can be abbreviated to their shortest
 non-ambiguous form and are case-sensitive. One or two dashes can be
 used. Some options have an alternate short form, indicated after a ``|``.
 
 Most options can also be set from your ipythonrc configuration file. See
 the provided example for more details on what the options do. Options
 given at the command line override the values set in the ipythonrc file.
 
 All options with a [no] prepended can be specified in negated form
 (-nooption instead of -option) to turn the feature off.
 
     -help  print a help message and exit.
 
     -pylab
 	this can only be given as the first option passed to IPython
 	(it will have no effect in any other position). It adds
 	special support for the matplotlib library
 	(http://matplotlib.sourceforge.ne), allowing interactive usage
 	of any of its backends as defined in the user's .matplotlibrc
 	file.  It automatically activates GTK or WX threading for
 	IPyhton if the choice of matplotlib backend requires it. It
 	also modifies the %run command to correctly execute (without
 	blocking) any matplotlib-based script which calls show() at
 	the end. See `Matplotlib support`_ for more details.
 
     -autocall <val>
 	Make IPython automatically call any callable object even if you
 	didn't type explicit parentheses. For example, 'str 43' becomes
 	'str(43)' automatically. The value can be '0' to disable the feature,
 	'1' for smart autocall, where it is not applied if there are no more
 	arguments on the line, and '2' for full autocall, where all callable
 	objects are automatically called (even if no arguments are
 	present). The default is '1'.
 
     -[no]autoindent    
 	Turn automatic indentation on/off.
 
     -[no]automagic 
 	make magic commands automatic (without needing their first character
 	to be %). Type %magic at the IPython prompt for more information.
 
     -[no]autoedit_syntax 
 	When a syntax error occurs after editing a file, automatically
 	open the file to the trouble causing line for convenient
 	fixing.
 
     -[no]banner		Print the initial information banner (default on).
 
     -c <command>
 	execute the given command string. This is similar to the -c
 	option in the normal Python interpreter.
 
     -cache_size, cs <n> 
 	size of the output cache (maximum number of entries to hold in
 	memory). The default is 1000, you can change it permanently in your
 	config file. Setting it to 0 completely disables the caching system,
 	and the minimum value accepted is 20 (if you provide a value less than
 	20, it is reset to 0 and a warning is issued) This limit is defined
 	because otherwise you'll spend more time re-flushing a too small cache
 	than working.
 
     -classic, cl 
 	Gives IPython a similar feel to the classic Python
 	prompt.
 
     -colors <scheme> 
 	Color scheme for prompts and exception reporting. Currently
 	implemented: NoColor, Linux and LightBG.
 
     -[no]color_info 
 	IPython can display information about objects via a set of functions,
 	and optionally can use colors for this, syntax highlighting source
 	code and various other elements.  However, because this information is
 	passed through a pager (like 'less') and many pagers get confused with
 	color codes, this option is off by default. You can test it and turn
 	it on permanently in your ipythonrc file if it works for you. As a
 	reference, the 'less' pager supplied with Mandrake 8.2 works ok, but
 	that in RedHat 7.2 doesn't.
 
 	Test it and turn it on permanently if it works with your
 	system. The magic function %color_info allows you to toggle this
 	interactively for testing.
 
     -[no]debug 
 	Show information about the loading process. Very useful to pin down
 	problems with your configuration files or to get details about
 	session restores.
 
     -[no]deep_reload: 
 	IPython can use the deep_reload module which reloads changes in
 	modules recursively (it replaces the reload() function, so you don't
 	need to change anything to use it).  deep_reload() forces a full
 	reload of modules whose code may have changed, which the default
 	reload() function does not.
 
 	When deep_reload is off, IPython will use the normal reload(),
 	but deep_reload will still be available as dreload(). This
 	feature is off by default [which means that you have both
 	normal reload() and dreload()].
 
     -editor <name>
 	Which editor to use with the %edit command. By default,
 	IPython will honor your EDITOR environment variable (if not
 	set, vi is the Unix default and notepad the Windows one).
 	Since this editor is invoked on the fly by IPython and is
 	meant for editing small code snippets, you may want to use a
 	small, lightweight editor here (in case your default EDITOR is
 	something like Emacs).
 
     -ipythondir <name> 
 	name of your IPython configuration directory IPYTHONDIR. This
 	can also be specified through the environment variable
 	IPYTHONDIR.
 
     -log, l 
 	generate a log file of all input. The file is named
 	ipython_log.py in your current directory (which prevents logs
 	from multiple IPython sessions from trampling each other). You
 	can use this to later restore a session by loading your
 	logfile as a file to be executed with option -logplay (see
 	below).
 
     -logfile, lf <name>   specify the name of your logfile.
 
     -logplay, lp <name> 
 
       you can replay a previous log. For restoring a session as close as
       possible to the state you left it in, use this option (don't just run
       the logfile). With -logplay, IPython will try to reconstruct the
       previous working environment in full, not just execute the commands in
       the logfile.
 
       When a session is restored, logging is automatically turned on
       again with the name of the logfile it was invoked with (it is
       read from the log header). So once you've turned logging on for
       a session, you can quit IPython and reload it as many times as
       you want and it will continue to log its history and restore
       from the beginning every time.
       
       Caveats: there are limitations in this option. The history
       variables _i*,_* and _dh don't get restored properly. In the
       future we will try to implement full session saving by writing
       and retrieving a 'snapshot' of the memory state of IPython. But
       our first attempts failed because of inherent limitations of
       Python's Pickle module, so this may have to wait.
 
     -[no]messages   
 	Print messages which IPython collects about its startup
 	process (default on).
 
     -[no]pdb
 	Automatically call the pdb debugger after every uncaught
 	exception. If you are used to debugging using pdb, this puts
 	you automatically inside of it after any call (either in
 	IPython or in code called by it) which triggers an exception
 	which goes uncaught.
 
     -pydb
 	Makes IPython use the third party "pydb" package as debugger,
 	instead of pdb. Requires that pydb is installed.
 	
     -[no]pprint
 	ipython can optionally use the pprint (pretty printer) module
 	for displaying results. pprint tends to give a nicer display
 	of nested data structures. If you like it, you can turn it on
 	permanently in your config file (default off).
 
     -profile, p <name>
 
 	assume that your config file is ipythonrc-<name> or
 	ipy_profile_<name>.py (looks in current dir first, then in
 	IPYTHONDIR).  This is a quick way to keep and load multiple
 	config files for different tasks, especially if you use the
 	include option of config files. You can keep a basic
 	IPYTHONDIR/ipythonrc file and then have other 'profiles' which
 	include this one and load extra things for particular
 	tasks. For example:
 
 	1. $HOME/.ipython/ipythonrc : load basic things you always want.
 	2. $HOME/.ipython/ipythonrc-math : load (1) and basic math-related modules.
 	3. $HOME/.ipython/ipythonrc-numeric : load (1) and Numeric and plotting modules.
 
 	Since it is possible to create an endless loop by having
 	circular file inclusions, IPython will stop if it reaches 15
 	recursive inclusions.
 
     -prompt_in1, pi1 <string>
 
         Specify the string used for input prompts. Note that if you are using
 	numbered prompts, the number is represented with a '\#' in the
 	string. Don't forget to quote strings with spaces embedded in
 	them. Default: 'In [\#]:'.  The :ref:`prompts section <prompts>`
 	discusses in detail all the available escapes to customize your
 	prompts.
 
     -prompt_in2, pi2 <string>
 	Similar to the previous option, but used for the continuation
 	prompts. The special sequence '\D' is similar to '\#', but
 	with all digits replaced dots (so you can have your
 	continuation prompt aligned with your input prompt).  Default:
 	' .\D.:' (note three spaces at the start for alignment with
 	'In [\#]').
 
     -prompt_out,po <string> 
 	String used for output prompts, also uses numbers like
 	prompt_in1. Default: 'Out[\#]:'
 
     -quick   start in bare bones mode (no config file loaded).
 
     -rcfile <name>   
 	name of your IPython resource configuration file. Normally
 	IPython loads ipythonrc (from current directory) or
 	IPYTHONDIR/ipythonrc.
 
 	If the loading of your config file fails, IPython starts with
 	a bare bones configuration (no modules loaded at all).
 
     -[no]readline
 	use the readline library, which is needed to support name
 	completion and command history, among other things.  It is
 	enabled by default, but may cause problems for users of
 	X/Emacs in Python comint or shell buffers.
 
 	Note that X/Emacs 'eterm' buffers (opened with M-x term) support
 	IPython's readline and syntax coloring fine, only 'emacs' (M-x
 	shell and C-c !) buffers do not.
 
     -screen_length, sl <n>
 	number of lines of your screen. This is used to control
 	printing of very long strings. Strings longer than this number
 	of lines will be sent through a pager instead of directly
 	printed.
 
 	The default value for this is 0, which means IPython will
 	auto-detect your screen size every time it needs to print certain
 	potentially long strings (this doesn't change the behavior of the
 	'print' keyword, it's only triggered internally). If for some
 	reason this isn't working well (it needs curses support), specify
 	it yourself. Otherwise don't change the default.
 
     -separate_in, si <string>
 
 	separator before input prompts.
 	Default: '\n'
 
     -separate_out, so <string>  
         separator before output prompts.
         Default: nothing.
 
     -separate_out2, so2
 	separator after output prompts.
 	Default: nothing.
 	For these three options, use the value 0 to specify no separator.
 
     -nosep   
 	shorthand for '-SeparateIn 0 -SeparateOut 0 -SeparateOut2
 	0'. Simply removes all input/output separators.
 
     -upgrade 
 	allows you to upgrade your IPYTHONDIR configuration when you
 	install a new version of IPython. Since new versions may
 	include new command line options or example files, this copies
 	updated ipythonrc-type files. However, it backs up (with a
 	.old extension) all files which it overwrites so that you can
 	merge back any customizations you might have in your personal
 	files. Note that you should probably use %upgrade instead,
 	it's a safer alternative.
 
 
     -Version    print version information and exit.
 
     -wxversion <string> 
 	Select a specific version of wxPython (used in conjunction
 	with -wthread). Requires the wxversion module, part of recent
 	wxPython distributions
 
     -xmode <modename>
 
 	Mode for exception reporting.
 
 	Valid modes: Plain, Context and Verbose.
 
 	* Plain: similar to python's normal traceback printing.
 	* Context: prints 5 lines of context source code around each
 	  line in the traceback.
 	* Verbose: similar to Context, but additionally prints the
 	  variables currently visible where the exception happened
 	  (shortening their strings if too long). This can potentially be
 	  very slow, if you happen to have a huge data structure whose
 	  string representation is complex to compute. Your computer may
 	  appear to freeze for a while with cpu usage at 100%. If this
 	  occurs, you can cancel the traceback with Ctrl-C (maybe hitting it
 	  more than once).
 
 Interactive use
 ===============
 
 Warning: IPython relies on the existence of a global variable called
 _ip which controls the shell itself. If you redefine _ip to anything,
 bizarre behavior will quickly occur.
 
 Other than the above warning, IPython is meant to work as a drop-in
 replacement for the standard interactive interpreter. As such, any code
 which is valid python should execute normally under IPython (cases where
 this is not true should be reported as bugs). It does, however, offer
 many features which are not available at a standard python prompt. What
 follows is a list of these.
 
 
 Caution for Windows users
 -------------------------
 
 Windows, unfortunately, uses the '\' character as a path
 separator. This is a terrible choice, because '\' also represents the
 escape character in most modern programming languages, including
 Python. For this reason, using '/' character is recommended if you
 have problems with ``\``.  However, in Windows commands '/' flags
 options, so you can not use it for the root directory. This means that
 paths beginning at the root must be typed in a contrived manner like:
 ``%copy \opt/foo/bar.txt \tmp``
 
 .. _magic:
 
 Magic command system
 --------------------
 
 IPython will treat any line whose first character is a % as a special
 call to a 'magic' function. These allow you to control the behavior of
 IPython itself, plus a lot of system-type features. They are all
 prefixed with a % character, but parameters are given without
 parentheses or quotes.
 
 Example: typing '%cd mydir' (without the quotes) changes you working
 directory to 'mydir', if it exists.
 
 If you have 'automagic' enabled (in your ipythonrc file, via the command
 line option -automagic or with the %automagic function), you don't need
 to type in the % explicitly. IPython will scan its internal list of
 magic functions and call one if it exists. With automagic on you can
 then just type 'cd mydir' to go to directory 'mydir'. The automagic
 system has the lowest possible precedence in name searches, so defining
 an identifier with the same name as an existing magic function will
 shadow it for automagic use. You can still access the shadowed magic
 function by explicitly using the % character at the beginning of the line.
 
 An example (with automagic on) should clarify all this::
 
     In [1]: cd ipython # %cd is called by automagic
 
     /home/fperez/ipython
 
     In [2]: cd=1 # now cd is just a variable
 
     In [3]: cd .. # and doesn't work as a function anymore
 
     ------------------------------
 
         File "<console>", line 1
 
           cd ..
 
               ^
 
     SyntaxError: invalid syntax
 
     In [4]: %cd .. # but %cd always works
 
     /home/fperez
 
     In [5]: del cd # if you remove the cd variable
 
     In [6]: cd ipython # automagic can work again
 
     /home/fperez/ipython
 
 You can define your own magic functions to extend the system. The
 following example defines a new magic command, %impall::
 
     import IPython.ipapi 
 
     ip = IPython.ipapi.get()
 
     def doimp(self, arg):
 
         ip = self.api
 
         ip.ex("import %s; reload(%s); from %s import *" % (
 
         arg,arg,arg)
 
         )
 
     ip.expose_magic('impall', doimp)
 
 You can also define your own aliased names for magic functions. In your
 ipythonrc file, placing a line like:
 
 execute __IP.magic_cl = __IP.magic_clear
 
 will define %cl as a new name for %clear.
 
 Type %magic for more information, including a list of all available
 magic functions at any time and their docstrings. You can also type
 %magic_function_name? (see sec. 6.4 <#sec:dyn-object-info> for
 information on the '?' system) to get information about any particular
 magic function you are interested in.
 
 
 Magic commands
 --------------
 
 The rest of this section is automatically generated for each release
 from the docstrings in the IPython code. Therefore the formatting is
 somewhat minimal, but this method has the advantage of having
 information always in sync with the code.
 
 A list of all the magic commands available in IPython's default
 installation follows. This is similar to what you'll see by simply
 typing %magic at the prompt, but that will also give you information
 about magic commands you may have added as part of your personal
 customizations.
 
 .. magic_start
 
 **%Exit**::
 
 	Exit IPython without confirmation.
 
 **%Pprint**::
 
 	Toggle pretty printing on/off.
 
 **%alias**::
 
 	Define an alias for a system command.
 
         '%alias alias_name cmd' defines 'alias_name' as an alias for 'cmd'
 
         Then, typing 'alias_name params' will execute the system command 'cmd
         params' (from your underlying operating system).
 
         Aliases have lower precedence than magic functions and Python normal
         variables, so if 'foo' is both a Python variable and an alias, the
         alias can not be executed until 'del foo' removes the Python variable.
 
         You can use the %l specifier in an alias definition to represent the
         whole line when the alias is called.  For example:
 
           In [2]: alias all echo "Input in brackets: <%l>"\
           In [3]: all hello world\
           Input in brackets: <hello world>
 
         You can also define aliases with parameters using %s specifiers (one
         per parameter):
         
           In [1]: alias parts echo first %s second %s\
           In [2]: %parts A B\
           first A second B\
           In [3]: %parts A\
           Incorrect number of arguments: 2 expected.\
           parts is an alias to: 'echo first %s second %s'
 
         Note that %l and %s are mutually exclusive.  You can only use one or
         the other in your aliases.
 
         Aliases expand Python variables just like system calls using ! or !! 
         do: all expressions prefixed with '$' get expanded.  For details of
         the semantic rules, see PEP-215:
         http://www.python.org/peps/pep-0215.html.  This is the library used by
         IPython for variable expansion.  If you want to access a true shell
         variable, an extra $ is necessary to prevent its expansion by IPython:
 
         In [6]: alias show echo\
         In [7]: PATH='A Python string'\
         In [8]: show $PATH\
         A Python string\
         In [9]: show $$PATH\
         /usr/local/lf9560/bin:/usr/local/intel/compiler70/ia32/bin:...
 
         You can use the alias facility to acess all of $PATH.  See the %rehash
         and %rehashx functions, which automatically create aliases for the
         contents of your $PATH.
 
         If called with no parameters, %alias prints the current alias table.
 
 **%autocall**::
 
 	Make functions callable without having to type parentheses.
 
         Usage:
 
            %autocall [mode]
 
         The mode can be one of: 0->Off, 1->Smart, 2->Full.  If not given, the
         value is toggled on and off (remembering the previous state).
 
         In more detail, these values mean:
 
         0 -> fully disabled
 
         1 -> active, but do not apply if there are no arguments on the line.
 
         In this mode, you get:
 
         In [1]: callable
         Out[1]: <built-in function callable>
 
         In [2]: callable 'hello'
         ------> callable('hello')
         Out[2]: False
 
         2 -> Active always.  Even if no arguments are present, the callable
         object is called:
 
         In [4]: callable
         ------> callable()
 
         Note that even with autocall off, you can still use '/' at the start of
         a line to treat the first argument on the command line as a function
         and add parentheses to it:
 
         In [8]: /str 43
         ------> str(43)
         Out[8]: '43'
 
 **%autoindent**::
 
 	Toggle autoindent on/off (if available).
 
 **%automagic**::
 
 	Make magic functions callable without having to type the initial %.
 
         Without argumentsl toggles on/off (when off, you must call it as
         %automagic, of course).  With arguments it sets the value, and you can
         use any of (case insensitive):
 
          - on,1,True: to activate
 
          - off,0,False: to deactivate.
 
         Note that magic functions have lowest priority, so if there's a
         variable whose name collides with that of a magic fn, automagic won't
         work for that function (you get the variable instead). However, if you
         delete the variable (del var), the previously shadowed magic function
         becomes visible to automagic again.
 
 **%bg**::
 
 	Run a job in the background, in a separate thread.
 
         For example,
 
           %bg myfunc(x,y,z=1)
 
         will execute 'myfunc(x,y,z=1)' in a background thread.  As soon as the
         execution starts, a message will be printed indicating the job
         number.  If your job number is 5, you can use
 
           myvar = jobs.result(5)  or  myvar = jobs[5].result
 
         to assign this result to variable 'myvar'.
 
         IPython has a job manager, accessible via the 'jobs' object.  You can
         type jobs? to get more information about it, and use jobs.<TAB> to see
         its attributes.  All attributes not starting with an underscore are
         meant for public use.
 
         In particular, look at the jobs.new() method, which is used to create
         new jobs.  This magic %bg function is just a convenience wrapper
         around jobs.new(), for expression-based jobs.  If you want to create a
         new job with an explicit function object and arguments, you must call
         jobs.new() directly.
 
         The jobs.new docstring also describes in detail several important
         caveats associated with a thread-based model for background job
         execution.  Type jobs.new? for details.
 
         You can check the status of all jobs with jobs.status().
 
         The jobs variable is set by IPython into the Python builtin namespace.
         If you ever declare a variable named 'jobs', you will shadow this
         name.  You can either delete your global jobs variable to regain
         access to the job manager, or make a new name and assign it manually
         to the manager (stored in IPython's namespace).  For example, to
         assign the job manager to the Jobs name, use:
 
           Jobs = __builtins__.jobs
 
 **%bookmark**::
 
 	Manage IPython's bookmark system.
 
         %bookmark <name>       - set bookmark to current dir
         %bookmark <name> <dir> - set bookmark to <dir>
         %bookmark -l           - list all bookmarks
         %bookmark -d <name>    - remove bookmark
         %bookmark -r           - remove all bookmarks
 
         You can later on access a bookmarked folder with:
           %cd -b <name>
         or simply '%cd <name>' if there is no directory called <name> AND
         there is such a bookmark defined.
 
         Your bookmarks persist through IPython sessions, but they are
         associated with each profile.
 
 **%cd**::
 
 	Change the current working directory.
 
         This command automatically maintains an internal list of directories
         you visit during your IPython session, in the variable _dh. The
         command %dhist shows this history nicely formatted. You can also
         do 'cd -<tab>' to see directory history conveniently.
 
         Usage:
 
           cd 'dir': changes to directory 'dir'.
 
           cd -: changes to the last visited directory.
 
           cd -<n>: changes to the n-th directory in the directory history.
 
           cd -b <bookmark_name>: jump to a bookmark set by %bookmark
              (note: cd <bookmark_name> is enough if there is no
               directory <bookmark_name>, but a bookmark with the name exists.)
               'cd -b <tab>' allows you to tab-complete bookmark names. 
 
         Options:
 
         -q: quiet.  Do not print the working directory after the cd command is
         executed.  By default IPython's cd command does print this directory,
         since the default prompts do not display path information.
         
         Note that !cd doesn't work for this purpose because the shell where
         !command runs is immediately discarded after executing 'command'.
 
 **%clear**::
 
 	 Clear various data (e.g. stored history data)
     
     %clear out - clear output history
     %clear in  - clear input history
     %clear shadow_compress - Compresses shadow history (to speed up ipython)
     %clear shadow_nuke - permanently erase all entries in shadow history
     %clear dhist - clear dir history
 
 **%color_info**::
 
 	Toggle color_info.
 
         The color_info configuration parameter controls whether colors are
         used for displaying object details (by things like %psource, %pfile or
         the '?' system). This function toggles this value with each call.
 
         Note that unless you have a fairly recent pager (less works better
         than more) in your system, using colored object information displays
         will not work properly. Test it and see.
 
 **%colors**::
 
 	Switch color scheme for prompts, info system and exception handlers.
 
         Currently implemented schemes: NoColor, Linux, LightBG.
 
         Color scheme names are not case-sensitive.
 
 **%cpaste**::
 
 	Allows you to paste & execute a pre-formatted code block from clipboard
         
         You must terminate the block with '--' (two minus-signs) alone on the
         line. You can also provide your own sentinel with '%paste -s %%' ('%%' 
         is the new sentinel for this operation)
         
         The block is dedented prior to execution to enable execution of method
         definitions. '>' and '+' characters at the beginning of a line are
         ignored, to allow pasting directly from e-mails or diff files. The
         executed block is also assigned to variable named 'pasted_block' for
         later editing with '%edit pasted_block'.
         
         You can also pass a variable name as an argument, e.g. '%cpaste foo'.
         This assigns the pasted block to variable 'foo' as string, without 
         dedenting or executing it.
         
         Do not be alarmed by garbled output on Windows (it's a readline bug). 
         Just press enter and type -- (and press enter again) and the block 
         will be what was just pasted.
         
         IPython statements (magics, shell escapes) are not supported (yet).
 
 **%debug**::
 
 	Activate the interactive debugger in post-mortem mode.
 
         If an exception has just occurred, this lets you inspect its stack
         frames interactively.  Note that this will always work only on the last
         traceback that occurred, so you must call this quickly after an
         exception that you wish to inspect has fired, because if another one
         occurs, it clobbers the previous one.
 
         If you want IPython to automatically do this on every exception, see
         the %pdb magic for more details.
 
 **%dhist**::
 
 	Print your history of visited directories.
 
         %dhist       -> print full history\
         %dhist n     -> print last n entries only\
         %dhist n1 n2 -> print entries between n1 and n2 (n1 not included)\
 
         This history is automatically maintained by the %cd command, and
         always available as the global list variable _dh. You can use %cd -<n>
         to go to directory number <n>.
         
         Note that most of time, you should view directory history by entering
         cd -<TAB>.
 
 **%dirs**::
 
 	Return the current directory stack.
 
 **%doctest_mode**::
 
 	Toggle doctest mode on and off.
 
         This mode allows you to toggle the prompt behavior between normal
         IPython prompts and ones that are as similar to the default IPython
         interpreter as possible.
 
         It also supports the pasting of code snippets that have leading '>>>'
         and '...' prompts in them.  This means that you can paste doctests from
         files or docstrings (even if they have leading whitespace), and the
         code will execute correctly.  You can then use '%history -tn' to see
         the translated history without line numbers; this will give you the
         input after removal of all the leading prompts and whitespace, which
         can be pasted back into an editor.
 
         With these features, you can switch into this mode easily whenever you
         need to do testing and changes to doctests, without having to leave
         your existing IPython session.
 
 **%ed**::
 
 	Alias to %edit.
 
 **%edit**::
 
 	Bring up an editor and execute the resulting code.
 
         Usage:
           %edit [options] [args]
 
         %edit runs IPython's editor hook.  The default version of this hook is
         set to call the __IPYTHON__.rc.editor command.  This is read from your
         environment variable $EDITOR.  If this isn't found, it will default to
         vi under Linux/Unix and to notepad under Windows.  See the end of this
         docstring for how to change the editor hook.
 
         You can also set the value of this editor via the command line option
         '-editor' or in your ipythonrc file. This is useful if you wish to use
         specifically for IPython an editor different from your typical default
         (and for Windows users who typically don't set environment variables).
 
         This command allows you to conveniently edit multi-line code right in
         your IPython session.
         
         If called without arguments, %edit opens up an empty editor with a
         temporary file and will execute the contents of this file when you
         close it (don't forget to save it!).
 
 
         Options:
 
         -n <number>: open the editor at a specified line number.  By default,
         the IPython editor hook uses the unix syntax 'editor +N filename', but
         you can configure this by providing your own modified hook if your
         favorite editor supports line-number specifications with a different
         syntax.
         
         -p: this will call the editor with the same data as the previous time
         it was used, regardless of how long ago (in your current session) it
         was.
 
         -r: use 'raw' input.  This option only applies to input taken from the
         user's history.  By default, the 'processed' history is used, so that
         magics are loaded in their transformed version to valid Python.  If
         this option is given, the raw input as typed as the command line is
         used instead.  When you exit the editor, it will be executed by
         IPython's own processor.
         
         -x: do not execute the edited code immediately upon exit. This is
         mainly useful if you are editing programs which need to be called with
         command line arguments, which you can then do using %run.
 
 
         Arguments:
 
         If arguments are given, the following possibilites exist:
 
         - The arguments are numbers or pairs of colon-separated numbers (like
         1 4:8 9). These are interpreted as lines of previous input to be
         loaded into the editor. The syntax is the same of the %macro command.
 
         - If the argument doesn't start with a number, it is evaluated as a
         variable and its contents loaded into the editor. You can thus edit
         any string which contains python code (including the result of
         previous edits).
 
         - If the argument is the name of an object (other than a string),
         IPython will try to locate the file where it was defined and open the
         editor at the point where it is defined. You can use `%edit function`
         to load an editor exactly at the point where 'function' is defined,
         edit it and have the file be executed automatically.
 
         If the object is a macro (see %macro for details), this opens up your
         specified editor with a temporary file containing the macro's data.
         Upon exit, the macro is reloaded with the contents of the file.
 
         Note: opening at an exact line is only supported under Unix, and some
         editors (like kedit and gedit up to Gnome 2.8) do not understand the
         '+NUMBER' parameter necessary for this feature. Good editors like
         (X)Emacs, vi, jed, pico and joe all do.
 
         - If the argument is not found as a variable, IPython will look for a
         file with that name (adding .py if necessary) and load it into the
         editor. It will execute its contents with execfile() when you exit,
         loading any code in the file into your interactive namespace.
 
         After executing your code, %edit will return as output the code you
         typed in the editor (except when it was an existing file). This way
         you can reload the code in further invocations of %edit as a variable,
         via _<NUMBER> or Out[<NUMBER>], where <NUMBER> is the prompt number of
         the output.
 
         Note that %edit is also available through the alias %ed.
 
         This is an example of creating a simple function inside the editor and
         then modifying it. First, start up the editor:
 
         In [1]: ed\
         Editing... done. Executing edited code...\
         Out[1]: 'def foo():\n    print "foo() was defined in an editing session"\n'
 
         We can then call the function foo():
         
         In [2]: foo()\
         foo() was defined in an editing session
 
         Now we edit foo.  IPython automatically loads the editor with the
         (temporary) file where foo() was previously defined:
         
         In [3]: ed foo\
         Editing... done. Executing edited code...
 
         And if we call foo() again we get the modified version:
         
         In [4]: foo()\
         foo() has now been changed!
 
         Here is an example of how to edit a code snippet successive
         times. First we call the editor:
 
         In [8]: ed\
         Editing... done. Executing edited code...\
         hello\
         Out[8]: "print 'hello'\n"
 
         Now we call it again with the previous output (stored in _):
 
         In [9]: ed _\
         Editing... done. Executing edited code...\
         hello world\
         Out[9]: "print 'hello world'\n"
 
         Now we call it with the output #8 (stored in _8, also as Out[8]):
 
         In [10]: ed _8\
         Editing... done. Executing edited code...\
         hello again\
         Out[10]: "print 'hello again'\n"
 
 
         Changing the default editor hook:
 
         If you wish to write your own editor hook, you can put it in a
         configuration file which you load at startup time.  The default hook
         is defined in the IPython.hooks module, and you can use that as a
         starting example for further modifications.  That file also has
         general instructions on how to set a new hook for use once you've
         defined it.
 
 **%env**::
 
 	List environment variables.
 
 **%exit**::
 
 	Exit IPython, confirming if configured to do so.
 
         You can configure whether IPython asks for confirmation upon exit by
         setting the confirm_exit flag in the ipythonrc file.
 
 **%hist**::
 
 	Alternate name for %history.
 
 **%history**::
 
 	Print input history (_i<n> variables), with most recent last.
     
     %history       -> print at most 40 inputs (some may be multi-line)\
     %history n     -> print at most n inputs\
     %history n1 n2 -> print inputs between n1 and n2 (n2 not included)\
     
     Each input's number <n> is shown, and is accessible as the
     automatically generated variable _i<n>.  Multi-line statements are
     printed starting at a new line for easy copy/paste.
     
 
     Options:
 
       -n: do NOT print line numbers. This is useful if you want to get a
       printout of many lines which can be directly pasted into a text
       editor.
 
       This feature is only available if numbered prompts are in use.
 
       -t: (default) print the 'translated' history, as IPython understands it.
       IPython filters your input and converts it all into valid Python source
       before executing it (things like magics or aliases are turned into
       function calls, for example). With this option, you'll see the native
       history instead of the user-entered version: '%cd /' will be seen as
       '_ip.magic("%cd /")' instead of '%cd /'.
       
       -r: print the 'raw' history, i.e. the actual commands you typed.
       
       -g: treat the arg as a pattern to grep for in (full) history.
       This includes the "shadow history" (almost all commands ever written).
       Use '%hist -g' to show full shadow history (may be very long).
       In shadow history, every index nuwber starts with 0.
 
       -f FILENAME: instead of printing the output to the screen, redirect it to
        the given file.  The file is always overwritten, though IPython asks for
        confirmation first if it already exists.
 
 **%logoff**::
 
 	Temporarily stop logging.
 
         You must have previously started logging.
 
 **%logon**::
 
 	Restart logging.
 
         This function is for restarting logging which you've temporarily
         stopped with %logoff. For starting logging for the first time, you
         must use the %logstart function, which allows you to specify an
         optional log filename.
 
 **%logstart**::
 
 	Start logging anywhere in a session.
 
         %logstart [-o|-r|-t] [log_name [log_mode]]
 
         If no name is given, it defaults to a file named 'ipython_log.py' in your
         current directory, in 'rotate' mode (see below).
 
         '%logstart name' saves to file 'name' in 'backup' mode.  It saves your
         history up to that point and then continues logging.
 
         %logstart takes a second optional parameter: logging mode. This can be one
         of (note that the modes are given unquoted):\
           append: well, that says it.\
           backup: rename (if exists) to name~ and start name.\
           global: single logfile in your home dir, appended to.\
           over  : overwrite existing log.\
           rotate: create rotating logs name.1~, name.2~, etc.
 
         Options:
 
           -o: log also IPython's output.  In this mode, all commands which
           generate an Out[NN] prompt are recorded to the logfile, right after
           their corresponding input line.  The output lines are always
           prepended with a '#[Out]# ' marker, so that the log remains valid
           Python code.
 
           Since this marker is always the same, filtering only the output from
           a log is very easy, using for example a simple awk call:
 
             awk -F'#\[Out\]# ' '{if($2) {print $2}}' ipython_log.py
 
           -r: log 'raw' input.  Normally, IPython's logs contain the processed
           input, so that user lines are logged in their final form, converted
           into valid Python.  For example, %Exit is logged as
           '_ip.magic("Exit").  If the -r flag is given, all input is logged
           exactly as typed, with no transformations applied.
 
           -t: put timestamps before each input line logged (these are put in
           comments).
 
 **%logstate**::
 
 	Print the status of the logging system.
 
 **%logstop**::
 
 	Fully stop logging and close log file.
 
         In order to start logging again, a new %logstart call needs to be made,
         possibly (though not necessarily) with a new filename, mode and other
         options.
 
 **%lsmagic**::
 
 	List currently available magic functions.
 
 **%macro**::
 
 	Define a set of input lines as a macro for future re-execution.
 
         Usage:\
           %macro [options] name n1-n2 n3-n4 ... n5 .. n6 ...
 
         Options:
         
           -r: use 'raw' input.  By default, the 'processed' history is used,
           so that magics are loaded in their transformed version to valid
           Python.  If this option is given, the raw input as typed as the
           command line is used instead.
 
         This will define a global variable called `name` which is a string
         made of joining the slices and lines you specify (n1,n2,... numbers
         above) from your input history into a single string. This variable
         acts like an automatic function which re-executes those lines as if
         you had typed them. You just type 'name' at the prompt and the code
         executes.
 
         The notation for indicating number ranges is: n1-n2 means 'use line
         numbers n1,...n2' (the endpoint is included).  That is, '5-7' means
         using the lines numbered 5,6 and 7.
 
         Note: as a 'hidden' feature, you can also use traditional python slice
         notation, where N:M means numbers N through M-1.
 
         For example, if your history contains (%hist prints it):
         
           44: x=1\
           45: y=3\
           46: z=x+y\
           47: print x\
           48: a=5\
           49: print 'x',x,'y',y\
 
         you can create a macro with lines 44 through 47 (included) and line 49
         called my_macro with:
 
           In [51]: %macro my_macro 44-47 49
 
         Now, typing `my_macro` (without quotes) will re-execute all this code
         in one pass.
 
         You don't need to give the line-numbers in order, and any given line
         number can appear multiple times. You can assemble macros with any
         lines from your input history in any order.
 
         The macro is a simple object which holds its value in an attribute,
         but IPython's display system checks for macros and executes them as
         code instead of printing them when you type their name.
 
         You can view a macro's contents by explicitly printing it with:
         
           'print macro_name'.
 
         For one-off cases which DON'T contain magic function calls in them you
         can obtain similar results by explicitly executing slices from your
         input history with:
 
           In [60]: exec In[44:48]+In[49]
 
 **%magic**::
 
 	Print information about the magic function system.
 
 **%mglob**::
 
 	    This program allows specifying filenames with "mglob" mechanism.
     Supported syntax in globs (wilcard matching patterns)::
     
      *.cpp ?ellowo*                
          - obvious. Differs from normal glob in that dirs are not included.
            Unix users might want to write this as: "*.cpp" "?ellowo*"
      rec:/usr/share=*.txt,*.doc    
          - get all *.txt and *.doc under /usr/share, 
            recursively
      rec:/usr/share
          - All files under /usr/share, recursively
      rec:*.py
          - All .py files under current working dir, recursively
      foo                           
          - File or dir foo
      !*.bak readme*                   
          - readme*, exclude files ending with .bak
      !.svn/ !.hg/ !*_Data/ rec:.
          - Skip .svn, .hg, foo_Data dirs (and their subdirs) in recurse.
            Trailing / is the key, \ does not work!
      dir:foo                       
          - the directory foo if it exists (not files in foo)
      dir:*                         
          - all directories in current folder
      foo.py bar.* !h* rec:*.py
          - Obvious. !h* exclusion only applies for rec:*.py.
            foo.py is *not* included twice.
      @filelist.txt
          - All files listed in 'filelist.txt' file, on separate lines.
 
 **%page**::
 
 	Pretty print the object and display it through a pager.
         
         %page [options] OBJECT
 
         If no object is given, use _ (last output).
         
         Options:
 
           -r: page str(object), don't pretty-print it.
 
 **%pdb**::
 
 	Control the automatic calling of the pdb interactive debugger.
 
         Call as '%pdb on', '%pdb 1', '%pdb off' or '%pdb 0'. If called without
         argument it works as a toggle.
 
         When an exception is triggered, IPython can optionally call the
         interactive pdb debugger after the traceback printout. %pdb toggles
         this feature on and off.
 
         The initial state of this feature is set in your ipythonrc
         configuration file (the variable is called 'pdb').
 
         If you want to just activate the debugger AFTER an exception has fired,
         without having to type '%pdb on' and rerunning your code, you can use
         the %debug magic.
 
 **%pdef**::
 
 	Print the definition header for any callable object.
 
         If the object is a class, print the constructor information.
 
 **%pdoc**::
 
 	Print the docstring for an object.
 
         If the given object is a class, it will print both the class and the
         constructor docstrings.
 
 **%pfile**::
 
 	Print (or run through pager) the file where an object is defined.
 
         The file opens at the line where the object definition begins. IPython
         will honor the environment variable PAGER if set, and otherwise will
         do its best to print the file in a convenient form.
 
         If the given argument is not an object currently defined, IPython will
         try to interpret it as a filename (automatically adding a .py extension
         if needed). You can thus use %pfile as a syntax highlighting code
         viewer.
 
 **%pinfo**::
 
 	Provide detailed information about an object.
     
         '%pinfo object' is just a synonym for object? or ?object.
 
 **%popd**::
 
 	Change to directory popped off the top of the stack.
 
 **%profile**::
 
 	Print your currently active IPyhton profile.
 
 **%prun**::
 
 	Run a statement through the python code profiler.
 
         Usage:\
           %prun [options] statement
 
         The given statement (which doesn't require quote marks) is run via the
         python profiler in a manner similar to the profile.run() function.
         Namespaces are internally managed to work correctly; profile.run
         cannot be used in IPython because it makes certain assumptions about
         namespaces which do not hold under IPython.
 
         Options:
 
         -l <limit>: you can place restrictions on what or how much of the
         profile gets printed. The limit value can be:
 
           * A string: only information for function names containing this string
           is printed.
 
           * An integer: only these many lines are printed.
 
           * A float (between 0 and 1): this fraction of the report is printed
           (for example, use a limit of 0.4 to see the topmost 40% only).
 
         You can combine several limits with repeated use of the option. For
         example, '-l __init__ -l 5' will print only the topmost 5 lines of
         information about class constructors.
 
         -r: return the pstats.Stats object generated by the profiling. This
         object has all the information about the profile in it, and you can
         later use it for further analysis or in other functions.
 
        -s <key>: sort profile by given key. You can provide more than one key
         by using the option several times: '-s key1 -s key2 -s key3...'. The
         default sorting key is 'time'.
 
         The following is copied verbatim from the profile documentation
         referenced below:
 
         When more than one key is provided, additional keys are used as
         secondary criteria when the there is equality in all keys selected
         before them.
         
         Abbreviations can be used for any key names, as long as the
         abbreviation is unambiguous.  The following are the keys currently
         defined:
 
                 Valid Arg       Meaning\
                   "calls"      call count\
                   "cumulative" cumulative time\
                   "file"       file name\
                   "module"     file name\
                   "pcalls"     primitive call count\
                   "line"       line number\
                   "name"       function name\
                   "nfl"        name/file/line\
                   "stdname"    standard name\
                   "time"       internal time
 
         Note that all sorts on statistics are in descending order (placing
         most time consuming items first), where as name, file, and line number
         searches are in ascending order (i.e., alphabetical). The subtle
         distinction between "nfl" and "stdname" is that the standard name is a
         sort of the name as printed, which means that the embedded line
         numbers get compared in an odd way.  For example, lines 3, 20, and 40
         would (if the file names were the same) appear in the string order
         "20" "3" and "40".  In contrast, "nfl" does a numeric compare of the
         line numbers.  In fact, sort_stats("nfl") is the same as
         sort_stats("name", "file", "line").
 
         -T <filename>: save profile results as shown on screen to a text
         file. The profile is still shown on screen.
 
         -D <filename>: save (via dump_stats) profile statistics to given
         filename. This data is in a format understod by the pstats module, and
         is generated by a call to the dump_stats() method of profile
         objects. The profile is still shown on screen.
 
         If you want to run complete programs under the profiler's control, use
         '%run -p [prof_opts] filename.py [args to program]' where prof_opts
         contains profiler specific options as described here.
         
         You can read the complete documentation for the profile module with:\
           In [1]: import profile; profile.help()
 
 **%psearch**::
 
 	Search for object in namespaces by wildcard.
 
         %psearch [options] PATTERN [OBJECT TYPE]
 
         Note: ? can be used as a synonym for %psearch, at the beginning or at
         the end: both a*? and ?a* are equivalent to '%psearch a*'.  Still, the
         rest of the command line must be unchanged (options come first), so
         for example the following forms are equivalent
 
         %psearch -i a* function
         -i a* function?
         ?-i a* function
 
         Arguments:
         
           PATTERN
 
           where PATTERN is a string containing * as a wildcard similar to its
           use in a shell.  The pattern is matched in all namespaces on the
           search path. By default objects starting with a single _ are not
           matched, many IPython generated objects have a single
           underscore. The default is case insensitive matching. Matching is
           also done on the attributes of objects and not only on the objects
           in a module.
 
           [OBJECT TYPE]
 
           Is the name of a python type from the types module. The name is
           given in lowercase without the ending type, ex. StringType is
           written string. By adding a type here only objects matching the
           given type are matched. Using all here makes the pattern match all
           types (this is the default).
 
         Options:
 
           -a: makes the pattern match even objects whose names start with a
           single underscore.  These names are normally ommitted from the
           search.
 
           -i/-c: make the pattern case insensitive/sensitive.  If neither of
           these options is given, the default is read from your ipythonrc
           file.  The option name which sets this value is
           'wildcards_case_sensitive'.  If this option is not specified in your
           ipythonrc file, IPython's internal default is to do a case sensitive
           search.
 
           -e/-s NAMESPACE: exclude/search a given namespace.  The pattern you
           specifiy can be searched in any of the following namespaces:
           'builtin', 'user', 'user_global','internal', 'alias', where
           'builtin' and 'user' are the search defaults.  Note that you should
           not use quotes when specifying namespaces.
 
           'Builtin' contains the python module builtin, 'user' contains all
           user data, 'alias' only contain the shell aliases and no python
           objects, 'internal' contains objects used by IPython.  The
           'user_global' namespace is only used by embedded IPython instances,
           and it contains module-level globals.  You can add namespaces to the
           search with -s or exclude them with -e (these options can be given
           more than once).
     
         Examples:
        
         %psearch a*            -> objects beginning with an a
         %psearch -e builtin a* -> objects NOT in the builtin space starting in a
         %psearch a* function   -> all functions beginning with an a
         %psearch re.e*         -> objects beginning with an e in module re
         %psearch r*.e*         -> objects that start with e in modules starting in r
         %psearch r*.* string   -> all strings in modules beginning with r
 
         Case sensitve search:
        
         %psearch -c a*         list all object beginning with lower case a
 
         Show objects beginning with a single _:
        
         %psearch -a _*         list objects beginning with a single underscore
 
 **%psource**::
 
 	Print (or run through pager) the source code for an object.
 
 **%pushd**::
 
 	Place the current dir on stack and change directory.
         
         Usage:\
           %pushd ['dirname']
 
 **%pwd**::
 
 	Return the current working directory path.
 
 **%pycat**::
 
 	Show a syntax-highlighted file through a pager.
 
         This magic is similar to the cat utility, but it will assume the file
         to be Python source and will show it with syntax highlighting.
 
 **%quickref**::
 
 	 Show a quick reference sheet
 
 **%quit**::
 
 	Exit IPython, confirming if configured to do so (like %exit)
 
 **%r**::
 
 	Repeat previous input.
 
         Note: Consider using the more powerfull %rep instead!
         
         If given an argument, repeats the previous command which starts with
         the same string, otherwise it just repeats the previous input.
 
         Shell escaped commands (with ! as first character) are not recognized
         by this system, only pure python code and magic commands.
 
 **%rehashdir**::
 
 	 Add executables in all specified dirs to alias table
      
     Usage:
 
     %rehashdir c:/bin;c:/tools
       - Add all executables under c:/bin and c:/tools to alias table, in 
       order to make them directly executable from any directory.
         
       Without arguments, add all executables in current directory.
 
 **%rehashx**::
 
 	Update the alias table with all executable files in $PATH.
 
         This version explicitly checks that every entry in $PATH is a file
         with execute access (os.X_OK), so it is much slower than %rehash.
 
         Under Windows, it checks executability as a match agains a
         '|'-separated string of extensions, stored in the IPython config
         variable win_exec_ext.  This defaults to 'exe|com|bat'.
         
         This function also resets the root module cache of module completer,
         used on slow filesystems.
 
 **%rep**::
 
 	 Repeat a command, or get command to input line for editing
 
     - %rep (no arguments):
     
     Place a string version of last computation result (stored in the special '_'
     variable) to the next input prompt. Allows you to create elaborate command
     lines without using copy-paste::
     
         $ l = ["hei", "vaan"]       
         $ "".join(l)        
         ==> heivaan        
         $ %rep        
         $ heivaan_ <== cursor blinking    
     
     %rep 45
     
     Place history line 45 to next input prompt. Use %hist to find out the
     number.
     
     %rep 1-4 6-7 3
     
     Repeat the specified lines immediately. Input slice syntax is the same as
     in %macro and %save.
     
     %rep foo
     
     Place the most recent line that has the substring "foo" to next input.
     (e.g. 'svn ci -m foobar').
 
 **%reset**::
 
 	Resets the namespace by removing all names defined by the user.
 
         Input/Output history are left around in case you need them.
 
 **%run**::
 
 	Run the named file inside IPython as a program.
 
         Usage:\
           %run [-n -i -t [-N<N>] -d [-b<N>] -p [profile options]] file [args]
         
         Parameters after the filename are passed as command-line arguments to
         the program (put in sys.argv). Then, control returns to IPython's
         prompt.
 
         This is similar to running at a system prompt:\
           $ python file args\
         but with the advantage of giving you IPython's tracebacks, and of
         loading all variables into your interactive namespace for further use
         (unless -p is used, see below).
 
         The file is executed in a namespace initially consisting only of
         __name__=='__main__' and sys.argv constructed as indicated. It thus
         sees its environment as if it were being run as a stand-alone program
         (except for sharing global objects such as previously imported
         modules). But after execution, the IPython interactive namespace gets
         updated with all variables defined in the program (except for __name__
         and sys.argv). This allows for very convenient loading of code for
         interactive work, while giving each program a 'clean sheet' to run in.
 
         Options:
         
         -n: __name__ is NOT set to '__main__', but to the running file's name
         without extension (as python does under import).  This allows running
         scripts and reloading the definitions in them without calling code
         protected by an ' if __name__ == "__main__" ' clause.
 
         -i: run the file in IPython's namespace instead of an empty one. This
         is useful if you are experimenting with code written in a text editor
         which depends on variables defined interactively.
 
         -e: ignore sys.exit() calls or SystemExit exceptions in the script
         being run.  This is particularly useful if IPython is being used to
         run unittests, which always exit with a sys.exit() call.  In such
         cases you are interested in the output of the test results, not in
         seeing a traceback of the unittest module.
 
         -t: print timing information at the end of the run.  IPython will give
         you an estimated CPU time consumption for your script, which under
         Unix uses the resource module to avoid the wraparound problems of
         time.clock().  Under Unix, an estimate of time spent on system tasks
         is also given (for Windows platforms this is reported as 0.0).
 
         If -t is given, an additional -N<N> option can be given, where <N>
         must be an integer indicating how many times you want the script to
         run.  The final timing report will include total and per run results.
 
         For example (testing the script uniq_stable.py):
 
             In [1]: run -t uniq_stable
 
             IPython CPU timings (estimated):\
               User  :    0.19597 s.\
               System:        0.0 s.\
 
             In [2]: run -t -N5 uniq_stable
 
             IPython CPU timings (estimated):\
             Total runs performed: 5\
               Times :      Total       Per run\
               User  :   0.910862 s,  0.1821724 s.\
               System:        0.0 s,        0.0 s.
 
         -d: run your program under the control of pdb, the Python debugger.
         This allows you to execute your program step by step, watch variables,
         etc.  Internally, what IPython does is similar to calling:
         
           pdb.run('execfile("YOURFILENAME")')
 
         with a breakpoint set on line 1 of your file.  You can change the line
         number for this automatic breakpoint to be <N> by using the -bN option
         (where N must be an integer).  For example:
 
           %run -d -b40 myscript
 
         will set the first breakpoint at line 40 in myscript.py.  Note that
         the first breakpoint must be set on a line which actually does
         something (not a comment or docstring) for it to stop execution.
 
         When the pdb debugger starts, you will see a (Pdb) prompt.  You must
         first enter 'c' (without qoutes) to start execution up to the first
         breakpoint.
 
         Entering 'help' gives information about the use of the debugger.  You
         can easily see pdb's full documentation with "import pdb;pdb.help()"
         at a prompt.
 
         -p: run program under the control of the Python profiler module (which
         prints a detailed report of execution times, function calls, etc).
 
         You can pass other options after -p which affect the behavior of the
         profiler itself. See the docs for %prun for details.
 
         In this mode, the program's variables do NOT propagate back to the
         IPython interactive namespace (because they remain in the namespace
         where the profiler executes them).
 
         Internally this triggers a call to %prun, see its documentation for
         details on the options available specifically for profiling.
 
         There is one special usage for which the text above doesn't apply:
         if the filename ends with .ipy, the file is run as ipython script,
         just as if the commands were written on IPython prompt.
 
 **%runlog**::
 
 	Run files as logs.
 
         Usage:\
           %runlog file1 file2 ...
 
         Run the named files (treating them as log files) in sequence inside
         the interpreter, and return to the prompt.  This is much slower than
         %run because each line is executed in a try/except block, but it
         allows running files with syntax errors in them.
 
         Normally IPython will guess when a file is one of its own logfiles, so
         you can typically use %run even for logs. This shorthand allows you to
         force any file to be treated as a log file.
 
 **%save**::
 
 	Save a set of lines to a given filename.
 
         Usage:\
           %save [options] filename n1-n2 n3-n4 ... n5 .. n6 ...
 
         Options:
         
           -r: use 'raw' input.  By default, the 'processed' history is used,
           so that magics are loaded in their transformed version to valid
           Python.  If this option is given, the raw input as typed as the
           command line is used instead.
 
         This function uses the same syntax as %macro for line extraction, but
         instead of creating a macro it saves the resulting string to the
         filename you specify.
 
         It adds a '.py' extension to the file if you don't do so yourself, and
         it asks for confirmation before overwriting existing files.
 
 **%sc**::
 
 	Shell capture - execute a shell command and capture its output.
 
         DEPRECATED. Suboptimal, retained for backwards compatibility.
         
         You should use the form 'var = !command' instead. Example:
          
          "%sc -l myfiles = ls ~" should now be written as
             
          "myfiles = !ls ~"
          
         myfiles.s, myfiles.l and myfiles.n still apply as documented
         below.
 
         --
         %sc [options] varname=command
 
         IPython will run the given command using commands.getoutput(), and
         will then update the user's interactive namespace with a variable
         called varname, containing the value of the call.  Your command can
         contain shell wildcards, pipes, etc.
 
         The '=' sign in the syntax is mandatory, and the variable name you
         supply must follow Python's standard conventions for valid names.
         
         (A special format without variable name exists for internal use)
 
         Options:
 
           -l: list output.  Split the output on newlines into a list before
           assigning it to the given variable.  By default the output is stored
           as a single string.
 
           -v: verbose.  Print the contents of the variable.
 
         In most cases you should not need to split as a list, because the
         returned value is a special type of string which can automatically
         provide its contents either as a list (split on newlines) or as a
         space-separated string.  These are convenient, respectively, either
         for sequential processing or to be passed to a shell command.
 
         For example:
 
             # Capture into variable a
             In [9]: sc a=ls *py
 
             # a is a string with embedded newlines
             In [10]: a
             Out[10]: 'setup.py win32_manual_post_install.py'
 
             # which can be seen as a list:
             In [11]: a.l
             Out[11]: ['setup.py', 'win32_manual_post_install.py']
 
             # or as a whitespace-separated string:
             In [12]: a.s
             Out[12]: 'setup.py win32_manual_post_install.py'
 
             # a.s is useful to pass as a single command line:
             In [13]: !wc -l $a.s
               146 setup.py
               130 win32_manual_post_install.py
               276 total
 
             # while the list form is useful to loop over:
             In [14]: for f in a.l:
                ....:      !wc -l $f
                ....:
             146 setup.py
             130 win32_manual_post_install.py
 
         Similiarly, the lists returned by the -l option are also special, in
         the sense that you can equally invoke the .s attribute on them to
         automatically get a whitespace-separated string from their contents:
 
             In [1]: sc -l b=ls *py
 
             In [2]: b
             Out[2]: ['setup.py', 'win32_manual_post_install.py']
 
             In [3]: b.s
             Out[3]: 'setup.py win32_manual_post_install.py'
 
         In summary, both the lists and strings used for ouptut capture have
         the following special attributes:
 
             .l (or .list) : value as list.
             .n (or .nlstr): value as newline-separated string.
             .s (or .spstr): value as space-separated string.
 
 **%store**::
 
 	Lightweight persistence for python variables.
 
     Example:
     
     ville@badger[~]|1> A = ['hello',10,'world']\
     ville@badger[~]|2> %store A\
     ville@badger[~]|3> Exit
     
     (IPython session is closed and started again...)
     
     ville@badger:~$ ipython -p pysh\
     ville@badger[~]|1> print A
     
     ['hello', 10, 'world']
     
     Usage:
     
     %store          - Show list of all variables and their current values\
     %store <var>    - Store the *current* value of the variable to disk\
     %store -d <var> - Remove the variable and its value from storage\
     %store -z       - Remove all variables from storage\
     %store -r       - Refresh all variables from store (delete current vals)\
     %store foo >a.txt  - Store value of foo to new file a.txt\
     %store foo >>a.txt - Append value of foo to file a.txt\   
     
     It should be noted that if you change the value of a variable, you
     need to %store it again if you want to persist the new value.
     
     Note also that the variables will need to be pickleable; most basic
     python types can be safely %stored.
     
     Also aliases can be %store'd across sessions.
 
 **%sx**::
 
 	Shell execute - run a shell command and capture its output.
 
         %sx command
 
         IPython will run the given command using commands.getoutput(), and
         return the result formatted as a list (split on '\n').  Since the
         output is _returned_, it will be stored in ipython's regular output
         cache Out[N] and in the '_N' automatic variables.
 
         Notes:
 
         1) If an input line begins with '!!', then %sx is automatically
         invoked.  That is, while:
           !ls
         causes ipython to simply issue system('ls'), typing
           !!ls
         is a shorthand equivalent to:
           %sx ls
         
         2) %sx differs from %sc in that %sx automatically splits into a list,
         like '%sc -l'.  The reason for this is to make it as easy as possible
         to process line-oriented shell output via further python commands.
         %sc is meant to provide much finer control, but requires more
         typing.
 
         3) Just like %sc -l, this is a list with special attributes:
 
           .l (or .list) : value as list.
           .n (or .nlstr): value as newline-separated string.
           .s (or .spstr): value as whitespace-separated string.
 
         This is very useful when trying to use such lists as arguments to
         system commands.
 
 **%system_verbose**::
 
 	Set verbose printing of system calls.
 
         If called without an argument, act as a toggle
 
 **%time**::
 
 	Time execution of a Python statement or expression.
 
         The CPU and wall clock times are printed, and the value of the
         expression (if any) is returned.  Note that under Win32, system time
         is always reported as 0, since it can not be measured.
 
         This function provides very basic timing functionality.  In Python
         2.3, the timeit module offers more control and sophistication, so this
         could be rewritten to use it (patches welcome).
         
         Some examples:
 
           In [1]: time 2**128
           CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s
           Wall time: 0.00
           Out[1]: 340282366920938463463374607431768211456L
 
           In [2]: n = 1000000
 
           In [3]: time sum(range(n))
           CPU times: user 1.20 s, sys: 0.05 s, total: 1.25 s
           Wall time: 1.37
           Out[3]: 499999500000L
 
           In [4]: time print 'hello world'
           hello world
           CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s
           Wall time: 0.00
 
           Note that the time needed by Python to compile the given expression
           will be reported if it is more than 0.1s.  In this example, the
           actual exponentiation is done by Python at compilation time, so while
           the expression can take a noticeable amount of time to compute, that
           time is purely due to the compilation:
 
           In [5]: time 3**9999;
           CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s
           Wall time: 0.00 s
 
           In [6]: time 3**999999;
           CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s
           Wall time: 0.00 s
           Compiler : 0.78 s
 
 **%timeit**::
 
 	Time execution of a Python statement or expression
 
         Usage:\
           %timeit [-n<N> -r<R> [-t|-c]] statement
 
         Time execution of a Python statement or expression using the timeit
         module.
 
         Options:
         -n<N>: execute the given statement <N> times in a loop. If this value
         is not given, a fitting value is chosen. 
         
         -r<R>: repeat the loop iteration <R> times and take the best result.
         Default: 3
         
         -t: use time.time to measure the time, which is the default on Unix.
         This function measures wall time.
         
         -c: use time.clock to measure the time, which is the default on
         Windows and measures wall time. On Unix, resource.getrusage is used
         instead and returns the CPU user time.
 
         -p<P>: use a precision of <P> digits to display the timing result.
         Default: 3
 
         
         Examples:\
           In [1]: %timeit pass
           10000000 loops, best of 3: 53.3 ns per loop
 
           In [2]: u = None
 
           In [3]: %timeit u is None
           10000000 loops, best of 3: 184 ns per loop
 
           In [4]: %timeit -r 4 u == None
           1000000 loops, best of 4: 242 ns per loop
 
           In [5]: import time
 
           In [6]: %timeit -n1 time.sleep(2)
           1 loops, best of 3: 2 s per loop
           
 
         The times reported by %timeit will be slightly higher than those
         reported by the timeit.py script when variables are accessed. This is
         due to the fact that %timeit executes the statement in the namespace
         of the shell, compared with timeit.py, which uses a single setup
         statement to import function or create variables. Generally, the bias
         does not matter as long as results from timeit.py are not mixed with
         those from %timeit.
 
 **%unalias**::
 
 	Remove an alias
 
 **%upgrade**::
 
 	 Upgrade your IPython installation
         
         This will copy the config files that don't yet exist in your 
         ipython dir from the system config dir. Use this after upgrading 
         IPython if you don't wish to delete your .ipython dir.
 
         Call with -nolegacy to get rid of ipythonrc* files (recommended for
         new users)
 
 **%which**::
 
 	 %which <cmd> => search PATH for files matching cmd. Also scans aliases.
 
     Traverses PATH and prints all files (not just executables!) that match the
     pattern on command line. Probably more useful in finding stuff
     interactively than 'which', which only prints the first matching item.
     
     Also discovers and expands aliases, so you'll see what will be executed
     when you call an alias.
     
     Example:
     
     [~]|62> %which d
     d -> ls -F --color=auto
       == c:\cygwin\bin\ls.exe
     c:\cygwin\bin\d.exe
     
     [~]|64> %which diff*
     diff3 -> diff3
       == c:\cygwin\bin\diff3.exe
     diff -> diff
       == c:\cygwin\bin\diff.exe
     c:\cygwin\bin\diff.exe
     c:\cygwin\bin\diff3.exe
 
 **%who**::
 
 	Print all interactive variables, with some minimal formatting.
 
         If any arguments are given, only variables whose type matches one of
         these are printed.  For example:
 
           %who function str
 
         will only list functions and strings, excluding all other types of
         variables.  To find the proper type names, simply use type(var) at a
         command line to see how python prints type names.  For example:
 
           In [1]: type('hello')\
           Out[1]: <type 'str'>
 
         indicates that the type name for strings is 'str'.
 
         %who always excludes executed names loaded through your configuration
         file and things which are internal to IPython.
 
         This is deliberate, as typically you may load many modules and the
         purpose of %who is to show you only what you've manually defined.
 
 **%who_ls**::
 
 	Return a sorted list of all interactive variables.
 
         If arguments are given, only variables of types matching these
         arguments are returned.
 
 **%whos**::
 
 	Like %who, but gives some extra information about each variable.
 
         The same type filtering of %who can be applied here.
 
         For all variables, the type is printed. Additionally it prints:
         
           - For {},[],(): their length.
 
           - For numpy and Numeric arrays, a summary with shape, number of
           elements, typecode and size in memory.
 
           - Everything else: a string representation, snipping their middle if
           too long.
 
 **%xmode**::
 
 	Switch modes for the exception handlers.
 
         Valid modes: Plain, Context and Verbose.
 
         If called without arguments, acts as a toggle.
 
 .. magic_end
 
 Access to the standard Python help
 ----------------------------------
 
 As of Python 2.1, a help system is available with access to object docstrings
 and the Python manuals. Simply type 'help' (no quotes) to access it. You can
 also type help(object) to obtain information about a given object, and
 help('keyword') for information on a keyword. As noted :ref:`here
 <accessing_help>`, you need to properly configure your environment variable
 PYTHONDOCS for this feature to work correctly.
 
 .. _dynamic_object_info:
 
 Dynamic object information
 --------------------------
 
 Typing ?word or word? prints detailed information about an object. If
 certain strings in the object are too long (docstrings, code, etc.) they
 get snipped in the center for brevity. This system gives access variable
 types and values, full source code for any object (if available),
 function prototypes and other useful information.
 
 Typing ??word or word?? gives access to the full information without
 snipping long strings. Long strings are sent to the screen through the
 less pager if longer than the screen and printed otherwise. On systems
 lacking the less command, IPython uses a very basic internal pager.
 
 The following magic functions are particularly useful for gathering
 information about your working environment. You can get more details by
 typing %magic or querying them individually (use %function_name? with or
 without the %), this is just a summary:
 
     * **%pdoc <object>**: Print (or run through a pager if too long) the
       docstring for an object. If the given object is a class, it will
       print both the class and the constructor docstrings.
     * **%pdef <object>**: Print the definition header for any callable
       object. If the object is a class, print the constructor information.
     * **%psource <object>**: Print (or run through a pager if too long)
       the source code for an object.
     * **%pfile <object>**: Show the entire source file where an object was
       defined via a pager, opening it at the line where the object
       definition begins.
     * **%who/%whos**: These functions give information about identifiers
       you have defined interactively (not things you loaded or defined
       in your configuration files). %who just prints a list of
       identifiers and %whos prints a table with some basic details about
       each identifier.
 
 Note that the dynamic object information functions (?/??, %pdoc, %pfile,
 %pdef, %psource) give you access to documentation even on things which
 are not really defined as separate identifiers. Try for example typing
 {}.get? or after doing import os, type os.path.abspath??.
 
 
 .. _readline:
 
 Readline-based features
 -----------------------
 
 These features require the GNU readline library, so they won't work if
 your Python installation lacks readline support. We will first describe
 the default behavior IPython uses, and then how to change it to suit
 your preferences.
 
 
 Command line completion
 +++++++++++++++++++++++
 
 At any time, hitting TAB will complete any available python commands or
 variable names, and show you a list of the possible completions if
 there's no unambiguous one. It will also complete filenames in the
 current directory if no python names match what you've typed so far.
 
 
 Search command history
 ++++++++++++++++++++++
 
 IPython provides two ways for searching through previous input and thus
 reduce the need for repetitive typing:
 
    1. Start typing, and then use Ctrl-p (previous,up) and Ctrl-n
       (next,down) to search through only the history items that match
       what you've typed so far. If you use Ctrl-p/Ctrl-n at a blank
       prompt, they just behave like normal arrow keys.
    2. Hit Ctrl-r: opens a search prompt. Begin typing and the system
       searches your history for lines that contain what you've typed so
       far, completing as much as it can.
 
 
 Persistent command history across sessions
 ++++++++++++++++++++++++++++++++++++++++++
 
 IPython will save your input history when it leaves and reload it next
 time you restart it. By default, the history file is named
 $IPYTHONDIR/history, but if you've loaded a named profile,
 '-PROFILE_NAME' is appended to the name. This allows you to keep
 separate histories related to various tasks: commands related to
 numerical work will not be clobbered by a system shell history, for
 example.
 
 
 Autoindent
 ++++++++++
 
 IPython can recognize lines ending in ':' and indent the next line,
 while also un-indenting automatically after 'raise' or 'return'.
 
 This feature uses the readline library, so it will honor your ~/.inputrc
 configuration (or whatever file your INPUTRC variable points to). Adding
 the following lines to your .inputrc file can make indenting/unindenting
 more convenient (M-i indents, M-u unindents)::
 
     $if Python 
     "\M-i": "    "  
     "\M-u": "\d\d\d\d"  
     $endif
 
 Note that there are 4 spaces between the quote marks after "M-i" above.
 
 Warning: this feature is ON by default, but it can cause problems with
 the pasting of multi-line indented code (the pasted code gets
 re-indented on each line). A magic function %autoindent allows you to
 toggle it on/off at runtime. You can also disable it permanently on in
 your ipythonrc file (set autoindent 0).
 
 
 Customizing readline behavior
 +++++++++++++++++++++++++++++
 
 All these features are based on the GNU readline library, which has an
 extremely customizable interface. Normally, readline is configured via a
 file which defines the behavior of the library; the details of the
 syntax for this can be found in the readline documentation available
 with your system or on the Internet. IPython doesn't read this file (if
 it exists) directly, but it does support passing to readline valid
 options via a simple interface. In brief, you can customize readline by
 setting the following options in your ipythonrc configuration file (note
 that these options can not be specified at the command line):
 
     * **readline_parse_and_bind**: this option can appear as many times as
       you want, each time defining a string to be executed via a
       readline.parse_and_bind() command. The syntax for valid commands
       of this kind can be found by reading the documentation for the GNU
       readline library, as these commands are of the kind which readline
       accepts in its configuration file.
     * **readline_remove_delims**: a string of characters to be removed
       from the default word-delimiters list used by readline, so that
       completions may be performed on strings which contain them. Do not
       change the default value unless you know what you're doing.
     * **readline_omit__names**: when tab-completion is enabled, hitting
       <tab> after a '.' in a name will complete all attributes of an
       object, including all the special methods whose names include
       double underscores (like __getitem__ or __class__). If you'd
       rather not see these names by default, you can set this option to
       1. Note that even when this option is set, you can still see those
       names by explicitly typing a _ after the period and hitting <tab>:
       'name._<tab>' will always complete attribute names starting with '_'.
       
       This option is off by default so that new users see all
       attributes of any objects they are dealing with.
 
 You will find the default values along with a corresponding detailed
 explanation in your ipythonrc file.
 
 
 Session logging and restoring
 -----------------------------
 
 You can log all input from a session either by starting IPython with the
 command line switches -log or -logfile (see :ref:`here <command_line_options>`)
 or by activating the logging at any moment with the magic function %logstart.
 
 Log files can later be reloaded with the -logplay option and IPython
 will attempt to 'replay' the log by executing all the lines in it, thus
 restoring the state of a previous session. This feature is not quite
 perfect, but can still be useful in many cases.
 
 The log files can also be used as a way to have a permanent record of
 any code you wrote while experimenting. Log files are regular text files
 which you can later open in your favorite text editor to extract code or
 to 'clean them up' before using them to replay a session.
 
 The %logstart function for activating logging in mid-session is used as
 follows:
 
 %logstart [log_name [log_mode]]
 
 If no name is given, it defaults to a file named 'log' in your
 IPYTHONDIR directory, in 'rotate' mode (see below).
 
 '%logstart name' saves to file 'name' in 'backup' mode. It saves your
 history up to that point and then continues logging.
 
 %logstart takes a second optional parameter: logging mode. This can be
 one of (note that the modes are given unquoted):
 
     * [over:] overwrite existing log_name.
     * [backup:] rename (if exists) to log_name~ and start log_name.
     * [append:] well, that says it.
     * [rotate:] create rotating logs log_name.1~, log_name.2~, etc.
 
 The %logoff and %logon functions allow you to temporarily stop and
 resume logging to a file which had previously been started with
 %logstart. They will fail (with an explanation) if you try to use them
 before logging has been started.
 
 .. _system_shell_access:
 
 System shell access
 -------------------
 
 Any input line beginning with a ! character is passed verbatim (minus
 the !, of course) to the underlying operating system. For example,
 typing !ls will run 'ls' in the current directory.
 
 Manual capture of command output
 --------------------------------
 
 If the input line begins with two exclamation marks, !!, the command is
 executed but its output is captured and returned as a python list, split
 on newlines. Any output sent by the subprocess to standard error is
 printed separately, so that the resulting list only captures standard
 output. The !! syntax is a shorthand for the %sx magic command.
 
 Finally, the %sc magic (short for 'shell capture') is similar to %sx,
 but allowing more fine-grained control of the capture details, and
 storing the result directly into a named variable. The direct use of 
 %sc is now deprecated, and you should ise the ``var = !cmd`` syntax
 instead.
 
 IPython also allows you to expand the value of python variables when
 making system calls. Any python variable or expression which you prepend
 with $ will get expanded before the system call is made::
 
     In [1]: pyvar='Hello world' 
     In [2]: !echo "A python variable: $pyvar"  
     A python variable: Hello world
 
 If you want the shell to actually see a literal $, you need to type it
 twice::
 
     In [3]: !echo "A system variable: $$HOME"  
     A system variable: /home/fperez
 
 You can pass arbitrary expressions, though you'll need to delimit them
 with {} if there is ambiguity as to the extent of the expression::
 
     In [5]: x=10 
     In [6]: y=20 
     In [13]: !echo $x+y  
     10+y  
     In [7]: !echo ${x+y}  
     30
 
 Even object attributes can be expanded::
 
     In [12]: !echo $sys.argv  
     [/home/fperez/usr/bin/ipython]
 
 
 System command aliases
 ----------------------
 
 The %alias magic function and the alias option in the ipythonrc
 configuration file allow you to define magic functions which are in fact
 system shell commands. These aliases can have parameters.
 
 '%alias alias_name cmd' defines 'alias_name' as an alias for 'cmd'
 
 Then, typing '%alias_name params' will execute the system command 'cmd
 params' (from your underlying operating system).
 
 You can also define aliases with parameters using %s specifiers (one per
 parameter). The following example defines the %parts function as an
 alias to the command 'echo first %s second %s' where each %s will be
 replaced by a positional parameter to the call to %parts::
 
     In [1]: alias parts echo first %s second %s 
     In [2]: %parts A B 
     first A second B  
     In [3]: %parts A  
     Incorrect number of arguments: 2 expected.  
     parts is an alias to: 'echo first %s second %s'
 
 If called with no parameters, %alias prints the table of currently
 defined aliases.
 
 The %rehash/rehashx magics allow you to load your entire $PATH as
 ipython aliases. See their respective docstrings (or sec. 6.2
 <#sec:magic> for further details).
 
 
 .. _dreload:
 
 Recursive reload
 ----------------
 
 The dreload function does a recursive reload of a module: changes made
 to the module since you imported will actually be available without
 having to exit.
 
 
 Verbose and colored exception traceback printouts
 -------------------------------------------------
 
 IPython provides the option to see very detailed exception tracebacks,
 which can be especially useful when debugging large programs. You can
 run any Python file with the %run function to benefit from these
 detailed tracebacks. Furthermore, both normal and verbose tracebacks can
 be colored (if your terminal supports it) which makes them much easier
 to parse visually.
 
 See the magic xmode and colors functions for details (just type %magic).
 
 These features are basically a terminal version of Ka-Ping Yee's cgitb
 module, now part of the standard Python library.
 
 
 .. _input_caching:
 
 Input caching system
 --------------------
 
 IPython offers numbered prompts (In/Out) with input and output caching
 (also referred to as 'input history'). All input is saved and can be 
 retrieved as variables (besides the usual arrow key recall), in 
 addition to the %rep magic command that brings a history entry
 up for editing on the next  command line.
 
 The following GLOBAL variables always exist (so don't overwrite them!):
 _i: stores previous input. _ii: next previous. _iii: next-next previous.
 _ih : a list of all input _ih[n] is the input from line n and this list
 is aliased to the global variable In. If you overwrite In with a
 variable of your own, you can remake the assignment to the internal list
 with a simple 'In=_ih'.
 
 Additionally, global variables named _i<n> are dynamically created (<n>
 being the prompt counter), such that
 _i<n> == _ih[<n>] == In[<n>].
 
 For example, what you typed at prompt 14 is available as _i14, _ih[14]
 and In[14].
 
 This allows you to easily cut and paste multi line interactive prompts
 by printing them out: they print like a clean string, without prompt
 characters. You can also manipulate them like regular variables (they
 are strings), modify or exec them (typing 'exec _i9' will re-execute the
 contents of input prompt 9, 'exec In[9:14]+In[18]' will re-execute lines
 9 through 13 and line 18).
 
 You can also re-execute multiple lines of input easily by using the
 magic %macro function (which automates the process and allows
 re-execution without having to type 'exec' every time). The macro system
 also allows you to re-execute previous lines which include magic
 function calls (which require special processing). Type %macro? or see
 sec. 6.2 <#sec:magic> for more details on the macro system.
 
 A history function %hist allows you to see any part of your input
 history by printing a range of the _i variables.
 
 You can also search ('grep') through your history by typing 
 '%hist -g somestring'. This also searches through the so called *shadow history*,
 which remembers all the commands (apart from multiline code blocks)
 you have ever entered. Handy for searching for svn/bzr URL's, IP adrresses
 etc. You can bring shadow history entries listed by '%hist -g' up for editing 
 (or re-execution by just pressing ENTER) with %rep command. Shadow history 
 entries are not available as _iNUMBER variables, and they are identified by 
 the '0' prefix in %hist -g output. That is, history entry 12 is a normal 
 history entry, but 0231 is a shadow history entry.
 
 Shadow history was added because the readline history is inherently very
 unsafe - if you have multiple IPython sessions open, the last session 
 to close will overwrite the history of previountly closed session. Likewise,
 if a crash occurs, history is never saved, whereas shadow history entries
 are added after entering every command (so a command executed 
 in another IPython session is immediately available in other IPython 
 sessions that are open).
 
 To conserve space, a command can exist in shadow history only once - it doesn't 
 make sense to store a common line like "cd .." a thousand times. The idea is 
 mainly to provide a reliable place where valuable, hard-to-remember commands can 
 always be retrieved, as opposed to providing an exact sequence of commands
 you have entered in actual order.
 
 Because shadow history has all the commands you have ever executed,
 time taken by %hist -g will increase oven time. If it ever starts to take
 too long (or it ends up containing sensitive information like passwords), 
 clear the shadow history by `%clear shadow_nuke`.
 
 Time taken to add entries to shadow history should be negligible, but 
 in any case, if you start noticing performance degradation after using 
 IPython for a long time (or running a script that floods the shadow history!), 
 you can 'compress' the shadow history by executing 
 `%clear shadow_compress`. In practice, this should never be necessary
 in normal use.
 
 .. _output_caching:
 
 Output caching system
 ---------------------
 
 For output that is returned from actions, a system similar to the input
 cache exists but using _ instead of _i. Only actions that produce a
 result (NOT assignments, for example) are cached. If you are familiar
 with Mathematica, IPython's _ variables behave exactly like
 Mathematica's % variables.
 
 The following GLOBAL variables always exist (so don't overwrite them!):
 
     * [_] (a single underscore) : stores previous output, like Python's
       default interpreter.
     * [__] (two underscores): next previous.
     * [___] (three underscores): next-next previous.
 
 Additionally, global variables named _<n> are dynamically created (<n>
 being the prompt counter), such that the result of output <n> is always
 available as _<n> (don't use the angle brackets, just the number, e.g.
 _21).
 
 These global variables are all stored in a global dictionary (not a
 list, since it only has entries for lines which returned a result)
 available under the names _oh and Out (similar to _ih and In). So the
 output from line 12 can be obtained as _12, Out[12] or _oh[12]. If you
 accidentally overwrite the Out variable you can recover it by typing
 'Out=_oh' at the prompt.
 
 This system obviously can potentially put heavy memory demands on your
 system, since it prevents Python's garbage collector from removing any
 previously computed results. You can control how many results are kept
 in memory with the option (at the command line or in your ipythonrc
 file) cache_size. If you set it to 0, the whole system is completely
 disabled and the prompts revert to the classic '>>>' of normal Python.
 
 
 Directory history
 -----------------
 
 Your history of visited directories is kept in the global list _dh, and
 the magic %cd command can be used to go to any entry in that list. The
 %dhist command allows you to view this history. Do ``cd -<TAB`` to
 conventiently view the directory history.
 
 
 Automatic parentheses and quotes
 --------------------------------
 
 These features were adapted from Nathan Gray's LazyPython. They are
 meant to allow less typing for common situations.
 
 
 Automatic parentheses
 ---------------------
 
 Callable objects (i.e. functions, methods, etc) can be invoked like this
 (notice the commas between the arguments)::
 
     >>> callable_ob arg1, arg2, arg3
 
 and the input will be translated to this::
 
     -> callable_ob(arg1, arg2, arg3)
 
 You can force automatic parentheses by using '/' as the first character
 of a line. For example::
 
     >>> /globals # becomes 'globals()'
 
 Note that the '/' MUST be the first character on the line! This won't work::
 
     >>> print /globals # syntax error
 
 In most cases the automatic algorithm should work, so you should rarely
 need to explicitly invoke /. One notable exception is if you are trying
 to call a function with a list of tuples as arguments (the parenthesis
 will confuse IPython)::
 
     In [1]: zip (1,2,3),(4,5,6) # won't work
 
 but this will work::
 
     In [2]: /zip (1,2,3),(4,5,6) 
     ---> zip ((1,2,3),(4,5,6))  
     Out[2]= [(1, 4), (2, 5), (3, 6)]
 
 IPython tells you that it has altered your command line by displaying
 the new command line preceded by ->. e.g.::
 
     In [18]: callable list 
     ----> callable (list)
 
 
 Automatic quoting
 -----------------
 
 You can force automatic quoting of a function's arguments by using ','
 or ';' as the first character of a line. For example::
 
     >>> ,my_function /home/me # becomes my_function("/home/me")
 
 If you use ';' instead, the whole argument is quoted as a single string
 (while ',' splits on whitespace)::
 
     >>> ,my_function a b c # becomes my_function("a","b","c")
 
     >>> ;my_function a b c # becomes my_function("a b c")
 
 Note that the ',' or ';' MUST be the first character on the line! This
 won't work::
 
     >>> x = ,my_function /home/me # syntax error
 
 IPython as your default Python environment
 ==========================================
 
 Python honors the environment variable PYTHONSTARTUP and will execute at
 startup the file referenced by this variable. If you put at the end of
 this file the following two lines of code::
 
     import IPython 
     IPython.Shell.IPShell().mainloop(sys_exit=1)
 
 then IPython will be your working environment anytime you start Python.
 The sys_exit=1 is needed to have IPython issue a call to sys.exit() when
 it finishes, otherwise you'll be back at the normal Python '>>>'
 prompt.
 
 This is probably useful to developers who manage multiple Python
 versions and don't want to have correspondingly multiple IPython
 versions. Note that in this mode, there is no way to pass IPython any
 command-line options, as those are trapped first by Python itself.
 
 .. _Embedding:
 
 Embedding IPython
 =================
 
 It is possible to start an IPython instance inside your own Python
 programs. This allows you to evaluate dynamically the state of your
 code, operate with your variables, analyze them, etc. Note however that
 any changes you make to values while in the shell do not propagate back
 to the running code, so it is safe to modify your values because you
 won't break your code in bizarre ways by doing so.
 
 This feature allows you to easily have a fully functional python
 environment for doing object introspection anywhere in your code with a
 simple function call. In some cases a simple print statement is enough,
 but if you need to do more detailed analysis of a code fragment this
 feature can be very valuable.
 
 It can also be useful in scientific computing situations where it is
 common to need to do some automatic, computationally intensive part and
 then stop to look at data, plots, etc.
 Opening an IPython instance will give you full access to your data and
 functions, and you can resume program execution once you are done with
 the interactive part (perhaps to stop again later, as many times as
 needed).
 
 The following code snippet is the bare minimum you need to include in
 your Python programs for this to work (detailed examples follow later)::
 
     from IPython.Shell import IPShellEmbed
 
     ipshell = IPShellEmbed()
 
     ipshell() # this call anywhere in your program will start IPython
 
 You can run embedded instances even in code which is itself being run at
 the IPython interactive prompt with '%run <filename>'. Since it's easy
 to get lost as to where you are (in your top-level IPython or in your
 embedded one), it's a good idea in such cases to set the in/out prompts
 to something different for the embedded instances. The code examples
 below illustrate this.
 
 You can also have multiple IPython instances in your program and open
 them separately, for example with different options for data
 presentation. If you close and open the same instance multiple times,
 its prompt counters simply continue from each execution to the next.
 
 Please look at the docstrings in the Shell.py module for more details on
 the use of this system.
 
 The following sample file illustrating how to use the embedding
 functionality is provided in the examples directory as example-embed.py.
 It should be fairly self-explanatory::
 
 
     #!/usr/bin/env python
 
     """An example of how to embed an IPython shell into a running program.
 
     Please see the documentation in the IPython.Shell module for more details.
 
     The accompanying file example-embed-short.py has quick code fragments for
     embedding which you can cut and paste in your code once you understand how
     things work.
 
     The code in this file is deliberately extra-verbose, meant for learning."""
 
     # The basics to get you going:
 
     # IPython sets the __IPYTHON__ variable so you can know if you have nested
     # copies running.
 
     # Try running this code both at the command line and from inside IPython (with
     # %run example-embed.py)
     try:
         __IPYTHON__
     except NameError:
         nested = 0
         args = ['']
     else:
         print "Running nested copies of IPython."
         print "The prompts for the nested copy have been modified"
         nested = 1
         # what the embedded instance will see as sys.argv:
         args = ['-pi1','In <\\#>: ','-pi2','   .\\D.: ',
                 '-po','Out<\\#>: ','-nosep']
 
     # First import the embeddable shell class
     from IPython.Shell import IPShellEmbed
 
     # Now create an instance of the embeddable shell. The first argument is a
     # string with options exactly as you would type them if you were starting
     # IPython at the system command line. Any parameters you want to define for
     # configuration can thus be specified here.
     ipshell = IPShellEmbed(args,
                            banner = 'Dropping into IPython',
                            exit_msg = 'Leaving Interpreter, back to program.')
 
     # Make a second instance, you can have as many as you want.
     if nested:
         args[1] = 'In2<\\#>'
     else:
         args = ['-pi1','In2<\\#>: ','-pi2','   .\\D.: ',
                 '-po','Out<\\#>: ','-nosep']
     ipshell2 = IPShellEmbed(args,banner = 'Second IPython instance.')
 
     print '\nHello. This is printed from the main controller program.\n'
 
     # You can then call ipshell() anywhere you need it (with an optional
     # message):
     ipshell('***Called from top level. '
             'Hit Ctrl-D to exit interpreter and continue program.\n'
             'Note that if you use %kill_embedded, you can fully deactivate\n'
             'This embedded instance so it will never turn on again')
 
     print '\nBack in caller program, moving along...\n'
 
     #---------------------------------------------------------------------------
     # More details:
 
     # IPShellEmbed instances don't print the standard system banner and
     # messages. The IPython banner (which actually may contain initialization
     # messages) is available as <instance>.IP.BANNER in case you want it.
 
     # IPShellEmbed instances print the following information everytime they
     # start:
 
     # - A global startup banner.
 
     # - A call-specific header string, which you can use to indicate where in the
     # execution flow the shell is starting.
 
     # They also print an exit message every time they exit.
 
     # Both the startup banner and the exit message default to None, and can be set
     # either at the instance constructor or at any other time with the
     # set_banner() and set_exit_msg() methods.
 
     # The shell instance can be also put in 'dummy' mode globally or on a per-call
     # basis. This gives you fine control for debugging without having to change
     # code all over the place.
 
     # The code below illustrates all this.
 
 
     # This is how the global banner and exit_msg can be reset at any point
     ipshell.set_banner('Entering interpreter - New Banner')
     ipshell.set_exit_msg('Leaving interpreter - New exit_msg')
 
     def foo(m):
         s = 'spam'
         ipshell('***In foo(). Try @whos, or print s or m:')
         print 'foo says m = ',m
 
     def bar(n):
         s = 'eggs'
         ipshell('***In bar(). Try @whos, or print s or n:')
         print 'bar says n = ',n
 
     # Some calls to the above functions which will trigger IPython:
     print 'Main program calling foo("eggs")\n'
     foo('eggs')
 
     # The shell can be put in 'dummy' mode where calls to it silently return. This
     # allows you, for example, to globally turn off debugging for a program with a
     # single call.
     ipshell.set_dummy_mode(1)
     print '\nTrying to call IPython which is now "dummy":'
     ipshell()
     print 'Nothing happened...'
     # The global 'dummy' mode can still be overridden for a single call
     print '\nOverriding dummy mode manually:'
     ipshell(dummy=0)
 
     # Reactivate the IPython shell
     ipshell.set_dummy_mode(0)
 
     print 'You can even have multiple embedded instances:'
     ipshell2()
 
     print '\nMain program calling bar("spam")\n'
     bar('spam')
 
     print 'Main program finished. Bye!'
 
     #********************** End of file <example-embed.py> ***********************
 
 Once you understand how the system functions, you can use the following
 code fragments in your programs which are ready for cut and paste::
 
 
     """Quick code snippets for embedding IPython into other programs.
 
     See example-embed.py for full details, this file has the bare minimum code for
     cut and paste use once you understand how to use the system."""
 
     #---------------------------------------------------------------------------
     # This code loads IPython but modifies a few things if it detects it's running
     # embedded in another IPython session (helps avoid confusion)
 
     try:
         __IPYTHON__
     except NameError:
         argv = ['']
         banner = exit_msg = ''
     else:
         # Command-line options for IPython (a list like sys.argv)
         argv = ['-pi1','In <\\#>:','-pi2','   .\\D.:','-po','Out<\\#>:']
         banner = '*** Nested interpreter ***'
         exit_msg = '*** Back in main IPython ***'
 
     # First import the embeddable shell class
     from IPython.Shell import IPShellEmbed
     # Now create the IPython shell instance. Put ipshell() anywhere in your code
     # where you want it to open.
     ipshell = IPShellEmbed(argv,banner=banner,exit_msg=exit_msg)
 
     #---------------------------------------------------------------------------
     # This code will load an embeddable IPython shell always with no changes for
     # nested embededings.
 
     from IPython.Shell import IPShellEmbed
     ipshell = IPShellEmbed()
     # Now ipshell() will open IPython anywhere in the code.
 
     #---------------------------------------------------------------------------
     # This code loads an embeddable shell only if NOT running inside
     # IPython. Inside IPython, the embeddable shell variable ipshell is just a
     # dummy function.
 
     try:
         __IPYTHON__
     except NameError:
         from IPython.Shell import IPShellEmbed
         ipshell = IPShellEmbed()
         # Now ipshell() will open IPython anywhere in the code
     else:
         # Define a dummy ipshell() so the same code doesn't crash inside an
         # interactive IPython
         def ipshell(): pass
 
     #******************* End of file <example-embed-short.py> ********************
 
 Using the Python debugger (pdb)
 ===============================
 
 Running entire programs via pdb
 -------------------------------
 
 pdb, the Python debugger, is a powerful interactive debugger which
 allows you to step through code, set breakpoints, watch variables,
 etc.  IPython makes it very easy to start any script under the control
 of pdb, regardless of whether you have wrapped it into a 'main()'
 function or not. For this, simply type '%run -d myscript' at an
 IPython prompt. See the %run command's documentation (via '%run?' or
 in Sec. magic_ for more details, including how to control where pdb
 will stop execution first.
 
 For more information on the use of the pdb debugger, read the included
 pdb.doc file (part of the standard Python distribution). On a stock
 Linux system it is located at /usr/lib/python2.3/pdb.doc, but the
 easiest way to read it is by using the help() function of the pdb module
 as follows (in an IPython prompt):
 
 In [1]: import pdb 
 In [2]: pdb.help()
 
 This will load the pdb.doc document in a file viewer for you automatically.
 
 
 Automatic invocation of pdb on exceptions
 -----------------------------------------
 
 IPython, if started with the -pdb option (or if the option is set in
 your rc file) can call the Python pdb debugger every time your code
 triggers an uncaught exception. This feature
 can also be toggled at any time with the %pdb magic command. This can be
 extremely useful in order to find the origin of subtle bugs, because pdb
 opens up at the point in your code which triggered the exception, and
 while your program is at this point 'dead', all the data is still
 available and you can walk up and down the stack frame and understand
 the origin of the problem.
 
 Furthermore, you can use these debugging facilities both with the
 embedded IPython mode and without IPython at all. For an embedded shell
 (see sec. Embedding_), simply call the constructor with
 '-pdb' in the argument string and automatically pdb will be called if an
 uncaught exception is triggered by your code.
 
 For stand-alone use of the feature in your programs which do not use
 IPython at all, put the following lines toward the top of your 'main'
 routine::
 
     import sys,IPython.ultraTB  
     sys.excepthook = IPython.ultraTB.FormattedTB(mode='Verbose',
     color_scheme='Linux', call_pdb=1)
 
 The mode keyword can be either 'Verbose' or 'Plain', giving either very
 detailed or normal tracebacks respectively. The color_scheme keyword can
 be one of 'NoColor', 'Linux' (default) or 'LightBG'. These are the same
 options which can be set in IPython with -colors and -xmode.
 
 This will give any of your programs detailed, colored tracebacks with
 automatic invocation of pdb.
 
 
 Extensions for syntax processing
 ================================
 
 This isn't for the faint of heart, because the potential for breaking
 things is quite high. But it can be a very powerful and useful feature.
 In a nutshell, you can redefine the way IPython processes the user input
 line to accept new, special extensions to the syntax without needing to
 change any of IPython's own code.
 
 In the IPython/Extensions directory you will find some examples
 supplied, which we will briefly describe now. These can be used 'as is'
 (and both provide very useful functionality), or you can use them as a
 starting point for writing your own extensions.
 
 
 Pasting of code starting with '>>> ' or '... '
 ----------------------------------------------
 
 In the python tutorial it is common to find code examples which have
 been taken from real python sessions. The problem with those is that all
 the lines begin with either '>>> ' or '... ', which makes it impossible
 to paste them all at once. One must instead do a line by line manual
 copying, carefully removing the leading extraneous characters.
 
 This extension identifies those starting characters and removes them
 from the input automatically, so that one can paste multi-line examples
 directly into IPython, saving a lot of time. Please look at the file
 InterpreterPasteInput.py in the IPython/Extensions directory for details
 on how this is done.
 
 IPython comes with a special profile enabling this feature, called
 tutorial. Simply start IPython via 'ipython -p tutorial' and the feature
 will be available. In a normal IPython session you can activate the
 feature by importing the corresponding module with:
 In [1]: import IPython.Extensions.InterpreterPasteInput
 
 The following is a 'screenshot' of how things work when this extension
 is on, copying an example from the standard tutorial::
 
     IPython profile: tutorial 
 
     *** Pasting of code with ">>>" or "..." has been enabled. 
 
     In [1]: >>> def fib2(n): # return Fibonacci series up to n 
        ...: ...     """Return a list containing the Fibonacci series up to
     n.""" 
        ...: ...     result = [] 
        ...: ...     a, b = 0, 1 
        ...: ...     while b < n: 
        ...: ...         result.append(b)    # see below 
        ...: ...         a, b = b, a+b 
        ...: ...     return result 
        ...: 
 
     In [2]: fib2(10) 
     Out[2]: [1, 1, 2, 3, 5, 8]
 
 Note that as currently written, this extension does not recognize
 IPython's prompts for pasting. Those are more complicated, since the
 user can change them very easily, they involve numbers and can vary in
 length. One could however extract all the relevant information from the
 IPython instance and build an appropriate regular expression. This is
 left as an exercise for the reader.
 
 
 Input of physical quantities with units
 ---------------------------------------
 
 The module PhysicalQInput allows a simplified form of input for physical
 quantities with units. This file is meant to be used in conjunction with
 the PhysicalQInteractive module (in the same directory) and
 Physics.PhysicalQuantities from Konrad Hinsen's ScientificPython
 (http://dirac.cnrs-orleans.fr/ScientificPython/).
 
 The Physics.PhysicalQuantities module defines PhysicalQuantity objects,
 but these must be declared as instances of a class. For example, to
 define v as a velocity of 3 m/s, normally you would write::
 
     In [1]: v = PhysicalQuantity(3,'m/s')
 
 Using the PhysicalQ_Input extension this can be input instead as: 
 In [1]: v = 3 m/s
 which is much more convenient for interactive use (even though it is
 blatantly invalid Python syntax).
 
 The physics profile supplied with IPython (enabled via 'ipython -p
 physics') uses these extensions, which you can also activate with:
 
 from math import * # math MUST be imported BEFORE PhysicalQInteractive 
 from IPython.Extensions.PhysicalQInteractive import * 
 import IPython.Extensions.PhysicalQInput
 
 
 Threading support
 =================
 
 WARNING: The threading support is still somewhat experimental, and it
 has only seen reasonable testing under Linux. Threaded code is
 particularly tricky to debug, and it tends to show extremely
 platform-dependent behavior. Since I only have access to Linux machines,
 I will have to rely on user's experiences and assistance for this area
 of IPython to improve under other platforms.
 
 IPython, via the -gthread , -qthread, -q4thread and -wthread options
 (described in Sec. `Threading options`_), can run in
 multithreaded mode to support pyGTK, Qt3, Qt4 and WXPython applications
 respectively. These GUI toolkits need to control the python main loop of
 execution, so under a normal Python interpreter, starting a pyGTK, Qt3,
 Qt4 or WXPython application will immediately freeze the shell.
 
 IPython, with one of these options (you can only use one at a time),
 separates the graphical loop and IPython's code execution run into
 different threads. This allows you to test interactively (with %run, for
 example) your GUI code without blocking.
 
 A nice mini-tutorial on using IPython along with the Qt Designer
 application is available at the SciPy wiki:
 http://www.scipy.org/Cookbook/Matplotlib/Qt_with_IPython_and_Designer.
 
 
 Tk issues
 ---------
 
 As indicated in Sec. `Threading options`_, a special -tk option is
 provided to try and allow Tk graphical applications to coexist
 interactively with WX, Qt or GTK ones. Whether this works at all,
 however, is very platform and configuration dependent. Please
 experiment with simple test cases before committing to using this
 combination of Tk and GTK/Qt/WX threading in a production environment.
 
 
 I/O pitfalls
 ------------
 
 Be mindful that the Python interpreter switches between threads every
 $N$ bytecodes, where the default value as of Python 2.3 is $N=100.$ This
 value can be read by using the sys.getcheckinterval() function, and it
 can be reset via sys.setcheckinterval(N). This switching of threads can
 cause subtly confusing effects if one of your threads is doing file I/O.
 In text mode, most systems only flush file buffers when they encounter a
 '\n'. An instruction as simple as:: 
 
   print >> filehandle, ''hello world''
 
 actually consists of several bytecodes, so it is possible that the
 newline does not reach your file before the next thread switch.
 Similarly, if you are writing to a file in binary mode, the file won't
 be flushed until the buffer fills, and your other thread may see
 apparently truncated files.
 
 For this reason, if you are using IPython's thread support and have (for
 example) a GUI application which will read data generated by files
 written to from the IPython thread, the safest approach is to open all
 of your files in unbuffered mode (the third argument to the file/open
 function is the buffering value)::
 
   filehandle = open(filename,mode,0)
 
 This is obviously a brute force way of avoiding race conditions with the
 file buffering. If you want to do it cleanly, and you have a resource
 which is being shared by the interactive IPython loop and your GUI
 thread, you should really handle it with thread locking and
 syncrhonization properties. The Python documentation discusses these.
 
 .. _interactive_demos:
 
 Interactive demos with IPython
 ==============================
 
 IPython ships with a basic system for running scripts interactively in
 sections, useful when presenting code to audiences. A few tags embedded
 in comments (so that the script remains valid Python code) divide a file
 into separate blocks, and the demo can be run one block at a time, with
 IPython printing (with syntax highlighting) the block before executing
 it, and returning to the interactive prompt after each block. The
 interactive namespace is updated after each block is run with the
 contents of the demo's namespace.
 
 This allows you to show a piece of code, run it and then execute
 interactively commands based on the variables just created. Once you
 want to continue, you simply execute the next block of the demo. The
 following listing shows the markup necessary for dividing a script into
 sections for execution as a demo::
 
 
     """A simple interactive demo to illustrate the use of IPython's Demo class.
 
     Any python script can be run as a demo, but that does little more than showing
     it on-screen, syntax-highlighted in one shot.  If you add a little simple
     markup, you can stop at specified intervals and return to the ipython prompt,
     resuming execution later.
     """
 
     print 'Hello, welcome to an interactive IPython demo.'
     print 'Executing this block should require confirmation before proceeding,'
     print 'unless auto_all has been set to true in the demo object'
 
     # The mark below defines a block boundary, which is a point where IPython will
     # stop execution and return to the interactive prompt.
     # Note that in actual interactive execution, 
     # <demo> --- stop ---
 
     x = 1
     y = 2
 
     # <demo> --- stop ---
 
     # the mark below makes this block as silent
     # <demo> silent
 
     print 'This is a silent block, which gets executed but not printed.'
 
     # <demo> --- stop ---
     # <demo> auto
     print 'This is an automatic block.'
     print 'It is executed without asking for confirmation, but printed.'
     z = x+y
 
     print 'z=',x
 
     # <demo> --- stop ---
     # This is just another normal block.
     print 'z is now:', z
 
     print 'bye!'
 
 In order to run a file as a demo, you must first make a Demo object out
 of it. If the file is named myscript.py, the following code will make a
 demo::
 
     from IPython.demo import Demo
 
     mydemo = Demo('myscript.py')
 
 This creates the mydemo object, whose blocks you run one at a time by
 simply calling the object with no arguments. If you have autocall active
 in IPython (the default), all you need to do is type::
 
     mydemo 
 
 and IPython will call it, executing each block. Demo objects can be
 restarted, you can move forward or back skipping blocks, re-execute the
 last block, etc. Simply use the Tab key on a demo object to see its
 methods, and call '?' on them to see their docstrings for more usage
 details. In addition, the demo module itself contains a comprehensive
 docstring, which you can access via::
 
     from IPython import demo
 
     demo?
 
 Limitations: It is important to note that these demos are limited to
 fairly simple uses. In particular, you can not put division marks in
 indented code (loops, if statements, function definitions, etc.)
 Supporting something like this would basically require tracking the
 internal execution state of the Python interpreter, so only top-level
 divisions are allowed. If you want to be able to open an IPython
 instance at an arbitrary point in a program, you can use IPython's
 embedding facilities, described in detail in Sec. 9
 
 
 .. _Matplotlib support:
 
 Plotting with matplotlib
 ========================
 
 The matplotlib library (http://matplotlib.sourceforge.net
 http://matplotlib.sourceforge.net) provides high quality 2D plotting for
 Python. Matplotlib can produce plots on screen using a variety of GUI
 toolkits, including Tk, GTK and WXPython. It also provides a number of
 commands useful for scientific computing, all with a syntax compatible
 with that of the popular Matlab program.
 
 IPython accepts the special option -pylab (see :ref:`here
 <command_line_options>`). This configures it to support matplotlib, honoring
 the settings in the .matplotlibrc file. IPython will detect the user's choice
 of matplotlib GUI backend, and automatically select the proper threading model
 to prevent blocking. It also sets matplotlib in interactive mode and modifies
 %run slightly, so that any matplotlib-based script can be executed using %run
 and the final show() command does not block the interactive shell.
 
 The -pylab option must be given first in order for IPython to configure its
 threading mode. However, you can still issue other options afterwards. This
 allows you to have a matplotlib-based environment customized with additional
 modules using the standard IPython profile mechanism (see :ref:`here
 <profiles>`): ``ipython -pylab -p myprofile`` will load the profile defined in
 ipythonrc-myprofile after configuring matplotlib.

docs/source/interactive/tutorial.txt

@@ -1,317 +1,315 b''
 .. _tutorial:
 
 ======================
 Quick IPython tutorial
 ======================
 
-.. contents::
-
 IPython can be used as an improved replacement for the Python prompt,
 and for that you don't really need to read any more of this manual. But
 in this section we'll try to summarize a few tips on how to make the
 most effective use of it for everyday Python development, highlighting
 things you might miss in the rest of the manual (which is getting long).
 We'll give references to parts in the manual which provide more detail
 when appropriate.
 
 The following article by Jeremy Jones provides an introductory tutorial
 about IPython: http://www.onlamp.com/pub/a/python/2005/01/27/ipython.html
 
 Highlights
 ==========
 
 Tab completion
 --------------
 
 TAB-completion, especially for attributes, is a convenient way to explore the
 structure of any object you're dealing with. Simply type object_name.<TAB> and
 a list of the object's attributes will be printed (see :ref:`the readline
 section <readline>` for more). Tab completion also works on file and directory
 names, which combined with IPython's alias system allows you to do from within
 IPython many of the things you normally would need the system shell for.
 
 Explore your objects
 --------------------
 
 Typing object_name? will print all sorts of details about any object,
 including docstrings, function definition lines (for call arguments) and
 constructor details for classes. The magic commands %pdoc, %pdef, %psource
 and %pfile will respectively print the docstring, function definition line,
 full source code and the complete file for any object (when they can be
 found). If automagic is on (it is by default), you don't need to type the '%'
 explicitly. See :ref:`this section <dynamic_object_info>` for more.
 
 The `%run` magic command
 ------------------------
 
 The %run magic command allows you to run any python script and load all of its
 data directly into the interactive namespace. Since the file is re-read from
 disk each time, changes you make to it are reflected immediately (in contrast
 to the behavior of import). I rarely use import for code I am testing, relying
 on %run instead. See :ref:`this section <magic>` for more on this and other
 magic commands, or type the name of any magic command and ? to get details on
 it. See also :ref:`this section <dreload>` for a recursive reload command. %run
 also has special flags for timing the execution of your scripts (-t) and for
 executing them under the control of either Python's pdb debugger (-d) or
 profiler (-p). With all of these, %run can be used as the main tool for
 efficient interactive development of code which you write in your editor of
 choice.
 
 Debug a Python script
 ---------------------
 
 Use the Python debugger, pdb. The %pdb command allows you to toggle on and off
 the automatic invocation of an IPython-enhanced pdb debugger (with coloring,
 tab completion and more) at any uncaught exception. The advantage of this is
 that pdb starts inside the function where the exception occurred, with all data
 still available. You can print variables, see code, execute statements and even
 walk up and down the call stack to track down the true source of the problem
 (which often is many layers in the stack above where the exception gets
 triggered). Running programs with %run and pdb active can be an efficient to
 develop and debug code, in many cases eliminating the need for print statements
 or external debugging tools. I often simply put a 1/0 in a place where I want
 to take a look so that pdb gets called, quickly view whatever variables I need
 to or test various pieces of code and then remove the 1/0. Note also that '%run
 -d' activates pdb and automatically sets initial breakpoints for you to step
 through your code, watch variables, etc.  The :ref:`output caching section
 <output_caching>` has more details.
 
 Use the output cache
 --------------------
 
 All output results are automatically stored in a global dictionary named Out
 and variables named _1, _2, etc. alias them. For example, the result of input
 line 4 is available either as Out[4] or as _4. Additionally, three variables
 named _, __ and ___ are always kept updated with the for the last three
 results. This allows you to recall any previous result and further use it for
 new calculations. See :ref:`the output caching section <output_caching>` for
 more.
 
 Suppress output
 ---------------
 
 Put a ';' at the end of a line to suppress the printing of output. This is
 useful when doing calculations which generate long output you are not
 interested in seeing. The _* variables and the Out[] list do get updated with
 the contents of the output, even if it is not printed. You can thus still
 access the generated results this way for further processing.
 
 Input cache
 -----------
 
 A similar system exists for caching input. All input is stored in a global
 list called In , so you can re-execute lines 22 through 28 plus line 34 by
 typing 'exec In[22:29]+In[34]' (using Python slicing notation). If you need
 to execute the same set of lines often, you can assign them to a macro with
 the %macro function. See :ref:`here <input_caching>` for more.
 
 Use your input history
 ----------------------
 
 The %hist command can show you all previous input, without line numbers if
 desired (option -n) so you can directly copy and paste code either back in
 IPython or in a text editor. You can also save all your history by turning on
 logging via %logstart; these logs can later be either reloaded as IPython
 sessions or used as code for your programs.
 
 Define your own system aliases
 ------------------------------
 
 Even though IPython gives you access to your system shell via the ! prefix,
 it is convenient to have aliases to the system commands you use most often.
 This allows you to work seamlessly from inside IPython with the same commands
 you are used to in your system shell. IPython comes with some pre-defined
 aliases and a complete system for changing directories, both via a stack (see
 %pushd, %popd and %dhist) and via direct %cd. The latter keeps a history of
 visited directories and allows you to go to any previously visited one.
 
 Call system shell commands
 --------------------------
 
 Use Python to manipulate the results of system commands. The '!!' special
 syntax, and the %sc and %sx magic commands allow you to capture system output
 into Python variables.
 
 Use Python variables when calling the shell
 -------------------------------------------
 
 Expand python variables when calling the shell (either via '!' and '!!' or via
 aliases) by prepending a $ in front of them. You can also expand complete
 python expressions. See :ref:`our shell section <system_shell_access>` for
 more details.
 
 Use profiles
 ------------
 
 Use profiles to maintain different configurations (modules to load, function
 definitions, option settings) for particular tasks. You can then have
 customized versions of IPython for specific purposes. :ref:`This section
 <profiles>` has more details.
 
 
 Embed IPython in your programs
 ------------------------------
 
 A few lines of code are enough to load a complete IPython inside your own
 programs, giving you the ability to work with your data interactively after
 automatic processing has been completed. See :ref:`here <embedding>` for more.
 
 Use the Python profiler
 -----------------------
 
 When dealing with performance issues, the %run command with a -p option
 allows you to run complete programs under the control of the Python profiler.
 The %prun command does a similar job for single Python expressions (like
 function calls).
 
 Use IPython to present interactive demos
 ----------------------------------------
 
 Use the IPython.demo.Demo class to load any Python script as an interactive
 demo. With a minimal amount of simple markup, you can control the execution of
 the script, stopping as needed. See :ref:`here <interactive_demos>` for more.
 
 Run doctests
 ------------
 
 Run your doctests from within IPython for development and debugging. The
 special %doctest_mode command toggles a mode where the prompt, output and
 exceptions display matches as closely as possible that of the default Python
 interpreter. In addition, this mode allows you to directly paste in code that
 contains leading '>>>' prompts, even if they have extra leading whitespace
 (as is common in doctest files). This combined with the '%history -tn' call
 to see your translated history (with these extra prompts removed and no line
 numbers) allows for an easy doctest workflow, where you can go from doctest
 to interactive execution to pasting into valid Python code as needed.
 
 Source code handling tips
 =========================
 
 IPython is a line-oriented program, without full control of the
 terminal. Therefore, it doesn't support true multiline editing. However,
 it has a number of useful tools to help you in dealing effectively with
 more complex editing.
 
 The %edit command gives a reasonable approximation of multiline editing,
 by invoking your favorite editor on the spot. IPython will execute the
 code you type in there as if it were typed interactively. Type %edit?
 for the full details on the edit command.
 
 If you have typed various commands during a session, which you'd like to
 reuse, IPython provides you with a number of tools. Start by using %hist
 to see your input history, so you can see the line numbers of all input.
 Let us say that you'd like to reuse lines 10 through 20, plus lines 24
 and 28. All the commands below can operate on these with the syntax::
 
     %command 10-20 24 28 
 
 where the command given can be:
 
     * %macro <macroname>: this stores the lines into a variable which,
       when called at the prompt, re-executes the input. Macros can be
       edited later using '%edit macroname', and they can be stored
       persistently across sessions with '%store macroname' (the storage
       system is per-profile). The combination of quick macros,
       persistent storage and editing, allows you to easily refine
       quick-and-dirty interactive input into permanent utilities, always
       available both in IPython and as files for general reuse.
     * %edit: this will open a text editor with those lines pre-loaded
       for further modification. It will then execute the resulting
       file's contents as if you had typed it at the prompt.
     * %save <filename>: this saves the lines directly to a named file on
       disk.
 
 While %macro saves input lines into memory for interactive re-execution,
 sometimes you'd like to save your input directly to a file. The %save
 magic does this: its input sytnax is the same as %macro, but it saves
 your input directly to a Python file. Note that the %logstart command
 also saves input, but it logs all input to disk (though you can
 temporarily suspend it and reactivate it with %logoff/%logon); %save
 allows you to select which lines of input you need to save.
 
 
 Lightweight 'version control'
 =============================
 
 When you call %edit with no arguments, IPython opens an empty editor
 with a temporary file, and it returns the contents of your editing
 session as a string variable. Thanks to IPython's output caching
 mechanism, this is automatically stored::
 
     In [1]: %edit
 
     IPython will make a temporary file named: /tmp/ipython_edit_yR-HCN.py
 
     Editing... done. Executing edited code...
 
     hello - this is a temporary file
 
     Out[1]: "print 'hello - this is a temporary file'\n"
 
 Now, if you call '%edit -p', IPython tries to open an editor with the
 same data as the last time you used %edit. So if you haven't used %edit
 in the meantime, this same contents will reopen; however, it will be
 done in a new file. This means that if you make changes and you later
 want to find an old version, you can always retrieve it by using its
 output number, via '%edit _NN', where NN is the number of the output
 prompt.
 
 Continuing with the example above, this should illustrate this idea::
 
     In [2]: edit -p
 
     IPython will make a temporary file named: /tmp/ipython_edit_nA09Qk.py
 
     Editing... done. Executing edited code...
 
     hello - now I made some changes
 
     Out[2]: "print 'hello - now I made some changes'\n"
 
     In [3]: edit _1
 
     IPython will make a temporary file named: /tmp/ipython_edit_gy6-zD.py
 
     Editing... done. Executing edited code...
 
     hello - this is a temporary file
 
     IPython version control at work :)
 
     Out[3]: "print 'hello - this is a temporary file'\nprint 'IPython version control at work :)'\n"
 
 
 This section was written after a contribution by Alexander Belchenko on
 the IPython user list.
 
 
 Effective logging
 =================
 
 A very useful suggestion sent in by Robert Kern follows:
 
 I recently happened on a nifty way to keep tidy per-project log files. I
 made a profile for my project (which is called "parkfield")::
 
     include ipythonrc
 
     # cancel earlier logfile invocation:
 
     logfile ''
 
     execute import time
 
     execute __cmd = '/Users/kern/research/logfiles/parkfield-%s.log rotate'
 
     execute __IP.magic_logstart(__cmd % time.strftime('%Y-%m-%d'))
 
 I also added a shell alias for convenience::
 
     alias parkfield="ipython -pylab -profile parkfield" 
 
 Now I have a nice little directory with everything I ever type in,
 organized by project and date.
 
 Contribute your own: If you have your own favorite tip on using IPython
 efficiently for a certain task (especially things which can't be done in
 the normal Python interpreter), don't hesitate to send it!

docs/source/license_and_copyright.txt

@@ -1,87 +1,91 b''
 .. _license:
 
 =====================
 License and Copyright
 =====================
 
 License
 =======
 
 IPython is licensed under the terms of the new or revised BSD license, as follows::
 
     Copyright (c) 2008, IPython Development Team
 
     All rights reserved.
 
-    Redistribution and use in source and binary forms, with or without modification,
-    are permitted provided that the following conditions are met:
-
-    Redistributions of source code must retain the above copyright notice, this list of
-    conditions and the following disclaimer.
-
-    Redistributions in binary form must reproduce the above copyright notice, this list
-    of conditions and the following disclaimer in the documentation and/or other
-    materials provided with the distribution.
-
-    Neither the name of the IPython Development Team nor the names of its contributors
-    may be used to endorse or promote products derived from this software without
-    specific prior written permission.
-
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
-    EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
-    IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
-    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-    NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-    PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-    WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-    POSSIBILITY OF SUCH DAMAGE.
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+
+    Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
+
+    Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+
+    Neither the name of the IPython Development Team nor the names of its
+    contributors may be used to endorse or promote products derived from this
+    software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+    IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+    THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+    PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+    CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+    EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+    PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+    PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+    LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+    NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 About the IPython Development Team
 ==================================
 
-Fernando Perez began IPython in 2001 based on code from Janko Hauser <[e-mail]> 
-and Nathaniel Gray <[e-mail]>.  Fernando is still the project lead.
+Fernando Perez began IPython in 2001 based on code from Janko Hauser
+<[e-mail]> and Nathaniel Gray <[e-mail]>. Fernando is still
+the project lead.
 
-The IPython Development Team is the set of all contributors to the IPython project.
-This includes all of the IPython subprojects. Here is a list of the currently active contributors:
+The IPython Development Team is the set of all contributors to the IPython
+project. This includes all of the IPython subprojects. Here is a list of the
+currently active contributors:
 
 	* Matthieu Brucher
 	* Ondrej Certik
 	* Laurent Dufrechou
 	* Robert Kern
 	* Brian E. Granger
 	* Fernando Perez (project leader)
 	* Benjamin Ragan-Kelley
 	* Ville M. Vainio
 	* Gael Varoququx
 	* Stefan van der Walt
 	* Tech-X Corporation
 	* Barry Wark
 
 If your name is missing, please add it.  
 
 Our Copyright Policy
 ====================
 
-IPython uses a shared copyright model. Each contributor maintains copyright over
-their contributions to IPython. But, it is important to note that these
-contributions are typically only changes to the repositories. Thus, the IPython
-source code, in its entirety is not the copyright of any single person or
-institution. Instead, it is the collective copyright of the entire IPython
+IPython uses a shared copyright model. Each contributor maintains copyright
+over their contributions to IPython. But, it is important to note that these
+contributions are typically only changes to the repositories. Thus, the
+IPython source code, in its entirety is not the copyright of any single person
+or institution. Instead, it is the collective copyright of the entire IPython
 Development Team. If individual contributors want to maintain a record of what
-changes/contributions they have specific copyright on, they should indicate their
-copyright in the commit message of the change, when they commit the change to
-one of the IPython repositories.
+changes/contributions they have specific copyright on, they should indicate
+their copyright in the commit message of the change, when they commit the
+change to one of the IPython repositories.
 
 Miscellaneous
 =============
 
 Some files (DPyGetOpt.py, for example) may be licensed under different
-conditions. Ultimately each file indicates clearly the conditions under
-which its author/authors have decided to publish the code.
+conditions. Ultimately each file indicates clearly the conditions under which
+its author/authors have decided to publish the code.
 
-Versions of IPython up to and including 0.6.3 were released under the
-GNU Lesser General Public License (LGPL), available at
+Versions of IPython up to and including 0.6.3 were released under the GNU
+Lesser General Public License (LGPL), available at
 http://www.gnu.org/copyleft/lesser.html.
  No newline at end of file

docs/source/parallel/index.txt

@@ -1,14 +1,16 b''
 .. _parallel_index:
 
 ====================================
 Using IPython for parallel computing
 ====================================
 
 .. toctree::
    :maxdepth: 2
 
    parallel_intro.txt
+   parallel_process.txt
    parallel_multiengine.txt
    parallel_task.txt
    parallel_mpi.txt
+   parallel_security.txt
 

docs/source/parallel/parallel_intro.txt

@@ -1,327 +1,205 b''
 .. _ip1par:
 
 ============================
 Overview and getting started
 ============================
 
-.. contents::
-
 Introduction
 ============
 
-This file gives an overview of IPython's sophisticated and
-powerful architecture for parallel and distributed computing. This
-architecture abstracts out parallelism in a very general way, which
-enables IPython to support many different styles of parallelism
-including:
+This section gives an overview of IPython's sophisticated and powerful
+architecture for parallel and distributed computing. This architecture
+abstracts out parallelism in a very general way, which enables IPython to
+support many different styles of parallelism including:
 
 * Single program, multiple data (SPMD) parallelism.
 * Multiple program, multiple data (MPMD) parallelism.
-* Message passing using ``MPI``.
+* Message passing using MPI.
 * Task farming.
 * Data parallel.
 * Combinations of these approaches.
 * Custom user defined approaches.
 
 Most importantly, IPython enables all types of parallel applications to
 be developed, executed, debugged and monitored *interactively*. Hence,
 the ``I`` in IPython.  The following are some example usage cases for IPython:
 
 * Quickly parallelize algorithms that are embarrassingly parallel
   using a number of simple approaches.  Many simple things can be
   parallelized interactively in one or two lines of code.
 
 * Steer traditional MPI applications on a supercomputer from an
   IPython session on your laptop.
 
 * Analyze and visualize large datasets (that could be remote and/or
   distributed) interactively using IPython and tools like
   matplotlib/TVTK.
 
 * Develop, test and debug new parallel algorithms 
   (that may use MPI) interactively.
 
 * Tie together multiple MPI jobs running on different systems into
   one giant distributed and parallel system.
 
 * Start a parallel job on your cluster and then have a remote 	
   collaborator connect to it and pull back data into their 
   local IPython session for plotting and analysis.
 
 * Run a set of tasks on a set of CPUs using dynamic load balancing.
 
 Architecture overview
 =====================
 
 The IPython architecture consists of three components:
 
 * The IPython engine.
 * The IPython controller.
 * Various controller clients.
 
 These components live in the :mod:`IPython.kernel` package and are
 installed with IPython.  They do, however, have additional dependencies
 that must be installed.  For more information, see our
 :ref:`installation documentation <install_index>`.
 
 IPython engine
 ---------------
 
 The IPython engine is a Python instance that takes Python commands over a
 network connection. Eventually, the IPython engine will be a full IPython
 interpreter, but for now, it is a regular Python interpreter. The engine
 can also handle incoming and outgoing Python objects sent over a network
 connection.  When multiple engines are started, parallel and distributed
 computing becomes possible. An important feature of an IPython engine is
 that it blocks while user code is being executed. Read on for how the
 IPython controller solves this problem to expose a clean asynchronous API
 to the user.
 
 IPython controller
 ------------------
 
 The IPython controller provides an interface for working with a set of
 engines. At an general level, the controller is a process to which
 IPython engines can connect. For each connected engine, the controller
 manages a queue. All actions that can be performed on the engine go
 through this queue. While the engines themselves block when user code is
 run, the controller hides that from the user to provide a fully
 asynchronous interface to a set of engines. 
 
 .. note::
 
     Because the controller listens on a network port for engines to 
     connect to it, it must be started *before* any engines are started.  
 
 The controller also provides a single point of contact for users who wish
 to utilize the engines connected to the controller. There are different
 ways of working with a controller. In IPython these ways correspond to different interfaces that the controller is adapted to.  Currently we have two default interfaces to the controller: 
 
-* The MultiEngine interface, which provides the simplest possible way of working
-  with engines interactively.
+* The MultiEngine interface, which provides the simplest possible way of
+  working with engines interactively.
 * The Task interface, which provides presents the engines as a load balanced
   task farming system.
 
 Advanced users can easily add new custom interfaces to enable other
 styles of parallelism. 
 
 .. note:: 
 
 	A single controller and set of engines can be accessed 
 	through multiple interfaces simultaneously.  This opens the
 	door for lots of interesting things.  
 
 Controller clients
 ------------------
 
 For each controller interface, there is a corresponding client. These
 clients allow users to interact with a set of engines through the
 interface.  Here are the two default clients:
 
 * The :class:`MultiEngineClient` class.
 * The :class:`TaskClient` class.
 
 Security
 --------
 
-By default (as long as `pyOpenSSL` is installed) all network connections between the controller and engines and the controller and clients are secure.  What does this mean?  First of all, all of the connections will be encrypted using SSL.  Second, the connections are authenticated.  We handle authentication in a `capabilities`__ based security model.  In this model,  a "capability (known in some systems as a key) is a communicable, unforgeable token of authority".  Put simply, a capability is like a key to your house.  If you have the key to your house, you can get in.  If not, you can't.  
-
-.. __: http://en.wikipedia.org/wiki/Capability-based_security
+By default (as long as `pyOpenSSL` is installed) all network connections between the controller and engines and the controller and clients are secure.  What does this mean?  First of all, all of the connections will be encrypted using SSL.  Second, the connections are authenticated.  We handle authentication in a capability based security model [Capability]_.  In this model,  a "capability (known in some systems as a key) is a communicable, unforgeable token of authority".  Put simply, a capability is like a key to your house.  If you have the key to your house, you can get in.  If not, you can't.  
 
 In our architecture, the controller is the only process that listens on network ports, and is thus responsible to creating these keys.  In IPython, these keys are known as Foolscap URLs, or FURLs, because of the underlying network protocol we are using.  As a user, you don't need to know anything about the details of these FURLs, other than that when the controller starts, it saves a set of FURLs to files named :file:`something.furl`.  The default location of these files is the :file:`~./ipython/security` directory.
 
-To connect and authenticate to the controller an engine or client simply needs to present an appropriate furl (that was originally created by the controller) to the controller.  Thus, the .furl files need to be copied to a location where the clients and engines can find them.  Typically, this is the :file:`~./ipython/security` directory on the host where the client/engine is running (which could be a different host than the controller).  Once the .furl files are copied over, everything should work fine.
+To connect and authenticate to the controller an engine or client simply needs to present an appropriate FURL (that was originally created by the controller) to the controller.  Thus, the FURL files need to be copied to a location where the clients and engines can find them.  Typically, this is the :file:`~./ipython/security` directory on the host where the client/engine is running (which could be a different host than the controller).  Once the FURL files are copied over, everything should work fine.
 
-Currently, there are three .furl files that the controller creates:
+Currently, there are three FURL files that the controller creates:
 
 ipcontroller-engine.furl
-    This ``.furl`` file is the key that gives an engine the ability to connect
+    This FURL file is the key that gives an engine the ability to connect
     to a controller.
 
 ipcontroller-tc.furl
-    This ``.furl`` file is the key that a :class:`TaskClient` must use to
+    This FURL file is the key that a :class:`TaskClient` must use to
     connect to the task interface of a controller.
     
 ipcontroller-mec.furl
-    This ``.furl`` file is the key that a :class:`MultiEngineClient` must use to
-    connect to the multiengine interface of a controller.
+    This FURL file is the key that a :class:`MultiEngineClient` must use
+    to connect to the multiengine interface of a controller.
 
-More details of how these ``.furl`` files are used are given below.
+More details of how these FURL files are used are given below.
+
+A detailed description of the security model and its implementation in IPython
+can be found :ref:`here <parallelsecurity>`.
 
 Getting Started
 ===============
 
 To use IPython for parallel computing, you need to start one instance of
-the controller and one or more instances of the engine. The controller
-and each engine can run on different machines or on the same machine.
-Because of this, there are many different possibilities for setting up
-the IP addresses and ports used by the various processes.
-
-Starting the controller and engine on your local machine
---------------------------------------------------------
-
-This is the simplest configuration that can be used and is useful for
-testing the system and on machines that have multiple cores and/or
-multple CPUs. The easiest way of getting started is to use the :command:`ipcluster`
-command::
-
-	$ ipcluster -n 4
-
-This will start an IPython controller and then 4 engines that connect to
-the controller. Lastly, the script will print out the Python commands
-that you can use to connect to the controller. It is that easy.
-
-.. warning::
-
-    The :command:`ipcluster` does not currently work on Windows.  We are
-    working on it though.
-
-Underneath the hood, the controller creates ``.furl`` files in the
-:file:`~./ipython/security` directory.  Because the engines are on the
-same host, they automatically find the needed :file:`ipcontroller-engine.furl`
-there and use it to connect to the controller.
-
-The :command:`ipcluster` script uses two other top-level
-scripts that you can also use yourself. These scripts are
-:command:`ipcontroller`, which starts the controller and :command:`ipengine` which
-starts one engine. To use these scripts to start things on your local
-machine, do the following.
-
-First start the controller::
-
-	$ ipcontroller
-	
-Next, start however many instances of the engine you want using (repeatedly) the command::
-
-	$ ipengine
-
-The engines should start and automatically connect to the controller using the ``.furl`` files in :file:`~./ipython/security`. You are now ready to use the controller and engines from IPython.
-
-.. warning:: 
-	
-	The order of the above operations is very important.  You *must*
- 	start the controller before the engines, since the engines connect 
-	to the controller as they get started.
-
-.. note::
-
-    On some platforms (OS X), to put the controller and engine into the background
-    you may need to give these commands in the form ``(ipcontroller &)`` 
-    and ``(ipengine &)`` (with the parentheses) for them to work properly. 
-
-
-Starting the controller and engines on different hosts
-------------------------------------------------------
-
-When the controller and engines are running on different hosts, things are
-slightly more complicated, but the underlying ideas are the same:
-
-1. Start the controller on a host using :command:`ipcontroler`.
-2. Copy :file:`ipcontroller-engine.furl` from :file:`~./ipython/security` on the controller's host to the host where the engines will run.
-3. Use :command:`ipengine` on the engine's hosts to start the engines.
+the controller and one or more instances of the engine. Initially, it is best to simply start a controller and engines on a single host using the :command:`ipcluster` command.  To start a controller and 4 engines on you localhost, just do::
 
-The only thing you have to be careful of is to tell :command:`ipengine` where the :file:`ipcontroller-engine.furl` file is located.  There are two ways you can do this:
+    $ ipcluster local -n 4
 
-* Put :file:`ipcontroller-engine.furl` in the :file:`~./ipython/security` directory
-  on the engine's host, where it will be found automatically.
-* Call :command:`ipengine` with the ``--furl-file=full_path_to_the_file`` flag.
-
-The ``--furl-file`` flag works like this::
-
-    $ ipengine --furl-file=/path/to/my/ipcontroller-engine.furl
-
-.. note::
-    
-    If the controller's and engine's hosts all have a shared file system  
-    (:file:`~./ipython/security` is the same on all of them), then things
-    will just work!
-
-Make .furl files persistent
----------------------------
-
-At fist glance it may seem that that managing the ``.furl`` files is a bit annoying.  Going back to the house and key analogy, copying the ``.furl`` around each time you start the controller is like having to make a new key everytime you want to unlock the door and enter your house.  As with your house, you want to be able to create the key (or ``.furl`` file) once, and then simply use it at any point in the future.
-
-This is possible.  The only thing you have to do is decide what ports the controller will listen on for the engines and clients.  This is done as follows::
-
-    $ ipcontroller --client-port=10101 --engine-port=10102
-
-Then, just copy the furl files over the first time and you are set.  You can start and stop the controller and engines any many times as you want in the future, just make sure to tell the controller to use the *same* ports.
-
-.. note::
-
-    You may ask the question: what ports does the controller listen on if you
-    don't tell is to use specific ones?  The default is to use high random port
-    numbers.  We do this for two reasons: i) to increase security through obcurity
-    and ii) to multiple controllers on a given host to start and automatically
-    use different ports.
-
-Starting engines using ``mpirun``
----------------------------------
-
-The IPython engines can be started using ``mpirun``/``mpiexec``, even if
-the engines don't call ``MPI_Init()`` or use the MPI API in any way. This is
-supported on modern MPI implementations like `Open MPI`_.. This provides
-an really nice way of starting a bunch of engine. On a system with MPI
-installed you can do::
-
-	mpirun -n 4 ipengine
-
-to start 4 engine on a cluster.  This works even if you don't have any
-Python-MPI bindings installed.
-
-.. _Open MPI: http://www.open-mpi.org/
-
-More details on using MPI with IPython can be found :ref:`here <parallelmpi>`.
-
-Log files
----------
-
-All of the components of IPython have log files associated with them.
-These log files can be extremely useful in debugging problems with
-IPython and can be found in the directory ``~/.ipython/log``.  Sending
-the log files to us will often help us to debug any problems.
-
-Next Steps
-==========
+More details about starting the IPython controller and engines can be found :ref:`here <parallel_process>`
 
 Once you have started the IPython controller and one or more engines, you
 are ready to use the engines to do something useful. To make sure
-everything is working correctly, try the following commands::
+everything is working correctly, try the following commands:
+
+.. sourcecode:: ipython
 
 	In [1]: from IPython.kernel import client
 	
 	In [2]: mec = client.MultiEngineClient()
 	
 	In [4]: mec.get_ids()
 	Out[4]: [0, 1, 2, 3]
 	
 	In [5]: mec.execute('print "Hello World"')
 	Out[5]: 
 	<Results List>
 	[0] In [1]: print "Hello World"
 	[0] Out[1]: Hello World
 
 	[1] In [1]: print "Hello World"
 	[1] Out[1]: Hello World
 
 	[2] In [1]: print "Hello World"
 	[2] Out[1]: Hello World
 
 	[3] In [1]: print "Hello World"
 	[3] Out[1]: Hello World
 
-Remember, a client also needs to present a ``.furl`` file to the controller.  How does this happen?  When a multiengine client is created with no arguments, the client tries to find the corresponding ``.furl`` file in the local :file:`~./ipython/security` directory.  If it finds it, you are set.  If you have put the ``.furl`` file in a different location or it has a different name, create the client like this::
+Remember, a client also needs to present a FURL file to the controller.  How does this happen?  When a multiengine client is created with no arguments, the client tries to find the corresponding FURL file in the local :file:`~./ipython/security` directory.  If it finds it, you are set.  If you have put the FURL file in a different location or it has a different name, create the client like this::
 
     mec = client.MultiEngineClient('/path/to/my/ipcontroller-mec.furl')
 
 Same thing hold true of creating a task client::
 
     tc = client.TaskClient('/path/to/my/ipcontroller-tc.furl')
 
 You are now ready to learn more about the :ref:`MultiEngine <parallelmultiengine>` and :ref:`Task <paralleltask>` interfaces to the controller.
 
 .. note:: 
 
     Don't forget that the engine, multiengine client and task client all have
-    *different* furl files.  You must move *each* of these around to an appropriate
-    location so that the engines and clients can use them to connect to the controller.
+    *different* furl files. You must move *each* of these around to an
+    appropriate location so that the engines and clients can use them to
+    connect to the controller.
+
+.. [Capability] Capability-based security, http://en.wikipedia.org/wiki/Capability-based_security
+

docs/source/parallel/parallel_mpi.txt

@@ -1,22 +1,157 b''
 .. _parallelmpi:
 
 =======================
 Using MPI with IPython
 =======================
 
-The simplest way of getting started with MPI is to install an MPI implementation
-(we recommend `Open MPI`_) and `mpi4py`_ and then start the engines using the
-``mpirun`` command::
-
-	mpirun -n 4 ipengine --mpi=mpi4py
-	
-This will automatically import `mpi4py`_ and make sure that `MPI_Init` is called
-at the right time. We also have built in support for `PyTrilinos`_, which can be
-used (assuming `PyTrilinos`_ is installed) by starting the engines with::
-
-	mpirun -n 4 ipengine --mpi=pytrilinos
-
-.. _MPI: http://www-unix.mcs.anl.gov/mpi/
-.. _mpi4py: http://mpi4py.scipy.org/
-.. _Open MPI: http://www.open-mpi.org/
-.. _PyTrilinos: http://trilinos.sandia.gov/packages/pytrilinos/
  No newline at end of file
+Often, a parallel algorithm will require moving data between the engines.  One way of accomplishing this is by doing a pull and then a push using the multiengine client.  However, this will be slow as all the data has to go through the controller to the client and then back through the controller, to its final destination.
+
+A much better way of moving data between engines is to use a message passing library, such as the Message Passing Interface (MPI) [MPI]_.  IPython's parallel computing architecture has been designed from the ground up to integrate with MPI.  This document describes how to use MPI with IPython.
+
+Additional installation requirements
+====================================
+
+If you want to use MPI with IPython, you will need to install:
+
+* A standard MPI implementation such as OpenMPI [OpenMPI]_ or MPICH.
+* The mpi4py [mpi4py]_ package.
+
+.. note::
+
+    The mpi4py package is not a strict requirement. However, you need to
+    have *some* way of calling MPI from Python. You also need some way of
+    making sure that :func:`MPI_Init` is called when the IPython engines start
+    up. There are a number of ways of doing this and a good number of
+    associated subtleties. We highly recommend just using mpi4py as it
+    takes care of most of these problems. If you want to do something
+    different, let us know and we can help you get started.
+
+Starting the engines with MPI enabled
+=====================================
+
+To use code that calls MPI, there are typically two things that MPI requires.
+
+1. The process that wants to call MPI must be started using
+   :command:`mpirun` or a batch system (like PBS) that has MPI support.
+2. Once the process starts, it must call :func:`MPI_Init`.
+
+There are a couple of ways that you can start the IPython engines and get these things to happen.
+
+Automatic starting using :command:`mpirun` and :command:`ipcluster`
+-------------------------------------------------------------------
+
+The easiest approach is to use the `mpirun` mode of :command:`ipcluster`, which will first start a controller and then a set of engines using :command:`mpirun`::
+
+    $ ipcluster mpirun -n 4
+
+This approach is best as interrupting :command:`ipcluster` will automatically
+stop and clean up the controller and engines.
+
+Manual starting using :command:`mpirun`
+---------------------------------------
+
+If you want to start the IPython engines using the :command:`mpirun`, just do::
+
+    $ mpirun -n 4 ipengine --mpi=mpi4py
+
+This requires that you already have a controller running and that the FURL
+files for the engines are in place. We also have built in support for
+PyTrilinos [PyTrilinos]_, which can be used (assuming is installed) by
+starting the engines with::
+
+    	mpirun -n 4 ipengine --mpi=pytrilinos
+
+Automatic starting using PBS and :command:`ipcluster`
+-----------------------------------------------------
+
+The :command:`ipcluster` command also has built-in integration with PBS. For more information on this approach, see our documentation on :ref:`ipcluster <parallel_process>`.
+
+Actually using MPI
+==================
+
+Once the engines are running with MPI enabled, you are ready to go.  You can now call any code that uses MPI in the IPython engines.  And, all of this can be done interactively.  Here we show a simple example that uses mpi4py [mpi4py]_.
+
+First, lets define a simply function that uses MPI to calculate the sum of a distributed array.  Save the following text in a file called :file:`psum.py`:
+
+.. sourcecode:: python
+
+    from mpi4py import MPI
+    import numpy as np
+    
+    def psum(a):
+        s = np.sum(a)
+        return MPI.COMM_WORLD.Allreduce(s,MPI.SUM)
+
+Now, start an IPython cluster in the same directory as :file:`psum.py`::
+
+    $ ipcluster mpirun -n 4
+
+Finally, connect to the cluster and use this function interactively.  In this case, we create a random array on each engine and sum up all the random arrays using our :func:`psum` function:
+
+.. sourcecode:: ipython
+
+    In [1]: from IPython.kernel import client
+    
+    In [2]: mec = client.MultiEngineClient()
+    
+    In [3]: mec.activate()
+    
+    In [4]: px import numpy as np
+    Parallel execution on engines: all
+    Out[4]: 
+    <Results List>
+    [0] In [13]: import numpy as np
+    [1] In [13]: import numpy as np
+    [2] In [13]: import numpy as np
+    [3] In [13]: import numpy as np
+    
+    In [6]: px a = np.random.rand(100)
+    Parallel execution on engines: all
+    Out[6]: 
+    <Results List>
+    [0] In [15]: a = np.random.rand(100)
+    [1] In [15]: a = np.random.rand(100)
+    [2] In [15]: a = np.random.rand(100)
+    [3] In [15]: a = np.random.rand(100)
+    
+    In [7]: px from psum import psum
+    Parallel execution on engines: all
+    Out[7]: 
+    <Results List>
+    [0] In [16]: from psum import psum
+    [1] In [16]: from psum import psum
+    [2] In [16]: from psum import psum
+    [3] In [16]: from psum import psum
+    
+    In [8]: px s = psum(a)
+    Parallel execution on engines: all
+    Out[8]: 
+    <Results List>
+    [0] In [17]: s = psum(a)
+    [1] In [17]: s = psum(a)
+    [2] In [17]: s = psum(a)
+    [3] In [17]: s = psum(a)
+    
+    In [9]: px print s
+    Parallel execution on engines: all
+    Out[9]: 
+    <Results List>
+    [0] In [18]: print s
+    [0] Out[18]: 187.451545803
+    
+    [1] In [18]: print s
+    [1] Out[18]: 187.451545803
+    
+    [2] In [18]: print s
+    [2] Out[18]: 187.451545803
+
+    [3] In [18]: print s
+    [3] Out[18]: 187.451545803
+
+Any Python code that makes calls to MPI can be used in this manner, including
+compiled C, C++ and Fortran libraries that have been exposed to Python.
+
+.. [MPI] Message Passing Interface.  http://www-unix.mcs.anl.gov/mpi/
+.. [mpi4py] MPI for Python. mpi4py: http://mpi4py.scipy.org/
+.. [OpenMPI] Open MPI. http://www.open-mpi.org/
+.. [PyTrilinos] PyTrilinos. http://trilinos.sandia.gov/packages/pytrilinos/
  No newline at end of file

docs/source/parallel/parallel_multiengine.txt

@@ -1,783 +1,828 b''
 .. _parallelmultiengine:
 
 ===============================
 IPython's multiengine interface
 ===============================
 
-.. contents::
-
 The multiengine interface represents one possible way of working with a set of
 IPython engines. The basic idea behind the multiengine interface is that the
 capabilities of each engine are directly and explicitly exposed to the user.
 Thus, in the multiengine interface, each engine is given an id that is used to
 identify the engine and give it work to do. This interface is very intuitive
 and is designed with interactive usage in mind, and is thus the best place for
 new users of IPython to begin.
 
 Starting the IPython controller and engines
 ===========================================
 
 To follow along with this tutorial, you will need to start the IPython
 controller and four IPython engines. The simplest way of doing this is to use
 the :command:`ipcluster` command::
 
-	$ ipcluster -n 4
+	$ ipcluster local -n 4
 	
 For more detailed information about starting the controller and engines, see
 our :ref:`introduction <ip1par>` to using IPython for parallel computing.
 
 Creating a ``MultiEngineClient`` instance
 =========================================
 
 The first step is to import the IPython :mod:`IPython.kernel.client` module
-and then create a :class:`MultiEngineClient` instance::
+and then create a :class:`MultiEngineClient` instance:
+
+.. sourcecode:: ipython
 
 	In [1]: from IPython.kernel import client
 	
 	In [2]: mec = client.MultiEngineClient()
 
 This form assumes that the :file:`ipcontroller-mec.furl` is in the
 :file:`~./ipython/security` directory on the client's host. If not, the
-location of the ``.furl`` file must be given as an argument to the
-constructor::
+location of the FURL file must be given as an argument to the
+constructor:
+
+.. sourcecode:: ipython
 
-    In[2]: mec = client.MultiEngineClient('/path/to/my/ipcontroller-mec.furl')
+    In [2]: mec = client.MultiEngineClient('/path/to/my/ipcontroller-mec.furl')
 
 To make sure there are engines connected to the controller, use can get a list
-of engine ids::
+of engine ids:
+
+.. sourcecode:: ipython
 
 	In [3]: mec.get_ids()
 	Out[3]: [0, 1, 2, 3]
 
 Here we see that there are four engines ready to do work for us.
 
 Quick and easy parallelism
 ==========================
 
 In many cases, you simply want to apply a Python function to a sequence of objects, but *in parallel*.  The multiengine interface provides two simple ways of accomplishing this:  a parallel version of :func:`map` and ``@parallel`` function decorator.
 
 Parallel map
 ------------
 
 Python's builtin :func:`map` functions allows a function to be applied to a
 sequence element-by-element. This type of code is typically trivial to
 parallelize. In fact, the multiengine interface in IPython already has a
-parallel version of :meth:`map` that works just like its serial counterpart::
+parallel version of :meth:`map` that works just like its serial counterpart:
+
+.. sourcecode:: ipython
 
 	In [63]: serial_result = map(lambda x:x**10, range(32))
 
 	In [64]: parallel_result = mec.map(lambda x:x**10, range(32))
 
 	In [65]: serial_result==parallel_result
 	Out[65]: True
 
 .. note::
 
     The multiengine interface version of :meth:`map` does not do any load
     balancing.  For a load balanced version, see the task interface.
 
 .. seealso::
 
     The :meth:`map` method has a number of options that can be controlled by
     the :meth:`mapper` method.  See its docstring for more information.
 
 Parallel function decorator
 ---------------------------
 
-Parallel functions are just like normal function, but they can be called on sequences and *in parallel*.  The multiengine interface provides a decorator that turns any Python function into a parallel function::
+Parallel functions are just like normal function, but they can be called on sequences and *in parallel*.  The multiengine interface provides a decorator that turns any Python function into a parallel function:
+
+.. sourcecode:: ipython
 
     In [10]: @mec.parallel()
        ....: def f(x):
        ....:     return 10.0*x**4
        ....: 
 
     In [11]: f(range(32))    # this is done in parallel
     Out[11]: 
     [0.0,10.0,160.0,...]
 
 See the docstring for the :meth:`parallel` decorator for options.
 
 Running Python commands
 =======================
 
 The most basic type of operation that can be performed on the engines is to
 execute Python code. Executing Python code can be done in blocking or
 non-blocking mode (blocking is default) using the :meth:`execute` method.
 
 Blocking execution
 ------------------
 
 In blocking mode, the :class:`MultiEngineClient` object (called ``mec`` in
 these examples) submits the command to the controller, which places the
 command in the engines' queues for execution. The :meth:`execute` call then
-blocks until the engines are done executing the command::
+blocks until the engines are done executing the command:
+
+.. sourcecode:: ipython
 
 	# The default is to run on all engines
 	In [4]: mec.execute('a=5')
 	Out[4]: 
 	<Results List>
 	[0] In [1]: a=5
 	[1] In [1]: a=5
 	[2] In [1]: a=5
 	[3] In [1]: a=5
 
 	In [5]: mec.execute('b=10')
 	Out[5]: 
 	<Results List>
 	[0] In [2]: b=10
 	[1] In [2]: b=10
 	[2] In [2]: b=10
 	[3] In [2]: b=10
 
 Python commands can be executed on specific engines by calling execute using
-the ``targets`` keyword argument::
+the ``targets`` keyword argument:
+
+.. sourcecode:: ipython
 
 	In [6]: mec.execute('c=a+b',targets=[0,2])
 	Out[6]: 
 	<Results List>
 	[0] In [3]: c=a+b
 	[2] In [3]: c=a+b
 
 
 	In [7]: mec.execute('c=a-b',targets=[1,3])
 	Out[7]: 
 	<Results List>
 	[1] In [3]: c=a-b
 	[3] In [3]: c=a-b
 
 
 	In [8]: mec.execute('print c')
 	Out[8]: 
 	<Results List>
 	[0] In [4]: print c
 	[0] Out[4]: 15
 
 	[1] In [4]: print c
 	[1] Out[4]: -5
 
 	[2] In [4]: print c
 	[2] Out[4]: 15
 
 	[3] In [4]: print c
 	[3] Out[4]: -5
 
 This example also shows one of the most important things about the IPython
 engines: they have a persistent user namespaces. The :meth:`execute` method
-returns a Python ``dict`` that contains useful information::
+returns a Python ``dict`` that contains useful information:
+
+.. sourcecode:: ipython
 
 	In [9]: result_dict = mec.execute('d=10; print d')
 
 	In [10]: for r in result_dict:
 	   ....:     print r
 	   ....:     
 	   ....:     
 	{'input': {'translated': 'd=10; print d', 'raw': 'd=10; print d'}, 'number': 5, 'id': 0, 'stdout': '10\n'}
 	{'input': {'translated': 'd=10; print d', 'raw': 'd=10; print d'}, 'number': 5, 'id': 1, 'stdout': '10\n'}
 	{'input': {'translated': 'd=10; print d', 'raw': 'd=10; print d'}, 'number': 5, 'id': 2, 'stdout': '10\n'}
 	{'input': {'translated': 'd=10; print d', 'raw': 'd=10; print d'}, 'number': 5, 'id': 3, 'stdout': '10\n'}
 
 Non-blocking execution
 ----------------------
 
 In non-blocking mode, :meth:`execute` submits the command to be executed and
 then returns a :class:`PendingResult` object immediately. The
 :class:`PendingResult` object gives you a way of getting a result at a later
 time through its :meth:`get_result` method or :attr:`r` attribute. This allows
 you to quickly submit long running commands without blocking your local
-Python/IPython session::
+Python/IPython session:
+
+.. sourcecode:: ipython
 
 	# In blocking mode
 	In [6]: mec.execute('import time')
 	Out[6]:
 	<Results List>
 	[0] In [1]: import time
 	[1] In [1]: import time
 	[2] In [1]: import time
 	[3] In [1]: import time
 
 	# In non-blocking mode
 	In [7]: pr = mec.execute('time.sleep(10)',block=False)
 
 	# Now block for the result
 	In [8]: pr.get_result()
 	Out[8]:
 	<Results List>
 	[0] In [2]: time.sleep(10)
 	[1] In [2]: time.sleep(10)
 	[2] In [2]: time.sleep(10)
 	[3] In [2]: time.sleep(10)
 
 	# Again in non-blocking mode
 	In [9]: pr = mec.execute('time.sleep(10)',block=False)
 
 	# Poll to see if the result is ready
 	In [10]: pr.get_result(block=False)
 
 	# A shorthand for get_result(block=True)
 	In [11]: pr.r
 	Out[11]:
 	<Results List>
 	[0] In [3]: time.sleep(10)
 	[1] In [3]: time.sleep(10)
 	[2] In [3]: time.sleep(10)
 	[3] In [3]: time.sleep(10)
 
 Often, it is desirable to wait until a set of :class:`PendingResult` objects
 are done. For this, there is a the method :meth:`barrier`. This method takes a
 tuple of :class:`PendingResult` objects and blocks until all of the associated
-results are ready::
+results are ready:
+
+.. sourcecode:: ipython
 
 	In [72]: mec.block=False
 
 	# A trivial list of PendingResults objects
 	In [73]: pr_list = [mec.execute('time.sleep(3)') for i in range(10)]
 
 	# Wait until all of them are done
 	In [74]: mec.barrier(pr_list)
 
 	# Then, their results are ready using get_result or the r attribute
 	In [75]: pr_list[0].r
 	Out[75]: 
 	<Results List>
 	[0] In [20]: time.sleep(3)
 	[1] In [19]: time.sleep(3)
 	[2] In [20]: time.sleep(3)
 	[3] In [19]: time.sleep(3)
 
 
 The ``block`` and ``targets`` keyword arguments and attributes
 --------------------------------------------------------------
 
 Most methods in the multiengine interface (like :meth:`execute`) accept
 ``block`` and ``targets`` as keyword arguments. As we have seen above, these
 keyword arguments control the blocking mode and which engines the command is
 applied to. The :class:`MultiEngineClient` class also has :attr:`block` and
 :attr:`targets` attributes that control the default behavior when the keyword
 arguments are not provided. Thus the following logic is used for :attr:`block`
 and :attr:`targets`:
 
 * If no keyword argument is provided, the instance attributes are used.
 * Keyword argument, if provided override the instance attributes.
 
-The following examples demonstrate how to use the instance attributes::
+The following examples demonstrate how to use the instance attributes:
+
+.. sourcecode:: ipython
 
 	In [16]: mec.targets = [0,2]
 
 	In [17]: mec.block = False
 
 	In [18]: pr = mec.execute('a=5')
 
 	In [19]: pr.r
 	Out[19]: 
 	<Results List>
 	[0] In [6]: a=5
 	[2] In [6]: a=5
 
 	# Note targets='all' means all engines
 	In [20]: mec.targets = 'all'
 
 	In [21]: mec.block = True
 
 	In [22]: mec.execute('b=10; print b')
 	Out[22]: 
 	<Results List>
 	[0] In [7]: b=10; print b
 	[0] Out[7]: 10
 
 	[1] In [6]: b=10; print b
 	[1] Out[6]: 10
 
 	[2] In [7]: b=10; print b
 	[2] Out[7]: 10
 
 	[3] In [6]: b=10; print b
 	[3] Out[6]: 10
 
 The :attr:`block` and :attr:`targets` instance attributes also determine the
 behavior of the parallel magic commands.
 
 
 Parallel magic commands
 -----------------------
 
 We provide a few IPython magic commands (``%px``, ``%autopx`` and ``%result``)
 that make it more pleasant to execute Python commands on the engines
 interactively. These are simply shortcuts to :meth:`execute` and
 :meth:`get_result`. The ``%px`` magic executes a single Python command on the
 engines specified by the :attr:`targets` attribute of the
-:class:`MultiEngineClient` instance (by default this is ``'all'``)::
+:class:`MultiEngineClient` instance (by default this is ``'all'``):
+
+.. sourcecode:: ipython
 
 	# Make this MultiEngineClient active for parallel magic commands
 	In [23]: mec.activate()
 
 	In [24]: mec.block=True
 
 	In [25]: import numpy
 
 	In [26]: %px import numpy
 	Executing command on Controller
 	Out[26]:
 	<Results List>
 	[0] In [8]: import numpy
 	[1] In [7]: import numpy
 	[2] In [8]: import numpy
 	[3] In [7]: import numpy
 
 
 	In [27]: %px a = numpy.random.rand(2,2)
 	Executing command on Controller
 	Out[27]:
 	<Results List>
 	[0] In [9]: a = numpy.random.rand(2,2)
 	[1] In [8]: a = numpy.random.rand(2,2)
 	[2] In [9]: a = numpy.random.rand(2,2)
 	[3] In [8]: a = numpy.random.rand(2,2)
 
 
 	In [28]: %px print numpy.linalg.eigvals(a)
 	Executing command on Controller
 	Out[28]:
 	<Results List>
 	[0] In [10]: print numpy.linalg.eigvals(a)
 	[0] Out[10]: [ 1.28167017  0.14197338]
 
 	[1] In [9]: print numpy.linalg.eigvals(a)
 	[1] Out[9]: [-0.14093616  1.27877273]
 
 	[2] In [10]: print numpy.linalg.eigvals(a)
 	[2] Out[10]: [-0.37023573  1.06779409]
 
 	[3] In [9]: print numpy.linalg.eigvals(a)
 	[3] Out[9]: [ 0.83664764 -0.25602658]
 
 The ``%result`` magic gets and prints the stdin/stdout/stderr of the last
 command executed on each engine. It is simply a shortcut to the
-:meth:`get_result` method::
+:meth:`get_result` method:
+
+.. sourcecode:: ipython
 
 	In [29]: %result
 	Out[29]:
 	<Results List>
 	[0] In [10]: print numpy.linalg.eigvals(a)
 	[0] Out[10]: [ 1.28167017  0.14197338]
 
 	[1] In [9]: print numpy.linalg.eigvals(a)
 	[1] Out[9]: [-0.14093616  1.27877273]
 
 	[2] In [10]: print numpy.linalg.eigvals(a)
 	[2] Out[10]: [-0.37023573  1.06779409]
 
 	[3] In [9]: print numpy.linalg.eigvals(a)
 	[3] Out[9]: [ 0.83664764 -0.25602658]
 
 The ``%autopx`` magic switches to a mode where everything you type is executed
-on the engines given by the :attr:`targets` attribute::
+on the engines given by the :attr:`targets` attribute:
+
+.. sourcecode:: ipython
 
 	In [30]: mec.block=False
 
 	In [31]: %autopx
 	Auto Parallel Enabled
 	Type %autopx to disable
 
 	In [32]: max_evals = []
 	<IPython.kernel.multiengineclient.PendingResult object at 0x17b8a70>
 
 	In [33]: for i in range(100):
 	   ....:     a = numpy.random.rand(10,10)
 	   ....:     a = a+a.transpose()
 	   ....:     evals = numpy.linalg.eigvals(a)
 	   ....:     max_evals.append(evals[0].real)
 	   ....:
 	   ....:
 	<IPython.kernel.multiengineclient.PendingResult object at 0x17af8f0>
 
 	In [34]: %autopx
 	Auto Parallel Disabled
 
 	In [35]: mec.block=True
 
 	In [36]: px print "Average max eigenvalue is: ", sum(max_evals)/len(max_evals)
 	Executing command on Controller
 	Out[36]:
 	<Results List>
 	[0] In [13]: print "Average max eigenvalue is: ", sum(max_evals)/len(max_evals)
 	[0] Out[13]: Average max eigenvalue is:  10.1387247332
 
 	[1] In [12]: print "Average max eigenvalue is: ", sum(max_evals)/len(max_evals)
 	[1] Out[12]: Average max eigenvalue is:  10.2076902286
 
 	[2] In [13]: print "Average max eigenvalue is: ", sum(max_evals)/len(max_evals)
 	[2] Out[13]: Average max eigenvalue is:  10.1891484655
 
 	[3] In [12]: print "Average max eigenvalue is: ", sum(max_evals)/len(max_evals)
 	[3] Out[12]: Average max eigenvalue is:  10.1158837784
 
 
 Moving Python objects around
 ============================
 
 In addition to executing code on engines, you can transfer Python objects to
 and from your IPython session and the engines. In IPython, these operations
 are called :meth:`push` (sending an object to the engines) and :meth:`pull`
 (getting an object from the engines).
 
 Basic push and pull
 -------------------
 
-Here are some examples of how you use :meth:`push` and :meth:`pull`::
+Here are some examples of how you use :meth:`push` and :meth:`pull`:
+
+.. sourcecode:: ipython
 
 	In [38]: mec.push(dict(a=1.03234,b=3453))
 	Out[38]: [None, None, None, None]
 
 	In [39]: mec.pull('a')
 	Out[39]: [1.03234, 1.03234, 1.03234, 1.03234]
 
 	In [40]: mec.pull('b',targets=0)
 	Out[40]: [3453]
 
 	In [41]: mec.pull(('a','b'))
 	Out[41]: [[1.03234, 3453], [1.03234, 3453], [1.03234, 3453], [1.03234, 3453]]
 
 	In [42]: mec.zip_pull(('a','b'))
 	Out[42]: [(1.03234, 1.03234, 1.03234, 1.03234), (3453, 3453, 3453, 3453)]
 
 	In [43]: mec.push(dict(c='speed'))
 	Out[43]: [None, None, None, None]
 
 	In [44]: %px print c
 	Executing command on Controller
 	Out[44]: 
 	<Results List>
 	[0] In [14]: print c
 	[0] Out[14]: speed
 
 	[1] In [13]: print c
 	[1] Out[13]: speed
 
 	[2] In [14]: print c
 	[2] Out[14]: speed
 
 	[3] In [13]: print c
 	[3] Out[13]: speed
 
 In non-blocking mode :meth:`push` and :meth:`pull` also return
-:class:`PendingResult` objects::
+:class:`PendingResult` objects:
+
+.. sourcecode:: ipython
 
 	In [47]: mec.block=False
 
 	In [48]: pr = mec.pull('a')
 
 	In [49]: pr.r
 	Out[49]: [1.03234, 1.03234, 1.03234, 1.03234]
 
 
 Push and pull for functions
 ---------------------------
 
 Functions can also be pushed and pulled using :meth:`push_function` and
-:meth:`pull_function`::
+:meth:`pull_function`:
 
+.. sourcecode:: ipython
 
     In [52]: mec.block=True
 
 	In [53]: def f(x):
 	   ....:     return 2.0*x**4
 	   ....: 
 
 	In [54]: mec.push_function(dict(f=f))
 	Out[54]: [None, None, None, None]
 
 	In [55]: mec.execute('y = f(4.0)')
 	Out[55]: 
 	<Results List>
 	[0] In [15]: y = f(4.0)
 	[1] In [14]: y = f(4.0)
 	[2] In [15]: y = f(4.0)
 	[3] In [14]: y = f(4.0)
 
 
 	In [56]: px print y
 	Executing command on Controller
 	Out[56]: 
 	<Results List>
 	[0] In [16]: print y
 	[0] Out[16]: 512.0
 
 	[1] In [15]: print y
 	[1] Out[15]: 512.0
 
 	[2] In [16]: print y
 	[2] Out[16]: 512.0
 
 	[3] In [15]: print y
 	[3] Out[15]: 512.0
 
 
 Dictionary interface
 --------------------
 
 As a shorthand to :meth:`push` and :meth:`pull`, the
 :class:`MultiEngineClient` class implements some of the Python dictionary
 interface. This make the remote namespaces of the engines appear as a local
-dictionary. Underneath, this uses :meth:`push` and :meth:`pull`::
+dictionary. Underneath, this uses :meth:`push` and :meth:`pull`:
+
+.. sourcecode:: ipython
 
 	In [50]: mec.block=True
 
 	In [51]: mec['a']=['foo','bar']
 
 	In [52]: mec['a']
 	Out[52]: [['foo', 'bar'], ['foo', 'bar'], ['foo', 'bar'], ['foo', 'bar']]
 
 Scatter and gather
 ------------------
 
 Sometimes it is useful to partition a sequence and push the partitions to
 different engines. In MPI language, this is know as scatter/gather and we
 follow that terminology. However, it is important to remember that in
 IPython's :class:`MultiEngineClient` class, :meth:`scatter` is from the
 interactive IPython session to the engines and :meth:`gather` is from the
 engines back to the interactive IPython session. For scatter/gather operations
-between engines, MPI should be used::
+between engines, MPI should be used:
+
+.. sourcecode:: ipython
 
 	In [58]: mec.scatter('a',range(16))
 	Out[58]: [None, None, None, None]
 
 	In [59]: px print a
 	Executing command on Controller
 	Out[59]: 
 	<Results List>
 	[0] In [17]: print a
 	[0] Out[17]: [0, 1, 2, 3]
 
 	[1] In [16]: print a
 	[1] Out[16]: [4, 5, 6, 7]
 
 	[2] In [17]: print a
 	[2] Out[17]: [8, 9, 10, 11]
 
 	[3] In [16]: print a
 	[3] Out[16]: [12, 13, 14, 15]
 
 
 	In [60]: mec.gather('a')
 	Out[60]: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
 
 Other things to look at
 =======================
 
 How to do parallel list comprehensions
 --------------------------------------
 
 In many cases list comprehensions are nicer than using the map function. While
 we don't have fully parallel list comprehensions, it is simple to get the
-basic effect using :meth:`scatter` and :meth:`gather`::
+basic effect using :meth:`scatter` and :meth:`gather`:
+
+.. sourcecode:: ipython
 
 	In [66]: mec.scatter('x',range(64))
 	Out[66]: [None, None, None, None]
 
 	In [67]: px y = [i**10 for i in x]
 	Executing command on Controller
 	Out[67]: 
 	<Results List>
 	[0] In [19]: y = [i**10 for i in x]
 	[1] In [18]: y = [i**10 for i in x]
 	[2] In [19]: y = [i**10 for i in x]
 	[3] In [18]: y = [i**10 for i in x]
 
 
 	In [68]: y = mec.gather('y')
 
 	In [69]: print y
 	[0, 1, 1024, 59049, 1048576, 9765625, 60466176, 282475249, 1073741824,...]
 
 Parallel exceptions
 -------------------
 
 In the multiengine interface, parallel commands can raise Python exceptions,
 just like serial commands. But, it is a little subtle, because a single
 parallel command can actually raise multiple exceptions (one for each engine
 the command was run on). To express this idea, the MultiEngine interface has a
 :exc:`CompositeError` exception class that will be raised in most cases. The
 :exc:`CompositeError` class is a special type of exception that wraps one or
-more other types of exceptions. Here is how it works::
+more other types of exceptions. Here is how it works:
+
+.. sourcecode:: ipython
 
 	In [76]: mec.block=True
 
 	In [77]: mec.execute('1/0')
 	---------------------------------------------------------------------------
 	CompositeError                            Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<ipython console> in <module>()
 
 	/ipython1-client-r3021/ipython1/kernel/multiengineclient.pyc in execute(self, lines, targets, block)
 	    432         targets, block = self._findTargetsAndBlock(targets, block)
 	    433         result = blockingCallFromThread(self.smultiengine.execute, lines,
 	--> 434             targets=targets, block=block)
 	    435         if block:
 	    436             result = ResultList(result)
 
 	/ipython1-client-r3021/ipython1/kernel/twistedutil.pyc in blockingCallFromThread(f, *a, **kw)
 	     72             result.raiseException()
 	     73         except Exception, e:
 	---> 74             raise e
 	     75     return result
 	     76 
 
 	CompositeError: one or more exceptions from call to method: execute
 	[0:execute]: ZeroDivisionError: integer division or modulo by zero
 	[1:execute]: ZeroDivisionError: integer division or modulo by zero
 	[2:execute]: ZeroDivisionError: integer division or modulo by zero
 	[3:execute]: ZeroDivisionError: integer division or modulo by zero
 
-Notice how the error message printed when :exc:`CompositeError` is raised has information about the individual exceptions that were raised on each engine.  If you want, you can even raise one of these original exceptions::
+Notice how the error message printed when :exc:`CompositeError` is raised has information about the individual exceptions that were raised on each engine.  If you want, you can even raise one of these original exceptions:
+
+.. sourcecode:: ipython
 
 	In [80]: try:
 	   ....:     mec.execute('1/0')
 	   ....: except client.CompositeError, e:
 	   ....:     e.raise_exception()
 	   ....:     
 	   ....:     
 	---------------------------------------------------------------------------
 	ZeroDivisionError                         Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<ipython console> in <module>()
 
 	/ipython1-client-r3021/ipython1/kernel/error.pyc in raise_exception(self, excid)
 	    156             raise IndexError("an exception with index %i does not exist"%excid)
 	    157         else:
 	--> 158             raise et, ev, etb
 	    159 
 	    160 def collect_exceptions(rlist, method):
 
 	ZeroDivisionError: integer division or modulo by zero
 
 If you are working in IPython, you can simple type ``%debug`` after one of
 these :exc:`CompositeError` exceptions is raised, and inspect the exception
-instance::
+instance:
+
+.. sourcecode:: ipython
 
 	In [81]: mec.execute('1/0')
 	---------------------------------------------------------------------------
 	CompositeError                            Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<ipython console> in <module>()
 
 	/ipython1-client-r3021/ipython1/kernel/multiengineclient.pyc in execute(self, lines, targets, block)
 	    432         targets, block = self._findTargetsAndBlock(targets, block)
 	    433         result = blockingCallFromThread(self.smultiengine.execute, lines,
 	--> 434             targets=targets, block=block)
 	    435         if block:
 	    436             result = ResultList(result)
 
 	/ipython1-client-r3021/ipython1/kernel/twistedutil.pyc in blockingCallFromThread(f, *a, **kw)
 	     72             result.raiseException()
 	     73         except Exception, e:
 	---> 74             raise e
 	     75     return result
 	     76 
 
 	CompositeError: one or more exceptions from call to method: execute
 	[0:execute]: ZeroDivisionError: integer division or modulo by zero
 	[1:execute]: ZeroDivisionError: integer division or modulo by zero
 	[2:execute]: ZeroDivisionError: integer division or modulo by zero
 	[3:execute]: ZeroDivisionError: integer division or modulo by zero
 
 	In [82]: %debug
 	> 
 	
 	/ipython1-client-r3021/ipython1/kernel/twistedutil.py(74)blockingCallFromThread()
 	     73         except Exception, e:
 	---> 74             raise e
 	     75     return result
 
 	# With the debugger running, e is the exceptions instance.  We can tab complete
 	# on it and see the extra methods that are available.
 	ipdb> e.
 	e.__class__         e.__getitem__       e.__new__           e.__setstate__      e.args
 	e.__delattr__       e.__getslice__      e.__reduce__        e.__str__           e.elist
 	e.__dict__          e.__hash__          e.__reduce_ex__     e.__weakref__       e.message
 	e.__doc__           e.__init__          e.__repr__          e._get_engine_str   e.print_tracebacks
 	e.__getattribute__  e.__module__        e.__setattr__       e._get_traceback    e.raise_exception
 	ipdb> e.print_tracebacks()
 	[0:execute]: 
 	---------------------------------------------------------------------------
 	ZeroDivisionError                         Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<string> in <module>()
 
 	ZeroDivisionError: integer division or modulo by zero
 
 	[1:execute]: 
 	---------------------------------------------------------------------------
 	ZeroDivisionError                         Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<string> in <module>()
 
 	ZeroDivisionError: integer division or modulo by zero
 
 	[2:execute]: 
 	---------------------------------------------------------------------------
 	ZeroDivisionError                         Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<string> in <module>()
 
 	ZeroDivisionError: integer division or modulo by zero
 
 	[3:execute]: 
 	---------------------------------------------------------------------------
 	ZeroDivisionError                         Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<string> in <module>()
 
 	ZeroDivisionError: integer division or modulo by zero
 
 .. note::
 
     The above example appears to be broken right now because of a change in 
     how we are using Twisted.
 
-All of this same error handling magic even works in non-blocking mode::
+All of this same error handling magic even works in non-blocking mode:
+
+.. sourcecode:: ipython
 
 	In [83]: mec.block=False
 
 	In [84]: pr = mec.execute('1/0')
 
 	In [85]: pr.r
 	---------------------------------------------------------------------------
 	CompositeError                            Traceback (most recent call last)
 
 	/ipython1-client-r3021/docs/examples/<ipython console> in <module>()
 
 	/ipython1-client-r3021/ipython1/kernel/multiengineclient.pyc in _get_r(self)
 	    170 
 	    171     def _get_r(self):
 	--> 172         return self.get_result(block=True)
 	    173 
 	    174     r = property(_get_r)
 
 	/ipython1-client-r3021/ipython1/kernel/multiengineclient.pyc in get_result(self, default, block)
 	    131                 return self.result
 	    132         try:
 	--> 133             result = self.client.get_pending_deferred(self.result_id, block)
 	    134         except error.ResultNotCompleted:
 	    135             return default
 
 	/ipython1-client-r3021/ipython1/kernel/multiengineclient.pyc in get_pending_deferred(self, deferredID, block)
 	    385 
 	    386     def get_pending_deferred(self, deferredID, block):
 	--> 387         return blockingCallFromThread(self.smultiengine.get_pending_deferred, deferredID, block)
 	    388 
 	    389     def barrier(self, pendingResults):
 
 	/ipython1-client-r3021/ipython1/kernel/twistedutil.pyc in blockingCallFromThread(f, *a, **kw)
 	     72             result.raiseException()
 	     73         except Exception, e:
 	---> 74             raise e
 	     75     return result
 	     76 
 
 	CompositeError: one or more exceptions from call to method: execute
 	[0:execute]: ZeroDivisionError: integer division or modulo by zero
 	[1:execute]: ZeroDivisionError: integer division or modulo by zero
 	[2:execute]: ZeroDivisionError: integer division or modulo by zero
 	[3:execute]: ZeroDivisionError: integer division or modulo by zero
 
 

docs/source/parallel/parallel_task.txt

@@ -1,93 +1,99 b''
 .. _paralleltask:
 
 ==========================
 The IPython task interface
 ==========================
 
-.. contents::
-
 The task interface to the controller presents the engines as a fault tolerant, dynamic load-balanced system or workers. Unlike the multiengine interface, in the task interface, the user have no direct access to individual engines. In some ways, this interface is simpler, but in other ways it is more powerful.
 
 Best of all the user can use both of these interfaces running at the same time to take advantage or both of their strengths.  When the user can break up the user's work into segments that do not depend on previous execution, the task interface is ideal.  But it also has more power and flexibility, allowing the user to guide the distribution of jobs, without having to assign tasks to engines explicitly.
 
 Starting the IPython controller and engines
 ===========================================
 
 To follow along with this tutorial, you will need to start the IPython
 controller and four IPython engines. The simplest way of doing this is to use
 the :command:`ipcluster` command::
 
-	$ ipcluster -n 4
+	$ ipcluster local -n 4
 	
 For more detailed information about starting the controller and engines, see
 our :ref:`introduction <ip1par>` to using IPython for parallel computing.
 
 Creating a ``TaskClient`` instance
 =========================================
 
 The first step is to import the IPython :mod:`IPython.kernel.client` module
-and then create a :class:`TaskClient` instance::
+and then create a :class:`TaskClient` instance:
+
+.. sourcecode:: ipython
 
 	In [1]: from IPython.kernel import client
 	
 	In [2]: tc = client.TaskClient()
 
 This form assumes that the :file:`ipcontroller-tc.furl` is in the
 :file:`~./ipython/security` directory on the client's host. If not, the
-location of the ``.furl`` file must be given as an argument to the
-constructor::
+location of the FURL file must be given as an argument to the
+constructor:
+
+.. sourcecode:: ipython
 
-    In[2]: mec = client.TaskClient('/path/to/my/ipcontroller-tc.furl')
+    In [2]: mec = client.TaskClient('/path/to/my/ipcontroller-tc.furl')
 
 Quick and easy parallelism
 ==========================
 
 In many cases, you simply want to apply a Python function to a sequence of objects, but *in parallel*.  Like the multiengine interface, the task interface provides two simple ways of accomplishing this:  a parallel version of :func:`map` and ``@parallel`` function decorator.  However, the verions in the task interface have one important difference:  they are dynamically load balanced.  Thus, if the execution time per item varies significantly, you should use the versions in the task interface.
 
 Parallel map
 ------------
 
-The parallel :meth:`map` in the task interface is similar to that in the multiengine interface::
+The parallel :meth:`map` in the task interface is similar to that in the multiengine interface:
+
+.. sourcecode:: ipython
 
 	In [63]: serial_result = map(lambda x:x**10, range(32))
 
 	In [64]: parallel_result = tc.map(lambda x:x**10, range(32))
 
 	In [65]: serial_result==parallel_result
 	Out[65]: True
 
 Parallel function decorator
 ---------------------------
 
-Parallel functions are just like normal function, but they can be called on sequences and *in parallel*.  The multiengine interface provides a decorator that turns any Python function into a parallel function::
+Parallel functions are just like normal function, but they can be called on sequences and *in parallel*.  The multiengine interface provides a decorator that turns any Python function into a parallel function:
+
+.. sourcecode:: ipython
 
     In [10]: @tc.parallel()
        ....: def f(x):
        ....:     return 10.0*x**4
        ....: 
 
     In [11]: f(range(32))    # this is done in parallel
     Out[11]: 
     [0.0,10.0,160.0,...]
 
 More details
 ============
 
 The :class:`TaskClient` has many more powerful features that allow quite a bit of flexibility in how tasks are defined and run.  The next places to look are in the following classes:
 
 * :class:`IPython.kernel.client.TaskClient`
 * :class:`IPython.kernel.client.StringTask`
 * :class:`IPython.kernel.client.MapTask`
 
 The following is an overview of how to use these classes together:
 
 1. Create a :class:`TaskClient`.
 2. Create one or more instances of :class:`StringTask` or :class:`MapTask`
    to define your tasks.
 3. Submit your tasks to using the :meth:`run` method of your
    :class:`TaskClient` instance.
 4. Use :meth:`TaskClient.get_task_result` to get the results of the
    tasks.
 
 We are in the process of developing more detailed information about the task interface.  For now, the docstrings of the :class:`TaskClient`, :class:`StringTask` and :class:`MapTask` classes should be consulted.