Add tests to ensure that %run does not modify __builtins__

I will open a ticket for this, the current code only has the failing tests,
I still need to find a fix.

IPython/Prompts.py

@@ -1,622 +1,626 b''
 # -*- coding: utf-8 -*-
 """
 Classes for handling input/output prompts.
 """
 
 #*****************************************************************************
 #       Copyright (C) 2008-2009 The IPython Development Team
 #       Copyright (C) 2001-2007 Fernando Perez <[e-mail]>
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #*****************************************************************************
 
 #****************************************************************************
 # Required modules
 import __builtin__
 import os
 import socket
 import sys
 import time
 
 # IPython's own
 from IPython import ColorANSI
 from IPython import Release
 from IPython.external.Itpl import ItplNS
 from IPython.ipapi import TryNext
 from IPython.ipstruct import Struct
 from IPython.macro import Macro
 
 from IPython.genutils import *
 
 #****************************************************************************
 #Color schemes for Prompts.
 
 PromptColors = ColorANSI.ColorSchemeTable()
 InputColors = ColorANSI.InputTermColors  # just a shorthand
 Colors = ColorANSI.TermColors  # just a shorthand
 
 PromptColors.add_scheme(ColorANSI.ColorScheme(
     'NoColor',
     in_prompt  = InputColors.NoColor,  # Input prompt
     in_number  = InputColors.NoColor,  # Input prompt number
     in_prompt2 = InputColors.NoColor, # Continuation prompt
     in_normal  = InputColors.NoColor,  # color off (usu. Colors.Normal)
     
     out_prompt = Colors.NoColor, # Output prompt
     out_number = Colors.NoColor, # Output prompt number
 
     normal = Colors.NoColor  # color off (usu. Colors.Normal)
     ))
 
 # make some schemes as instances so we can copy them for modification easily:
 __PColLinux =  ColorANSI.ColorScheme(
     'Linux',
     in_prompt  = InputColors.Green,
     in_number  = InputColors.LightGreen,
     in_prompt2 = InputColors.Green,
     in_normal  = InputColors.Normal,  # color off (usu. Colors.Normal)
 
     out_prompt = Colors.Red,
     out_number = Colors.LightRed,
 
     normal = Colors.Normal
     )
 # Don't forget to enter it into the table!
 PromptColors.add_scheme(__PColLinux)
 
 # Slightly modified Linux for light backgrounds
 __PColLightBG  = __PColLinux.copy('LightBG')
 
 __PColLightBG.colors.update(
     in_prompt  = InputColors.Blue,
     in_number  = InputColors.LightBlue,
     in_prompt2 = InputColors.Blue
 )
 PromptColors.add_scheme(__PColLightBG)
 
 del Colors,InputColors
 
 #-----------------------------------------------------------------------------
 def multiple_replace(dict, text):
     """ Replace in 'text' all occurences of any key in the given
     dictionary by its corresponding value.  Returns the new string."""
 
     # Function by Xavier Defrang, originally found at:
     # http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/81330
 
     # Create a regular expression  from the dictionary keys
     regex = re.compile("(%s)" % "|".join(map(re.escape, dict.keys())))
     # For each match, look-up corresponding value in dictionary
     return regex.sub(lambda mo: dict[mo.string[mo.start():mo.end()]], text)
 
 #-----------------------------------------------------------------------------
 # Special characters that can be used in prompt templates, mainly bash-like
 
 # If $HOME isn't defined (Windows), make it an absurd string so that it can
 # never be expanded out into '~'.  Basically anything which can never be a
 # reasonable directory name will do, we just want the $HOME -> '~' operation
 # to become a no-op.  We pre-compute $HOME here so it's not done on every
 # prompt call.
 
 # FIXME:
 
 # - This should be turned into a class which does proper namespace management,
 # since the prompt specials need to be evaluated in a certain namespace.
 # Currently it's just globals, which need to be managed manually by code
 # below.
 
 # - I also need to split up the color schemes from the prompt specials
 # somehow.  I don't have a clean design for that quite yet.
 
 HOME = os.environ.get("HOME","//////:::::ZZZZZ,,,~~~")
 
 # We precompute a few more strings here for the prompt_specials, which are
 # fixed once ipython starts.  This reduces the runtime overhead of computing
 # prompt strings.
 USER           = os.environ.get("USER")
 HOSTNAME       = socket.gethostname()
 HOSTNAME_SHORT = HOSTNAME.split(".")[0]
 ROOT_SYMBOL    = "$#"[os.name=='nt' or os.getuid()==0]
 
 prompt_specials_color = {
     # Prompt/history count
     '%n' : '${self.col_num}' '${self.cache.prompt_count}' '${self.col_p}',
     r'\#': '${self.col_num}' '${self.cache.prompt_count}' '${self.col_p}',
     # Just the prompt counter number, WITHOUT any coloring wrappers, so users
     # can get numbers displayed in whatever color they want.
     r'\N': '${self.cache.prompt_count}',
+
     # Prompt/history count, with the actual digits replaced by dots.  Used
     # mainly in continuation prompts (prompt_in2)
+    #r'\D': '${"."*len(str(self.cache.prompt_count))}',
+    # More robust form of the above expression, that uses __builtins__
     r'\D': '${"."*__builtins__.len(__builtins__.str(self.cache.prompt_count))}',
+
     # Current working directory
     r'\w': '${os.getcwd()}',
     # Current time
     r'\t' : '${time.strftime("%H:%M:%S")}',
     # Basename of current working directory.
     # (use os.sep to make this portable across OSes)
     r'\W' : '${os.getcwd().split("%s")[-1]}' % os.sep,
     # These X<N> are an extension to the normal bash prompts.  They return
     # N terms of the path, after replacing $HOME with '~'
     r'\X0': '${os.getcwd().replace("%s","~")}' % HOME,
     r'\X1': '${self.cwd_filt(1)}',
     r'\X2': '${self.cwd_filt(2)}',
     r'\X3': '${self.cwd_filt(3)}',
     r'\X4': '${self.cwd_filt(4)}',
     r'\X5': '${self.cwd_filt(5)}',
     # Y<N> are similar to X<N>, but they show '~' if it's the directory
     # N+1 in the list.  Somewhat like %cN in tcsh.
     r'\Y0': '${self.cwd_filt2(0)}',
     r'\Y1': '${self.cwd_filt2(1)}',
     r'\Y2': '${self.cwd_filt2(2)}',
     r'\Y3': '${self.cwd_filt2(3)}',
     r'\Y4': '${self.cwd_filt2(4)}',
     r'\Y5': '${self.cwd_filt2(5)}',
     # Hostname up to first .
     r'\h': HOSTNAME_SHORT,
     # Full hostname
     r'\H': HOSTNAME,
     # Username of current user
     r'\u': USER,
     # Escaped '\'
     '\\\\': '\\',
     # Newline
     r'\n': '\n',
     # Carriage return
     r'\r': '\r',
     # Release version
     r'\v': Release.version,
     # Root symbol ($ or #)
     r'\$': ROOT_SYMBOL,
     }
 
 # A copy of the prompt_specials dictionary but with all color escapes removed,
 # so we can correctly compute the prompt length for the auto_rewrite method.
 prompt_specials_nocolor = prompt_specials_color.copy()
 prompt_specials_nocolor['%n'] = '${self.cache.prompt_count}'
 prompt_specials_nocolor[r'\#'] = '${self.cache.prompt_count}'
 
 # Add in all the InputTermColors color escapes as valid prompt characters.
 # They all get added as \\C_COLORNAME, so that we don't have any conflicts
 # with a color name which may begin with a letter used by any other of the
 # allowed specials.  This of course means that \\C will never be allowed for
 # anything else.
 input_colors = ColorANSI.InputTermColors
 for _color in dir(input_colors):
     if _color[0] != '_':
         c_name = r'\C_'+_color
         prompt_specials_color[c_name] = getattr(input_colors,_color)
         prompt_specials_nocolor[c_name] = ''
 
 # we default to no color for safety.  Note that prompt_specials is a global
 # variable used by all prompt objects.
 prompt_specials = prompt_specials_nocolor
 
 #-----------------------------------------------------------------------------
 def str_safe(arg):
     """Convert to a string, without ever raising an exception.
 
     If str(arg) fails, <ERROR: ... > is returned, where ... is the exception
     error message."""
 
     try:
         out = str(arg)
     except UnicodeError:
         try:
             out = arg.encode('utf_8','replace')
         except Exception,msg:
             # let's keep this little duplication here, so that the most common
             # case doesn't suffer from a double try wrapping.
             out = '<ERROR: %s>' % msg
     except Exception,msg:
         out = '<ERROR: %s>' % msg
     return out
 
 class BasePrompt(object):
     """Interactive prompt similar to Mathematica's."""
 
     def _get_p_template(self):
         return self._p_template
 
     def _set_p_template(self,val):
         self._p_template = val
         self.set_p_str()
 
     p_template = property(_get_p_template,_set_p_template,
                           doc='Template for prompt string creation')
 
     def __init__(self,cache,sep,prompt,pad_left=False):
 
         # Hack: we access information about the primary prompt through the
         # cache argument.  We need this, because we want the secondary prompt
         # to be aligned with the primary one.  Color table info is also shared
         # by all prompt classes through the cache.  Nice OO spaghetti code!
         self.cache = cache
         self.sep = sep
         
         # regexp to count the number of spaces at the end of a prompt
         # expression, useful for prompt auto-rewriting
         self.rspace = re.compile(r'(\s*)$')
         # Flag to left-pad prompt strings to match the length of the primary
         # prompt
         self.pad_left = pad_left
 
         # Set template to create each actual prompt (where numbers change).
         # Use a property
         self.p_template = prompt
         self.set_p_str()
 
     def set_p_str(self):
         """ Set the interpolating prompt strings.
 
         This must be called every time the color settings change, because the
         prompt_specials global may have changed."""
 
         import os,time  # needed in locals for prompt string handling
         loc = locals()
         try:
             self.p_str = ItplNS('%s%s%s' %
                                 ('${self.sep}${self.col_p}',
                                  multiple_replace(prompt_specials, self.p_template),
                                  '${self.col_norm}'),self.cache.user_ns,loc)
     
             self.p_str_nocolor = ItplNS(multiple_replace(prompt_specials_nocolor,
                                                          self.p_template),
                                         self.cache.user_ns,loc)
         except:
             print "Illegal prompt template (check $ usage!):",self.p_template
             self.p_str = self.p_template
             self.p_str_nocolor = self.p_template
 
     def write(self,msg):  # dbg
         sys.stdout.write(msg)
         return ''
 
     def __str__(self):
         """Return a string form of the prompt.
 
         This for is useful for continuation and output prompts, since it is
         left-padded to match lengths with the primary one (if the
         self.pad_left attribute is set)."""
 
         out_str = str_safe(self.p_str)
         if self.pad_left:
             # We must find the amount of padding required to match lengths,
             # taking the color escapes (which are invisible on-screen) into
             # account.
             esc_pad = len(out_str) - len(str_safe(self.p_str_nocolor))
             format = '%%%ss' % (len(str(self.cache.last_prompt))+esc_pad)
             return format % out_str
         else:
             return out_str
 
     # these path filters are put in as methods so that we can control the
     # namespace where the prompt strings get evaluated
     def cwd_filt(self,depth):
         """Return the last depth elements of the current working directory.
 
         $HOME is always replaced with '~'.
         If depth==0, the full path is returned."""
 
         cwd = os.getcwd().replace(HOME,"~")
         out = os.sep.join(cwd.split(os.sep)[-depth:])
         if out:
             return out
         else:
             return os.sep
 
     def cwd_filt2(self,depth):
         """Return the last depth elements of the current working directory.
 
         $HOME is always replaced with '~'.
         If depth==0, the full path is returned."""
 
         full_cwd = os.getcwd()
         cwd = full_cwd.replace(HOME,"~").split(os.sep)
         if '~' in cwd and len(cwd) == depth+1:
             depth += 1
         drivepart = ''
         if sys.platform == 'win32' and len(cwd) > depth:
             drivepart = os.path.splitdrive(full_cwd)[0]
         out = drivepart + '/'.join(cwd[-depth:])
 
         if out:
             return out
         else:
             return os.sep
 
     def __nonzero__(self):
         """Implement boolean behavior.
 
         Checks whether the p_str attribute is non-empty"""
 
         return bool(self.p_template)
 
 class Prompt1(BasePrompt):
     """Input interactive prompt similar to Mathematica's."""
 
     def __init__(self,cache,sep='\n',prompt='In [\\#]: ',pad_left=True):
         BasePrompt.__init__(self,cache,sep,prompt,pad_left)
 
     def set_colors(self):
         self.set_p_str()
         Colors = self.cache.color_table.active_colors # shorthand
         self.col_p = Colors.in_prompt
         self.col_num = Colors.in_number
         self.col_norm = Colors.in_normal
         # We need a non-input version of these escapes for the '--->'
         # auto-call prompts used in the auto_rewrite() method.
         self.col_p_ni = self.col_p.replace('\001','').replace('\002','') 
         self.col_norm_ni = Colors.normal        
         
     def __str__(self):
         self.cache.prompt_count += 1
         self.cache.last_prompt = str_safe(self.p_str_nocolor).split('\n')[-1]
         return str_safe(self.p_str)
 
     def auto_rewrite(self):
         """Print a string of the form '--->' which lines up with the previous
         input string. Useful for systems which re-write the user input when
         handling automatically special syntaxes."""
 
         curr = str(self.cache.last_prompt)
         nrspaces = len(self.rspace.search(curr).group())
         return '%s%s>%s%s' % (self.col_p_ni,'-'*(len(curr)-nrspaces-1),
                               ' '*nrspaces,self.col_norm_ni)
 
 class PromptOut(BasePrompt):
     """Output interactive prompt similar to Mathematica's."""
 
     def __init__(self,cache,sep='',prompt='Out[\\#]: ',pad_left=True):
         BasePrompt.__init__(self,cache,sep,prompt,pad_left)
         if not self.p_template:
             self.__str__ = lambda: ''
 
     def set_colors(self):
         self.set_p_str()
         Colors = self.cache.color_table.active_colors # shorthand
         self.col_p = Colors.out_prompt
         self.col_num = Colors.out_number
         self.col_norm = Colors.normal
 
 class Prompt2(BasePrompt):
     """Interactive continuation prompt."""
     
     def __init__(self,cache,prompt='   .\\D.: ',pad_left=True):
         self.cache = cache
         self.p_template = prompt
         self.pad_left = pad_left
         self.set_p_str()
 
     def set_p_str(self):
         import os,time  # needed in locals for prompt string handling
         loc = locals()
         self.p_str = ItplNS('%s%s%s' %
                             ('${self.col_p2}',
                              multiple_replace(prompt_specials, self.p_template),
                              '$self.col_norm'),
                             self.cache.user_ns,loc)
         self.p_str_nocolor = ItplNS(multiple_replace(prompt_specials_nocolor,
                                                      self.p_template),
                                     self.cache.user_ns,loc)
 
     def set_colors(self):
         self.set_p_str()
         Colors = self.cache.color_table.active_colors
         self.col_p2 = Colors.in_prompt2
         self.col_norm = Colors.in_normal
         # FIXME (2004-06-16) HACK: prevent crashes for users who haven't
         # updated their prompt_in2 definitions.  Remove eventually.
         self.col_p = Colors.out_prompt
         self.col_num = Colors.out_number
 
 
 #-----------------------------------------------------------------------------
 class CachedOutput:
     """Class for printing output from calculations while keeping a cache of
     reults. It dynamically creates global variables prefixed with _ which
     contain these results.
 
     Meant to be used as a sys.displayhook replacement, providing numbered
     prompts and cache services.
 
     Initialize with initial and final values for cache counter (this defines
     the maximum size of the cache."""
 
     def __init__(self,shell,cache_size,Pprint,
                  colors='NoColor',input_sep='\n',
                  output_sep='\n',output_sep2='',
                  ps1 = None, ps2 = None,ps_out = None,pad_left=True):
 
         cache_size_min = 3
         if cache_size <= 0:
             self.do_full_cache = 0
             cache_size = 0
         elif cache_size < cache_size_min:
             self.do_full_cache = 0
             cache_size = 0
             warn('caching was disabled (min value for cache size is %s).' %
                  cache_size_min,level=3)
         else:
             self.do_full_cache = 1
 
         self.cache_size = cache_size
         self.input_sep = input_sep
 
         # we need a reference to the user-level namespace
         self.shell = shell
         self.user_ns = shell.user_ns
         # and to the user's input
         self.input_hist = shell.input_hist
         # and to the user's logger, for logging output
         self.logger = shell.logger
 
         # Set input prompt strings and colors
         if cache_size == 0:
             if ps1.find('%n') > -1 or ps1.find(r'\#') > -1 \
                    or ps1.find(r'\N') > -1:
                 ps1 = '>>> '
             if ps2.find('%n') > -1 or ps2.find(r'\#') > -1 \
                    or ps2.find(r'\N') > -1:
                 ps2 = '... '
         self.ps1_str = self._set_prompt_str(ps1,'In [\\#]: ','>>> ')
         self.ps2_str = self._set_prompt_str(ps2,'   .\\D.: ','... ')
         self.ps_out_str = self._set_prompt_str(ps_out,'Out[\\#]: ','')
 
         self.color_table = PromptColors
         self.prompt1 = Prompt1(self,sep=input_sep,prompt=self.ps1_str,
                                pad_left=pad_left)
         self.prompt2 = Prompt2(self,prompt=self.ps2_str,pad_left=pad_left)
         self.prompt_out = PromptOut(self,sep='',prompt=self.ps_out_str,
                                     pad_left=pad_left)
         self.set_colors(colors)
 
         # other more normal stuff
         # b/c each call to the In[] prompt raises it by 1, even the first.
         self.prompt_count = 0
         # Store the last prompt string each time, we need it for aligning
         # continuation and auto-rewrite prompts
         self.last_prompt = ''
         self.Pprint = Pprint
         self.output_sep = output_sep
         self.output_sep2 = output_sep2
         self._,self.__,self.___ = '','',''
         self.pprint_types = map(type,[(),[],{}])
         
         # these are deliberately global:
         to_user_ns = {'_':self._,'__':self.__,'___':self.___}
         self.user_ns.update(to_user_ns)
 
     def _set_prompt_str(self,p_str,cache_def,no_cache_def):
         if p_str is None:
             if self.do_full_cache:
                 return cache_def
             else:
                 return no_cache_def
         else:
             return p_str
                 
     def set_colors(self,colors):
         """Set the active color scheme and configure colors for the three
         prompt subsystems."""
 
         # FIXME: the prompt_specials global should be gobbled inside this
         # class instead.  Do it when cleaning up the whole 3-prompt system.
         global prompt_specials
         if colors.lower()=='nocolor':
             prompt_specials = prompt_specials_nocolor
         else:
             prompt_specials = prompt_specials_color
         
         self.color_table.set_active_scheme(colors)
         self.prompt1.set_colors()
         self.prompt2.set_colors()
         self.prompt_out.set_colors()
 
     def __call__(self,arg=None):
         """Printing with history cache management.
         
         This is invoked everytime the interpreter needs to print, and is
         activated by setting the variable sys.displayhook to it."""
 
         # If something injected a '_' variable in __builtin__, delete
         # ipython's automatic one so we don't clobber that.  gettext() in
         # particular uses _, so we need to stay away from it.
         if '_' in __builtin__.__dict__:
             try:
                 del self.user_ns['_']
             except KeyError:
                 pass
         if arg is not None:
             cout_write = Term.cout.write # fast lookup
             # first handle the cache and counters
 
             # do not print output if input ends in ';'
             try:
                 if self.input_hist[self.prompt_count].endswith(';\n'):
                     return
             except IndexError:
                 # some uses of ipshellembed may fail here
                 pass
             # don't use print, puts an extra space
             cout_write(self.output_sep)
             outprompt = self.shell.hooks.generate_output_prompt()
             if self.do_full_cache:
                 cout_write(outprompt)
 
             # and now call a possibly user-defined print mechanism
             manipulated_val = self.display(arg)
             
             # user display hooks can change the variable to be stored in
             # output history
             
             if manipulated_val is not None:
                 arg = manipulated_val
                 
             # avoid recursive reference when displaying _oh/Out
             if arg is not self.user_ns['_oh']:
                 self.update(arg)
 
             if self.logger.log_output:
                 self.logger.log_write(repr(arg),'output')
             cout_write(self.output_sep2)
             Term.cout.flush()
 
     def _display(self,arg):
         """Default printer method, uses pprint.
 
         Do ip.set_hook("result_display", my_displayhook) for custom result
         display, e.g. when your own objects need special formatting.
         """
         try:
             return IPython.generics.result_display(arg)
         except TryNext:            
             return self.shell.hooks.result_display(arg)
 
     # Assign the default display method:
     display = _display
 
     def update(self,arg):
         #print '***cache_count', self.cache_count # dbg
         if len(self.user_ns['_oh']) >= self.cache_size and self.do_full_cache:
             warn('Output cache limit (currently '+
                   `self.cache_size`+' entries) hit.\n'
                  'Flushing cache and resetting history counter...\n'
                  'The only history variables available will be _,__,___ and _1\n'
                  'with the current result.')
 
             self.flush()
         # Don't overwrite '_' and friends if '_' is in __builtin__ (otherwise
         # we cause buggy behavior for things like gettext).
         if '_' not in __builtin__.__dict__:
             self.___ = self.__
             self.__ = self._
             self._ = arg
             self.user_ns.update({'_':self._,'__':self.__,'___':self.___})
             
         # hackish access to top-level  namespace to create _1,_2... dynamically
         to_main = {}
         if self.do_full_cache:
             new_result = '_'+`self.prompt_count`
             to_main[new_result] = arg
             self.user_ns.update(to_main)
             self.user_ns['_oh'][self.prompt_count] = arg
 
     def flush(self):
         if not self.do_full_cache:
             raise ValueError,"You shouldn't have reached the cache flush "\
                   "if full caching is not enabled!"
         # delete auto-generated vars from global namespace
         
         for n in range(1,self.prompt_count + 1):
             key = '_'+`n`
             try:
                 del self.user_ns[key]
             except: pass
         self.user_ns['_oh'].clear()
         
         if '_' not in __builtin__.__dict__:
             self.user_ns.update({'_':None,'__':None, '___':None})
         import gc
         gc.collect() # xxx needed?
 

IPython/testing/plugin/ipdoctest.py

@@ -1,875 +1,885 b''
 """Nose Plugin that supports IPython doctests.
 
 Limitations:
 
 - When generating examples for use as doctests, make sure that you have
   pretty-printing OFF.  This can be done either by starting ipython with the
   flag '--nopprint', by setting pprint to 0 in your ipythonrc file, or by
   interactively disabling it with %Pprint.  This is required so that IPython
   output matches that of normal Python, which is used by doctest for internal
   execution.
 
 - Do not rely on specific prompt numbers for results (such as using
   '_34==True', for example).  For IPython tests run via an external process the
   prompt numbers may be different, and IPython tests run as normal python code
   won't even have these special _NN variables set at all.
 """
 
 #-----------------------------------------------------------------------------
 # Module imports
 
 # From the standard library
 import __builtin__
 import commands
 import doctest
 import inspect
 import logging
 import os
 import re
 import sys
 import traceback
 import unittest
 
 from inspect import getmodule
 from StringIO import StringIO
 
 # We are overriding the default doctest runner, so we need to import a few
 # things from doctest directly
 from doctest import (REPORTING_FLAGS, REPORT_ONLY_FIRST_FAILURE,
                      _unittest_reportflags, DocTestRunner,
                      _extract_future_flags, pdb, _OutputRedirectingPdb,
                      _exception_traceback,
                      linecache)
 
 # Third-party modules
 import nose.core
 
 from nose.plugins import doctests, Plugin
 from nose.util import anyp, getpackage, test_address, resolve_name, tolist
 
 #-----------------------------------------------------------------------------
 # Module globals and other constants
 
 log = logging.getLogger(__name__)
 
 ###########################################################################
 # *** HACK ***
 # We must start our own ipython object and heavily muck with it so that all the
 # modifications IPython makes to system behavior don't send the doctest
 # machinery into a fit.  This code should be considered a gross hack, but it
 # gets the job done.
 
 
 # Hack to modify the %run command so we can sync the user's namespace with the
 # test globals.  Once we move over to a clean magic system, this will be done
 # with much less ugliness.
 
 class py_file_finder(object):
     def __init__(self,test_filename):
         self.test_filename = test_filename
         
     def __call__(self,name):
         from IPython.genutils import get_py_filename
         try:
             return get_py_filename(name)
         except IOError:
             test_dir = os.path.dirname(self.test_filename)
             new_path = os.path.join(test_dir,name)
             return get_py_filename(new_path)
     
 
 def _run_ns_sync(self,arg_s,runner=None):
     """Modified version of %run that syncs testing namespaces.
 
     This is strictly needed for running doctests that call %run.
     """
 
-    finder = py_file_finder(_run_ns_sync.test_filename)
+    # When tests call %run directly (not via doctest) these function attributes
+    # are not set
+    try:
+        fname = _run_ns_sync.test_filename
+    except AttributeError:
+        fname = arg_s
+
+    finder = py_file_finder(fname)
     out = _ip.IP.magic_run_ori(arg_s,runner,finder)
-    _run_ns_sync.test_globs.update(_ip.user_ns)
+    
+    # Simliarly, there is no test_globs when a test is NOT a doctest
+    if hasattr(_run_ns_sync,'test_globs'):
+        _run_ns_sync.test_globs.update(_ip.user_ns)
     return out
 
 
 class ipnsdict(dict):
     """A special subclass of dict for use as an IPython namespace in doctests.
 
     This subclass adds a simple checkpointing capability so that when testing
     machinery clears it (we use it as the test execution context), it doesn't
     get completely destroyed.
     """
     
     def __init__(self,*a):
         dict.__init__(self,*a)
         self._savedict = {}
         
     def clear(self):
         dict.clear(self)
         self.update(self._savedict)
 
     def _checkpoint(self):
         self._savedict.clear()
         self._savedict.update(self)
 
     def update(self,other):
         self._checkpoint()
         dict.update(self,other)
         # If '_' is in the namespace, python won't set it when executing code,
         # and we have examples that test it.  So we ensure that the namespace
         # is always 'clean' of it before it's used for test code execution.
         self.pop('_',None)
         
 
 def start_ipython():
     """Start a global IPython shell, which we need for IPython-specific syntax.
     """
 
     # This function should only ever run once!
     if hasattr(start_ipython,'already_called'):
         return
     start_ipython.already_called = True
 
     # Ok,  first time we're called, go ahead
     import new
 
     import IPython
 
     def xsys(cmd):
         """Execute a command and print its output.
 
         This is just a convenience function to replace the IPython system call
         with one that is more doctest-friendly.
         """
         cmd = _ip.IP.var_expand(cmd,depth=1)
         sys.stdout.write(commands.getoutput(cmd))
         sys.stdout.flush()
 
     # Store certain global objects that IPython modifies
     _displayhook = sys.displayhook
     _excepthook = sys.excepthook
     _main = sys.modules.get('__main__')
 
     # Start IPython instance.  We customize it to start with minimal frills.
     user_ns,global_ns = IPython.ipapi.make_user_namespaces(ipnsdict(),dict())
     IPython.Shell.IPShell(['--colors=NoColor','--noterm_title'],
                           user_ns,global_ns)
 
     # Deactivate the various python system hooks added by ipython for
     # interactive convenience so we don't confuse the doctest system
     sys.modules['__main__'] = _main
     sys.displayhook = _displayhook
     sys.excepthook = _excepthook
 
     # So that ipython magics and aliases can be doctested (they work by making
     # a call into a global _ip object)
     _ip = IPython.ipapi.get()
     __builtin__._ip = _ip
 
     # Modify the IPython system call with one that uses getoutput, so that we
     # can capture subcommands and print them to Python's stdout, otherwise the
     # doctest machinery would miss them.
     _ip.system = xsys
 
     # Also patch our %run function in.
     im = new.instancemethod(_run_ns_sync,_ip.IP, _ip.IP.__class__)
     _ip.IP.magic_run_ori = _ip.IP.magic_run
     _ip.IP.magic_run = im
 
 # The start call MUST be made here.  I'm not sure yet why it doesn't work if
 # it is made later, at plugin initialization time, but in all my tests, that's
 # the case.
 start_ipython()
 
 # *** END HACK ***
 ###########################################################################
 
 # Classes and functions
 
 def is_extension_module(filename):
     """Return whether the given filename is an extension module.
 
     This simply checks that the extension is either .so or .pyd.
     """
     return os.path.splitext(filename)[1].lower() in ('.so','.pyd')
 
 
 class DocTestSkip(object):
     """Object wrapper for doctests to be skipped."""
     
     ds_skip = """Doctest to skip.
     >>> 1 #doctest: +SKIP
     """
 
     def __init__(self,obj):
         self.obj = obj
 
     def __getattribute__(self,key):
         if key == '__doc__':
             return DocTestSkip.ds_skip
         else:
             return getattr(object.__getattribute__(self,'obj'),key)
 
 # Modified version of the one in the stdlib, that fixes a python bug (doctests
 # not found in extension modules, http://bugs.python.org/issue3158)
 class DocTestFinder(doctest.DocTestFinder):
 
     def _from_module(self, module, object):
         """
         Return true if the given object is defined in the given
         module.
         """
         if module is None:
             return True
         elif inspect.isfunction(object):
             return module.__dict__ is object.func_globals
         elif inspect.isbuiltin(object):
             return module.__name__ == object.__module__
         elif inspect.isclass(object):
             return module.__name__ == object.__module__
         elif inspect.ismethod(object):
             # This one may be a bug in cython that fails to correctly set the
             # __module__ attribute of methods, but since the same error is easy
             # to make by extension code writers, having this safety in place
             # isn't such a bad idea
             return module.__name__ == object.im_class.__module__
         elif inspect.getmodule(object) is not None:
             return module is inspect.getmodule(object)
         elif hasattr(object, '__module__'):
             return module.__name__ == object.__module__
         elif isinstance(object, property):
             return True # [XX] no way not be sure.
         else:
             raise ValueError("object must be a class or function")
 
     def _find(self, tests, obj, name, module, source_lines, globs, seen):
         """
         Find tests for the given object and any contained objects, and
         add them to `tests`.
         """
 
         if hasattr(obj,"skip_doctest"):
             #print 'SKIPPING DOCTEST FOR:',obj  # dbg
             obj = DocTestSkip(obj)
 
         doctest.DocTestFinder._find(self,tests, obj, name, module,
                                     source_lines, globs, seen)
 
         # Below we re-run pieces of the above method with manual modifications,
         # because the original code is buggy and fails to correctly identify
         # doctests in extension modules.
 
         # Local shorthands
         from inspect import isroutine, isclass, ismodule
 
         # Look for tests in a module's contained objects.
         if inspect.ismodule(obj) and self._recurse:
             for valname, val in obj.__dict__.items():
                 valname1 = '%s.%s' % (name, valname)
                 if ( (isroutine(val) or isclass(val))
                      and self._from_module(module, val) ):
 
                     self._find(tests, val, valname1, module, source_lines,
                                globs, seen)
 
         # Look for tests in a class's contained objects.
         if inspect.isclass(obj) and self._recurse:
             #print 'RECURSE into class:',obj  # dbg
             for valname, val in obj.__dict__.items():
                 # Special handling for staticmethod/classmethod.
                 if isinstance(val, staticmethod):
                     val = getattr(obj, valname)
                 if isinstance(val, classmethod):
                     val = getattr(obj, valname).im_func
 
                 # Recurse to methods, properties, and nested classes.
                 if ((inspect.isfunction(val) or inspect.isclass(val) or
                      inspect.ismethod(val) or
                       isinstance(val, property)) and
                       self._from_module(module, val)):
                     valname = '%s.%s' % (name, valname)
                     self._find(tests, val, valname, module, source_lines,
                                globs, seen)
 
 
 class IPDoctestOutputChecker(doctest.OutputChecker):
     """Second-chance checker with support for random tests.
     
     If the default comparison doesn't pass, this checker looks in the expected
     output string for flags that tell us to ignore the output.
     """
 
     random_re = re.compile(r'#\s*random\s+')
     
     def check_output(self, want, got, optionflags):
         """Check output, accepting special markers embedded in the output.
 
         If the output didn't pass the default validation but the special string
         '#random' is included, we accept it."""
 
         # Let the original tester verify first, in case people have valid tests
         # that happen to have a comment saying '#random' embedded in.
         ret = doctest.OutputChecker.check_output(self, want, got,
                                                  optionflags)
         if not ret and self.random_re.search(want):
             #print >> sys.stderr, 'RANDOM OK:',want  # dbg
             return True
 
         return ret
 
 
 class DocTestCase(doctests.DocTestCase):
     """Proxy for DocTestCase: provides an address() method that
     returns the correct address for the doctest case. Otherwise
     acts as a proxy to the test case. To provide hints for address(),
     an obj may also be passed -- this will be used as the test object
     for purposes of determining the test address, if it is provided.
     """
 
     # Note: this method was taken from numpy's nosetester module.
 
     # Subclass nose.plugins.doctests.DocTestCase to work around a bug in
     # its constructor that blocks non-default arguments from being passed
     # down into doctest.DocTestCase
 
     def __init__(self, test, optionflags=0, setUp=None, tearDown=None,
                  checker=None, obj=None, result_var='_'):
         self._result_var = result_var
         doctests.DocTestCase.__init__(self, test,
                                       optionflags=optionflags,
                                       setUp=setUp, tearDown=tearDown,
                                       checker=checker)
         # Now we must actually copy the original constructor from the stdlib
         # doctest class, because we can't call it directly and a bug in nose
         # means it never gets passed the right arguments.
 
         self._dt_optionflags = optionflags
         self._dt_checker = checker
         self._dt_test = test
         self._dt_setUp = setUp
         self._dt_tearDown = tearDown
 
         # XXX - store this runner once in the object!
         runner = IPDocTestRunner(optionflags=optionflags,
                                  checker=checker, verbose=False)
         self._dt_runner = runner
 
 
         # Each doctest should remember what directory it was loaded from...
         self._ori_dir = os.getcwd()
 
     # Modified runTest from the default stdlib
     def runTest(self):
         test = self._dt_test
         runner = self._dt_runner
         
         old = sys.stdout
         new = StringIO()
         optionflags = self._dt_optionflags
 
         if not (optionflags & REPORTING_FLAGS):
             # The option flags don't include any reporting flags,
             # so add the default reporting flags
             optionflags |= _unittest_reportflags
 
         try:
             # Save our current directory and switch out to the one where the
             # test was originally created, in case another doctest did a
             # directory change.  We'll restore this in the finally clause.
             curdir = os.getcwd()
             os.chdir(self._ori_dir)
 
             runner.DIVIDER = "-"*70
             failures, tries = runner.run(test,out=new.write,
                                          clear_globs=False)
         finally:
             sys.stdout = old
             os.chdir(curdir)
 
         if failures:
             raise self.failureException(self.format_failure(new.getvalue()))
 
     def setUp(self):
         """Modified test setup that syncs with ipython namespace"""
         
         if isinstance(self._dt_test.examples[0],IPExample):
             # for IPython examples *only*, we swap the globals with the ipython
             # namespace, after updating it with the globals (which doctest
             # fills with the necessary info from the module being tested).
             _ip.IP.user_ns.update(self._dt_test.globs)
             self._dt_test.globs = _ip.IP.user_ns
 
         doctests.DocTestCase.setUp(self)
 
 
 # A simple subclassing of the original with a different class name, so we can
 # distinguish and treat differently IPython examples from pure python ones.
 class IPExample(doctest.Example): pass
 
 
 class IPExternalExample(doctest.Example):
     """Doctest examples to be run in an external process."""
 
     def __init__(self, source, want, exc_msg=None, lineno=0, indent=0,
                  options=None):
         # Parent constructor
         doctest.Example.__init__(self,source,want,exc_msg,lineno,indent,options)
 
         # An EXTRA newline is needed to prevent pexpect hangs
         self.source += '\n'
 
 
 class IPDocTestParser(doctest.DocTestParser):
     """
     A class used to parse strings containing doctest examples.
 
     Note: This is a version modified to properly recognize IPython input and
     convert any IPython examples into valid Python ones.
     """
     # This regular expression is used to find doctest examples in a
     # string.  It defines three groups: `source` is the source code
     # (including leading indentation and prompts); `indent` is the
     # indentation of the first (PS1) line of the source code; and
     # `want` is the expected output (including leading indentation).
 
     # Classic Python prompts or default IPython ones
     _PS1_PY = r'>>>'
     _PS2_PY = r'\.\.\.'
 
     _PS1_IP = r'In\ \[\d+\]:'
     _PS2_IP = r'\ \ \ \.\.\.+:'
 
     _RE_TPL = r'''
         # Source consists of a PS1 line followed by zero or more PS2 lines.
         (?P<source>
             (?:^(?P<indent> [ ]*) (?P<ps1> %s) .*)    # PS1 line
             (?:\n           [ ]*  (?P<ps2> %s) .*)*)  # PS2 lines
         \n? # a newline
         # Want consists of any non-blank lines that do not start with PS1.
         (?P<want> (?:(?![ ]*$)    # Not a blank line
                      (?![ ]*%s)   # Not a line starting with PS1
                      (?![ ]*%s)   # Not a line starting with PS2
                      .*$\n?       # But any other line
                   )*)
                   '''
 
     _EXAMPLE_RE_PY = re.compile( _RE_TPL % (_PS1_PY,_PS2_PY,_PS1_PY,_PS2_PY),
                                  re.MULTILINE | re.VERBOSE)
 
     _EXAMPLE_RE_IP = re.compile( _RE_TPL % (_PS1_IP,_PS2_IP,_PS1_IP,_PS2_IP),
                                  re.MULTILINE | re.VERBOSE)
 
     # Mark a test as being fully random.  In this case, we simply append the
     # random marker ('#random') to each individual example's output.  This way
     # we don't need to modify any other code.
     _RANDOM_TEST = re.compile(r'#\s*all-random\s+')
 
     # Mark tests to be executed in an external process - currently unsupported.
     _EXTERNAL_IP = re.compile(r'#\s*ipdoctest:\s*EXTERNAL')
     
     def ip2py(self,source):
         """Convert input IPython source into valid Python."""
         out = []
         newline = out.append
         #print 'IPSRC:\n',source,'\n###'  # dbg
         # The input source must be first stripped of all bracketing whitespace
         # and turned into lines, so it looks to the parser like regular user
         # input
         for lnum,line in enumerate(source.strip().splitlines()):
             newline(_ip.IP.prefilter(line,lnum>0))
         newline('')  # ensure a closing newline, needed by doctest
         #print "PYSRC:", '\n'.join(out)  # dbg
         return '\n'.join(out)
 
     def parse(self, string, name='<string>'):
         """
         Divide the given string into examples and intervening text,
         and return them as a list of alternating Examples and strings.
         Line numbers for the Examples are 0-based.  The optional
         argument `name` is a name identifying this string, and is only
         used for error messages.
         """
 
         #print 'Parse string:\n',string # dbg
 
         string = string.expandtabs()
         # If all lines begin with the same indentation, then strip it.
         min_indent = self._min_indent(string)
         if min_indent > 0:
             string = '\n'.join([l[min_indent:] for l in string.split('\n')])
 
         output = []
         charno, lineno = 0, 0
 
         # We make 'all random' tests by adding the '# random' mark to every
         # block of output in the test.
         if self._RANDOM_TEST.search(string):
             random_marker = '\n# random'
         else:
             random_marker = ''
 
         # Whether to convert the input from ipython to python syntax
         ip2py = False
         # Find all doctest examples in the string.  First, try them as Python
         # examples, then as IPython ones
         terms = list(self._EXAMPLE_RE_PY.finditer(string))
         if terms:
             # Normal Python example
             #print '-'*70  # dbg
             #print 'PyExample, Source:\n',string  # dbg
             #print '-'*70  # dbg
             Example = doctest.Example
         else:
             # It's an ipython example.  Note that IPExamples are run
             # in-process, so their syntax must be turned into valid python.
             # IPExternalExamples are run out-of-process (via pexpect) so they
             # don't need any filtering (a real ipython will be executing them).
             terms = list(self._EXAMPLE_RE_IP.finditer(string))
             if self._EXTERNAL_IP.search(string):
                 #print '-'*70  # dbg
                 #print 'IPExternalExample, Source:\n',string  # dbg
                 #print '-'*70  # dbg
                 Example = IPExternalExample
             else:
                 #print '-'*70  # dbg
                 #print 'IPExample, Source:\n',string  # dbg
                 #print '-'*70  # dbg
                 Example = IPExample
                 ip2py = True
 
         for m in terms:
             # Add the pre-example text to `output`.
             output.append(string[charno:m.start()])
             # Update lineno (lines before this example)
             lineno += string.count('\n', charno, m.start())
             # Extract info from the regexp match.
             (source, options, want, exc_msg) = \
                      self._parse_example(m, name, lineno,ip2py)
 
             # Append the random-output marker (it defaults to empty in most
             # cases, it's only non-empty for 'all-random' tests):
             want += random_marker
                 
             if Example is IPExternalExample:
                 options[doctest.NORMALIZE_WHITESPACE] = True
                 want += '\n'
 
             # Create an Example, and add it to the list.
             if not self._IS_BLANK_OR_COMMENT(source):
                 output.append(Example(source, want, exc_msg,
                                       lineno=lineno,
                                       indent=min_indent+len(m.group('indent')),
                                       options=options))
             # Update lineno (lines inside this example)
             lineno += string.count('\n', m.start(), m.end())
             # Update charno.
             charno = m.end()
         # Add any remaining post-example text to `output`.
         output.append(string[charno:])
         return output
 
     def _parse_example(self, m, name, lineno,ip2py=False):
         """
         Given a regular expression match from `_EXAMPLE_RE` (`m`),
         return a pair `(source, want)`, where `source` is the matched
         example's source code (with prompts and indentation stripped);
         and `want` is the example's expected output (with indentation
         stripped).
 
         `name` is the string's name, and `lineno` is the line number
         where the example starts; both are used for error messages.
 
         Optional:
         `ip2py`: if true, filter the input via IPython to convert the syntax
         into valid python.
         """
 
         # Get the example's indentation level.
         indent = len(m.group('indent'))
 
         # Divide source into lines; check that they're properly
         # indented; and then strip their indentation & prompts.
         source_lines = m.group('source').split('\n')
 
         # We're using variable-length input prompts
         ps1 = m.group('ps1')
         ps2 = m.group('ps2')
         ps1_len = len(ps1)
 
         self._check_prompt_blank(source_lines, indent, name, lineno,ps1_len)
         if ps2:
             self._check_prefix(source_lines[1:], ' '*indent + ps2, name, lineno)
 
         source = '\n'.join([sl[indent+ps1_len+1:] for sl in source_lines])
 
         if ip2py:
             # Convert source input from IPython into valid Python syntax
             source = self.ip2py(source)
 
         # Divide want into lines; check that it's properly indented; and
         # then strip the indentation.  Spaces before the last newline should
         # be preserved, so plain rstrip() isn't good enough.
         want = m.group('want')
         want_lines = want.split('\n')
         if len(want_lines) > 1 and re.match(r' *$', want_lines[-1]):
             del want_lines[-1]  # forget final newline & spaces after it
         self._check_prefix(want_lines, ' '*indent, name,
                            lineno + len(source_lines))
 
         # Remove ipython output prompt that might be present in the first line
         want_lines[0] = re.sub(r'Out\[\d+\]: \s*?\n?','',want_lines[0])
 
         want = '\n'.join([wl[indent:] for wl in want_lines])
 
         # If `want` contains a traceback message, then extract it.
         m = self._EXCEPTION_RE.match(want)
         if m:
             exc_msg = m.group('msg')
         else:
             exc_msg = None
 
         # Extract options from the source.
         options = self._find_options(source, name, lineno)
 
         return source, options, want, exc_msg
 
     def _check_prompt_blank(self, lines, indent, name, lineno, ps1_len):
         """
         Given the lines of a source string (including prompts and
         leading indentation), check to make sure that every prompt is
         followed by a space character.  If any line is not followed by
         a space character, then raise ValueError.
 
         Note: IPython-modified version which takes the input prompt length as a
         parameter, so that prompts of variable length can be dealt with.
         """
         space_idx = indent+ps1_len
         min_len = space_idx+1
         for i, line in enumerate(lines):
             if len(line) >=  min_len and line[space_idx] != ' ':
                 raise ValueError('line %r of the docstring for %s '
                                  'lacks blank after %s: %r' %
                                  (lineno+i+1, name,
                                   line[indent:space_idx], line))
 
 
 SKIP = doctest.register_optionflag('SKIP')
 
 
 class IPDocTestRunner(doctest.DocTestRunner,object):
     """Test runner that synchronizes the IPython namespace with test globals.
     """
     
     def run(self, test, compileflags=None, out=None, clear_globs=True):
 
         # Hack: ipython needs access to the execution context of the example,
         # so that it can propagate user variables loaded by %run into
         # test.globs.  We put them here into our modified %run as a function
         # attribute.  Our new %run will then only make the namespace update
         # when called (rather than unconconditionally updating test.globs here
         # for all examples, most of which won't be calling %run anyway).
         _run_ns_sync.test_globs = test.globs
         _run_ns_sync.test_filename = test.filename
         
         return super(IPDocTestRunner,self).run(test,
                                                compileflags,out,clear_globs)
 
 
 class DocFileCase(doctest.DocFileCase):
     """Overrides to provide filename
     """
     def address(self):
         return (self._dt_test.filename, None, None)
 
 
 class ExtensionDoctest(doctests.Doctest):
     """Nose Plugin that supports doctests in extension modules.
     """
     name = 'extdoctest'   # call nosetests with --with-extdoctest
     enabled = True
 
     def __init__(self,exclude_patterns=None):
         """Create a new ExtensionDoctest plugin.
 
         Parameters
         ----------
 
         exclude_patterns : sequence of strings, optional
           These patterns are compiled as regular expressions, subsequently used
           to exclude any filename which matches them from inclusion in the test
           suite (using pattern.search(), NOT pattern.match() ).
         """
 
         if exclude_patterns is None:
             exclude_patterns = []
         self.exclude_patterns = map(re.compile,exclude_patterns)
         doctests.Doctest.__init__(self)
 
     def options(self, parser, env=os.environ):
         Plugin.options(self, parser, env)
         parser.add_option('--doctest-tests', action='store_true',
                           dest='doctest_tests',
                           default=env.get('NOSE_DOCTEST_TESTS',True),
                           help="Also look for doctests in test modules. "
                           "Note that classes, methods and functions should "
                           "have either doctests or non-doctest tests, "
                           "not both. [NOSE_DOCTEST_TESTS]")
         parser.add_option('--doctest-extension', action="append",
                           dest="doctestExtension",
                           help="Also look for doctests in files with "
                           "this extension [NOSE_DOCTEST_EXTENSION]")
         # Set the default as a list, if given in env; otherwise
         # an additional value set on the command line will cause
         # an error.
         env_setting = env.get('NOSE_DOCTEST_EXTENSION')
         if env_setting is not None:
             parser.set_defaults(doctestExtension=tolist(env_setting))
 
 
     def configure(self, options, config):
         Plugin.configure(self, options, config)
         self.doctest_tests = options.doctest_tests
         self.extension = tolist(options.doctestExtension)
 
         self.parser = doctest.DocTestParser()
         self.finder = DocTestFinder()
         self.checker = IPDoctestOutputChecker()
         self.globs = None
         self.extraglobs = None
 
 
     def loadTestsFromExtensionModule(self,filename):
         bpath,mod = os.path.split(filename)
         modname = os.path.splitext(mod)[0]
         try:
             sys.path.append(bpath)
             module = __import__(modname)
             tests = list(self.loadTestsFromModule(module))
         finally:
             sys.path.pop()
         return tests
 
     # NOTE: the method below is almost a copy of the original one in nose, with
     # a  few modifications to control output checking.
 
     def loadTestsFromModule(self, module):
         #print '*** ipdoctest - lTM',module  # dbg
         
         if not self.matches(module.__name__):
             log.debug("Doctest doesn't want module %s", module)
             return
 
         tests = self.finder.find(module,globs=self.globs,
                                  extraglobs=self.extraglobs)
         if not tests:
             return
 
         # always use whitespace and ellipsis options
         optionflags = doctest.NORMALIZE_WHITESPACE | doctest.ELLIPSIS
 
         tests.sort()
         module_file = module.__file__
         if module_file[-4:] in ('.pyc', '.pyo'):
             module_file = module_file[:-1]
         for test in tests:
             if not test.examples:
                 continue
             if not test.filename:
                 test.filename = module_file
             
             yield DocTestCase(test,
                               optionflags=optionflags,
                               checker=self.checker)
 
 
     def loadTestsFromFile(self, filename):
         if is_extension_module(filename):
             for t in self.loadTestsFromExtensionModule(filename):
                 yield t
         else:
             if self.extension and anyp(filename.endswith, self.extension):
                 name = os.path.basename(filename)
                 dh = open(filename)
                 try:
                     doc = dh.read()
                 finally:
                     dh.close()
                 test = self.parser.get_doctest(
                     doc, globs={'__file__': filename}, name=name,
                     filename=filename, lineno=0)
                 if test.examples:
                     #print 'FileCase:',test.examples  # dbg
                     yield DocFileCase(test)
                 else:
                     yield False # no tests to load
 
     def wantFile(self,filename):
         """Return whether the given filename should be scanned for tests.
 
         Modified version that accepts extension modules as valid containers for
         doctests.
         """
         #print '*** ipdoctest- wantFile:',filename  # dbg
 
         for pat in self.exclude_patterns:
             if pat.search(filename):
                 #print '###>>> SKIP:',filename  # dbg
                 return False
 
         if is_extension_module(filename):
             return True
         else:
             return doctests.Doctest.wantFile(self,filename)
 
 
 class IPythonDoctest(ExtensionDoctest):
     """Nose Plugin that supports doctests in extension modules.
     """
     name = 'ipdoctest'   # call nosetests with --with-ipdoctest
     enabled = True
     
     def makeTest(self, obj, parent):
         """Look for doctests in the given object, which will be a
         function, method or class.
         """
         # always use whitespace and ellipsis options
         optionflags = doctest.NORMALIZE_WHITESPACE | doctest.ELLIPSIS
 
         doctests = self.finder.find(obj, module=getmodule(parent))
         if doctests:
             for test in doctests:
                 if len(test.examples) == 0:
                     continue
 
                 yield DocTestCase(test, obj=obj,
                                   optionflags=optionflags,
                                   checker=self.checker)
 
     def options(self, parser, env=os.environ):
         Plugin.options(self, parser, env)
         parser.add_option('--ipdoctest-tests', action='store_true',
                           dest='ipdoctest_tests',
                           default=env.get('NOSE_IPDOCTEST_TESTS',True),
                           help="Also look for doctests in test modules. "
                           "Note that classes, methods and functions should "
                           "have either doctests or non-doctest tests, "
                           "not both. [NOSE_IPDOCTEST_TESTS]")
         parser.add_option('--ipdoctest-extension', action="append",
                           dest="ipdoctest_extension",
                           help="Also look for doctests in files with "
                           "this extension [NOSE_IPDOCTEST_EXTENSION]")
         # Set the default as a list, if given in env; otherwise
         # an additional value set on the command line will cause
         # an error.
         env_setting = env.get('NOSE_IPDOCTEST_EXTENSION')
         if env_setting is not None:
             parser.set_defaults(ipdoctest_extension=tolist(env_setting))
 
     def configure(self, options, config):
         Plugin.configure(self, options, config)
         self.doctest_tests = options.ipdoctest_tests
         self.extension = tolist(options.ipdoctest_extension)
 
         self.parser = IPDocTestParser()
         self.finder = DocTestFinder(parser=self.parser)
         self.checker = IPDoctestOutputChecker()
         self.globs = None
         self.extraglobs = None

IPython/tests/test_magic.py

@@ -1,151 +1,203 b''
 """Tests for various magic functions.
 
 Needs to be run by nose (to make ipython session available).
 """
 
 # Standard library imports
 import os
 import sys
 
 # Third-party imports
 import nose.tools as nt
 
 # From our own code
 from IPython.testing import decorators as dec
-
 #-----------------------------------------------------------------------------
 # Test functions begin
 
 def test_rehashx():
     # clear up everything
     _ip.IP.alias_table.clear()
     del _ip.db['syscmdlist']
     
     _ip.magic('rehashx')
     # Practically ALL ipython development systems will have more than 10 aliases
 
     assert len(_ip.IP.alias_table) > 10
     for key, val in _ip.IP.alias_table.items():
         # we must strip dots from alias names
         assert '.' not in key
 
     # rehashx must fill up syscmdlist
     scoms = _ip.db['syscmdlist']
     assert len(scoms) > 10
 
 
 def doctest_run_ns():
     """Classes declared %run scripts must be instantiable afterwards.
 
     In [11]: run tclass foo
 
     In [12]: isinstance(f(),foo)
     Out[12]: True
     """
 
     
 def doctest_run_ns2():
     """Classes declared %run scripts must be instantiable afterwards.
 
     In [4]: run tclass C-first_pass
 
     In [5]: run tclass C-second_pass
     tclass.py: deleting object: C-first_pass
     """
 
 
 def doctest_hist_f():
     """Test %hist -f with temporary filename.
 
     In [9]: import tempfile
 
     In [10]: tfile = tempfile.mktemp('.py','tmp-ipython-')
 
     In [11]: %history -n -f $tfile 3
     """
 
+def doctest_run_builtins():
+    """Check that %run doesn't damage __builtins__ via a doctest.
+
+    This is similar to the test_run_builtins, but I want *both* forms of the
+    test to catch any possible glitches in our testing machinery, since that
+    modifies %run somewhat.  So for this, we have both a normal test (below)
+    and a doctest (this one).
+
+    In [1]: import tempfile
+
+    In [2]: bid1 = id(__builtins__)
+
+    In [3]: f = tempfile.NamedTemporaryFile()
+
+    In [4]: f.write('pass\\n')
+
+    In [5]: f.flush()
+
+    In [6]: print 'B1:',type(__builtins__)
+    B1: <type 'module'>
+
+    In [7]: %run $f.name
+
+    In [8]: bid2 = id(__builtins__)
+
+    In [9]: print 'B2:',type(__builtins__)
+    B2: <type 'module'>
+
+    In [10]: bid1 == bid2
+    Out[10]: True
+    """
+
+def test_run_builtins():
+    """Check that %run doesn't damage __builtins__ """
+    import sys
+    import tempfile
+    import types
+
+    # Make an empty file and put 'pass' in it
+    f = tempfile.NamedTemporaryFile()
+    f.write('pass\n')
+    f.flush()
+
+    # Our first test is that the id of __builtins__ is not modified by %run
+    bid1 = id(__builtins__)
+    _ip.magic('run %s' % f.name)
+    bid2 = id(__builtins__)
+    yield nt.assert_equals,bid1,bid2
+    # However, the above could pass if __builtins__ was already modified to be
+    # a dict (it should be a module) by a previous use of %run.  So we also
+    # check explicitly that it really is a module:
+    yield nt.assert_equals,type(__builtins__),type(sys)
+    
 
 def doctest_hist_r():
     """Test %hist -r
 
     XXX - This test is not recording the output correctly.  Not sure why...
 
     In [6]: x=1
 
     In [7]: hist -n -r 2
     x=1  # random
     hist -n -r 2  # random
     """
 
 
 def test_obj_del():
     """Test that object's __del__ methods are called on exit."""
     test_dir = os.path.dirname(__file__)
     del_file = os.path.join(test_dir,'obj_del.py')
     out = _ip.IP.getoutput('ipython %s' % del_file)
     nt.assert_equals(out,'obj_del.py: object A deleted')
 
 
 def test_shist():
     # Simple tests of ShadowHist class - test generator.
     import os, shutil, tempfile
 
     from IPython.Extensions import pickleshare
     from IPython.history import ShadowHist
     
     tfile = tempfile.mktemp('','tmp-ipython-')
     
     db = pickleshare.PickleShareDB(tfile)
     s = ShadowHist(db)
     s.add('hello')
     s.add('world')
     s.add('hello')
     s.add('hello')
     s.add('karhu')
 
     yield nt.assert_equals,s.all(),[(1, 'hello'), (2, 'world'), (3, 'karhu')]
     
     yield nt.assert_equal,s.get(2),'world'
     
     shutil.rmtree(tfile)
     
 @dec.skipif_not_numpy
 def test_numpy_clear_array_undec():
     _ip.ex('import numpy as np')
     _ip.ex('a = np.empty(2)')
     
     yield nt.assert_true,'a' in _ip.user_ns
     _ip.magic('clear array')
     yield nt.assert_false,'a' in _ip.user_ns
     
 
 @dec.skip()
 def test_fail_dec(*a,**k):
     yield nt.assert_true, False
 
 @dec.skip('This one shouldn not run')
 def test_fail_dec2(*a,**k):
     yield nt.assert_true, False
 
 @dec.skipknownfailure
 def test_fail_dec3(*a,**k):
     yield nt.assert_true, False
 
 
 def doctest_refbug():
     """Very nasty problem with references held by multiple runs of a script.
     See: https://bugs.launchpad.net/ipython/+bug/269966
 
     In [1]: _ip.IP.clear_main_mod_cache()
     
     In [2]: run refbug
 
     In [3]: call_f()
     lowercased: hello
 
     In [4]: run refbug
 
     In [5]: call_f()
     lowercased: hello
     lowercased: hello
     """