Fix problem with rc_override.

EmbeddedSphinxShell is instantiated at import time, this patch works around
the issue.

IPython/Shell.py

@@ -1,1246 +1,1261 b''
 # -*- coding: utf-8 -*-
 """IPython Shell classes.
 
 All the matplotlib support code was co-developed with John Hunter,
 matplotlib's author.
 """
 
 #*****************************************************************************
 #       Copyright (C) 2001-2006 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.
 #*****************************************************************************
 
 # Code begins
 # Stdlib imports
 import __builtin__
 import __main__
 import Queue
 import inspect
 import os
 import sys
 import thread
 import threading
 import time
 
 from signal import signal, SIGINT
 
 try:
     import ctypes
     HAS_CTYPES = True
 except ImportError:
     HAS_CTYPES = False
 
 # IPython imports
 import IPython
 from IPython import ultraTB, ipapi
 from IPython.Magic import Magic
 from IPython.genutils import Term,warn,error,flag_calls, ask_yes_no
 from IPython.iplib import InteractiveShell
 from IPython.ipmaker import make_IPython
 from IPython.ipstruct import Struct
 from IPython.testing import decorators as testdec
 
 # Globals
 # global flag to pass around information about Ctrl-C without exceptions
 KBINT = False
 
 # global flag to turn on/off Tk support.
 USE_TK = False
 
 # ID for the main thread, used for cross-thread exceptions
 MAIN_THREAD_ID = thread.get_ident()
 
 # Tag when runcode() is active, for exception handling
 CODE_RUN = None
 
 # Default timeout for waiting for multithreaded shells (in seconds)
 GUI_TIMEOUT = 10
 
 #-----------------------------------------------------------------------------
 # This class is trivial now, but I want to have it in to publish a clean
 # interface. Later when the internals are reorganized, code that uses this
 # shouldn't have to change.
 
 class IPShell:
     """Create an IPython instance."""
     
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,
                  debug=1,shell_class=InteractiveShell):
         self.IP = make_IPython(argv,user_ns=user_ns,
                                user_global_ns=user_global_ns,
                                debug=debug,shell_class=shell_class)
 
     def mainloop(self,sys_exit=0,banner=None):
         self.IP.mainloop(banner)
         if sys_exit:
             sys.exit()
 
 #-----------------------------------------------------------------------------
 def kill_embedded(self,parameter_s=''):
     """%kill_embedded : deactivate for good the current embedded IPython.
 
     This function (after asking for confirmation) sets an internal flag so that
     an embedded IPython will never activate again.  This is useful to
     permanently disable a shell that is being called inside a loop: once you've
     figured out what you needed from it, you may then kill it and the program
     will then continue to run without the interactive shell interfering again.
     """
     
     kill = ask_yes_no("Are you sure you want to kill this embedded instance "
                      "(y/n)? [y/N] ",'n')
     if kill:
         self.shell.embedded_active = False
         print "This embedded IPython will not reactivate anymore once you exit."
     
 class IPShellEmbed:
     """Allow embedding an IPython shell into a running program.
 
     Instances of this class are callable, with the __call__ method being an
     alias to the embed() method of an InteractiveShell instance.
 
     Usage (see also the example-embed.py file for a running example):
 
     ipshell = IPShellEmbed([argv,banner,exit_msg,rc_override])
 
     - argv: list containing valid command-line options for IPython, as they
     would appear in sys.argv[1:].
 
     For example, the following command-line options:
 
       $ ipython -prompt_in1 'Input <\\#>' -colors LightBG
 
     would be passed in the argv list as:
 
       ['-prompt_in1','Input <\\#>','-colors','LightBG']
 
     - banner: string which gets printed every time the interpreter starts.
 
     - exit_msg: string which gets printed every time the interpreter exits.
 
     - rc_override: a dict or Struct of configuration options such as those
     used by IPython. These options are read from your ~/.ipython/ipythonrc
     file when the Shell object is created. Passing an explicit rc_override
     dict with any options you want allows you to override those values at
     creation time without having to modify the file. This way you can create
     embeddable instances configured in any way you want without editing any
     global files (thus keeping your interactive IPython configuration
     unchanged).
 
     Then the ipshell instance can be called anywhere inside your code:
     
     ipshell(header='') -> Opens up an IPython shell.
 
     - header: string printed by the IPython shell upon startup. This can let
     you know where in your code you are when dropping into the shell. Note
     that 'banner' gets prepended to all calls, so header is used for
     location-specific information.
 
     For more details, see the __call__ method below.
 
     When the IPython shell is exited with Ctrl-D, normal program execution
     resumes.
 
     This functionality was inspired by a posting on comp.lang.python by cmkl
     <[e-mail]> on Dec. 06/01 concerning similar uses of pyrepl, and
     by the IDL stop/continue commands."""
 
     def __init__(self,argv=None,banner='',exit_msg=None,rc_override=None,
                  user_ns=None):
         """Note that argv here is a string, NOT a list."""
         self.set_banner(banner)
         self.set_exit_msg(exit_msg)
         self.set_dummy_mode(0)
 
         # sys.displayhook is a global, we need to save the user's original
         # Don't rely on __displayhook__, as the user may have changed that.
         self.sys_displayhook_ori = sys.displayhook
 
         # save readline completer status
         try:
             #print 'Save completer',sys.ipcompleter  # dbg
             self.sys_ipcompleter_ori = sys.ipcompleter
         except:
             pass # not nested with IPython
         
         self.IP = make_IPython(argv,rc_override=rc_override,
                                embedded=True,
                                user_ns=user_ns)
 
         ip = ipapi.IPApi(self.IP)
         ip.expose_magic("kill_embedded",kill_embedded)
 
         # copy our own displayhook also
         self.sys_displayhook_embed = sys.displayhook
         # and leave the system's display hook clean
         sys.displayhook = self.sys_displayhook_ori
         # don't use the ipython crash handler so that user exceptions aren't
         # trapped
         sys.excepthook = ultraTB.FormattedTB(color_scheme = self.IP.rc.colors,
                                              mode = self.IP.rc.xmode,
                                              call_pdb = self.IP.rc.pdb)
         self.restore_system_completer()
 
     def restore_system_completer(self):
         """Restores the readline completer which was in place.
 
         This allows embedded IPython within IPython not to disrupt the
         parent's completion.
         """
         
         try:
             self.IP.readline.set_completer(self.sys_ipcompleter_ori)
             sys.ipcompleter = self.sys_ipcompleter_ori
         except:
             pass
 
     def __call__(self,header='',local_ns=None,global_ns=None,dummy=None):
         """Activate the interactive interpreter.
 
         __call__(self,header='',local_ns=None,global_ns,dummy=None) -> Start
         the interpreter shell with the given local and global namespaces, and
         optionally print a header string at startup.
 
         The shell can be globally activated/deactivated using the
         set/get_dummy_mode methods. This allows you to turn off a shell used
         for debugging globally.
 
         However, *each* time you call the shell you can override the current
         state of dummy_mode with the optional keyword parameter 'dummy'. For
         example, if you set dummy mode on with IPShell.set_dummy_mode(1), you
         can still have a specific call work by making it as IPShell(dummy=0).
 
         The optional keyword parameter dummy controls whether the call
         actually does anything.  """
 
         # If the user has turned it off, go away
         if not self.IP.embedded_active:
             return
 
         # Normal exits from interactive mode set this flag, so the shell can't
         # re-enter (it checks this variable at the start of interactive mode).
         self.IP.exit_now = False
 
         # Allow the dummy parameter to override the global __dummy_mode
         if dummy or (dummy != 0 and self.__dummy_mode):
             return
 
         # Set global subsystems (display,completions) to our values
         sys.displayhook = self.sys_displayhook_embed
         if self.IP.has_readline:
             self.IP.set_completer()
 
         if self.banner and header:
             format = '%s\n%s\n'
         else:
             format = '%s%s\n'
         banner =  format % (self.banner,header)
 
         # Call the embedding code with a stack depth of 1 so it can skip over
         # our call and get the original caller's namespaces.
         self.IP.embed_mainloop(banner,local_ns,global_ns,stack_depth=1)
 
         if self.exit_msg:
             print self.exit_msg
             
         # Restore global systems (display, completion)
         sys.displayhook = self.sys_displayhook_ori
         self.restore_system_completer()
     
     def set_dummy_mode(self,dummy):
         """Sets the embeddable shell's dummy mode parameter.
 
         set_dummy_mode(dummy): dummy = 0 or 1.
 
         This parameter is persistent and makes calls to the embeddable shell
         silently return without performing any action. This allows you to
         globally activate or deactivate a shell you're using with a single call.
 
         If you need to manually"""
 
         if dummy not in [0,1,False,True]:
             raise ValueError,'dummy parameter must be boolean'
         self.__dummy_mode = dummy
 
     def get_dummy_mode(self):
         """Return the current value of the dummy mode parameter.
         """
         return self.__dummy_mode
     
     def set_banner(self,banner):
         """Sets the global banner.
 
         This banner gets prepended to every header printed when the shell
         instance is called."""
 
         self.banner = banner
 
     def set_exit_msg(self,exit_msg):
         """Sets the global exit_msg.
 
         This exit message gets printed upon exiting every time the embedded
         shell is called. It is None by default. """
 
         self.exit_msg = exit_msg
 
 #-----------------------------------------------------------------------------
 if HAS_CTYPES:
     #  Add async exception support.  Trick taken from:
     # http://sebulba.wikispaces.com/recipe+thread2
     def _async_raise(tid, exctype):
         """raises the exception, performs cleanup if needed"""
         if not inspect.isclass(exctype):
             raise TypeError("Only types can be raised (not instances)")
         # Explicit cast to c_long is necessary for 64-bit support:
         # See https://bugs.launchpad.net/ipython/+bug/237073
         res = ctypes.pythonapi.PyThreadState_SetAsyncExc(ctypes.c_long(tid),
                                                          ctypes.py_object(exctype))
         if res == 0:
             raise ValueError("invalid thread id")
         elif res != 1:
             # If it returns a number greater than one, you're in trouble, 
             # and you should call it again with exc=NULL to revert the effect
             ctypes.pythonapi.PyThreadState_SetAsyncExc(tid, 0)
             raise SystemError("PyThreadState_SetAsyncExc failed")
 
     def sigint_handler(signum,stack_frame):
         """Sigint handler for threaded apps.
 
         This is a horrible hack to pass information about SIGINT _without_
         using exceptions, since I haven't been able to properly manage
         cross-thread exceptions in GTK/WX.  In fact, I don't think it can be
         done (or at least that's my understanding from a c.l.py thread where
         this was discussed)."""
 
         global KBINT
 
         if CODE_RUN:
             _async_raise(MAIN_THREAD_ID,KeyboardInterrupt)
         else:
             KBINT = True
             print '\nKeyboardInterrupt - Press <Enter> to continue.',
             Term.cout.flush()
 
 else:
     def sigint_handler(signum,stack_frame):
         """Sigint handler for threaded apps.
 
         This is a horrible hack to pass information about SIGINT _without_
         using exceptions, since I haven't been able to properly manage
         cross-thread exceptions in GTK/WX.  In fact, I don't think it can be
         done (or at least that's my understanding from a c.l.py thread where
         this was discussed)."""
 
         global KBINT
 
         print '\nKeyboardInterrupt - Press <Enter> to continue.',
         Term.cout.flush()
         # Set global flag so that runsource can know that Ctrl-C was hit
         KBINT = True
 
 
 class MTInteractiveShell(InteractiveShell):
     """Simple multi-threaded shell."""
 
     # Threading strategy taken from:
     # http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/65109, by Brian
     # McErlean and John Finlay.  Modified with corrections by Antoon Pardon,
     # from the pygtk mailing list, to avoid lockups with system calls.
 
     # class attribute to indicate whether the class supports threads or not.
     # Subclasses with thread support should override this as needed.
     isthreaded = True
 
     def __init__(self,name,usage=None,rc=Struct(opts=None,args=None),
                  user_ns=None,user_global_ns=None,banner2='',
                  gui_timeout=GUI_TIMEOUT,**kw):
         """Similar to the normal InteractiveShell, but with threading control"""
         
         InteractiveShell.__init__(self,name,usage,rc,user_ns,
                                   user_global_ns,banner2)
 
         # Timeout we wait for GUI thread
         self.gui_timeout = gui_timeout
 
         # A queue to hold the code to be executed. 
         self.code_queue = Queue.Queue()
 
         # Stuff to do at closing time
         self._kill = None
         on_kill = kw.get('on_kill', [])
         # Check that all things to kill are callable:
         for t in on_kill:
             if not callable(t):
                 raise TypeError,'on_kill must be a list of callables'
         self.on_kill = on_kill
         # thread identity of the "worker thread" (that may execute code directly)
         self.worker_ident = None
         
     def runsource(self, source, filename="<input>", symbol="single"):
         """Compile and run some source in the interpreter.
 
         Modified version of code.py's runsource(), to handle threading issues.
         See the original for full docstring details."""
                 
         global KBINT
         
         # If Ctrl-C was typed, we reset the flag and return right away
         if KBINT:
             KBINT = False
             return False
 
         if self._kill:
             # can't queue new code if we are being killed
             return True
         
         try:
             code = self.compile(source, filename, symbol)
         except (OverflowError, SyntaxError, ValueError):
             # Case 1
             self.showsyntaxerror(filename)
             return False
 
         if code is None:
             # Case 2
             return True
 
         # shortcut - if we are in worker thread, or the worker thread is not
         # running, execute directly (to allow recursion and prevent deadlock if
         # code is run early in IPython construction)
         
         if (self.worker_ident is None
             or self.worker_ident == thread.get_ident() ):
             InteractiveShell.runcode(self,code)
             return False
 
         # Case 3
         # Store code in queue, so the execution thread can handle it.
 
         completed_ev, received_ev = threading.Event(), threading.Event() 
         
         self.code_queue.put((code,completed_ev, received_ev))
         # first make sure the message was received, with timeout
         received_ev.wait(self.gui_timeout)
         if not received_ev.isSet():
             # the mainloop is dead, start executing code directly
             print "Warning: Timeout for mainloop thread exceeded"
             print "switching to nonthreaded mode (until mainloop wakes up again)"
             self.worker_ident = None
         else:
             completed_ev.wait()
         return False
 
     def runcode(self):
         """Execute a code object.
 
         Multithreaded wrapper around IPython's runcode()."""
         
         global CODE_RUN
         
         # we are in worker thread, stash out the id for runsource() 
         self.worker_ident = thread.get_ident()
 
         if self._kill:
             print >>Term.cout, 'Closing threads...',
             Term.cout.flush()
             for tokill in self.on_kill:
                 tokill()
             print >>Term.cout, 'Done.'
             # allow kill() to return
             self._kill.set()
             return True
 
         # Install sigint handler.  We do it every time to ensure that if user
         # code modifies it, we restore our own handling.
         try:
             signal(SIGINT,sigint_handler)
         except SystemError:
             # This happens under Windows, which seems to have all sorts
             # of problems with signal handling.  Oh well...
             pass
 
         # Flush queue of pending code by calling the run methood of the parent
         # class with all items which may be in the queue.
         code_to_run = None
         while 1:
             try:
                 code_to_run, completed_ev, received_ev = self.code_queue.get_nowait()                
             except Queue.Empty:
                 break
             received_ev.set()
             
             # Exceptions need to be raised differently depending on which
             # thread is active.  This convoluted try/except is only there to
             # protect against asynchronous exceptions, to ensure that a KBINT
             # at the wrong time doesn't deadlock everything.  The global
             # CODE_TO_RUN is set to true/false as close as possible to the
             # runcode() call, so that the KBINT handler is correctly informed.
             try:
                 try:
                    CODE_RUN = True
                    InteractiveShell.runcode(self,code_to_run)
                 except KeyboardInterrupt:
                    print "Keyboard interrupted in mainloop"
                    while not self.code_queue.empty():
                       code, ev1,ev2 = self.code_queue.get_nowait()
                       ev1.set()
                       ev2.set()                      
                    break
             finally:
                 CODE_RUN = False
                 # allow runsource() return from wait
                 completed_ev.set()
                 
         
         # This MUST return true for gtk threading to work
         return True
 
     def kill(self):
         """Kill the thread, returning when it has been shut down."""
         self._kill = threading.Event()
         self._kill.wait()
 
 class MatplotlibShellBase:
     """Mixin class to provide the necessary modifications to regular IPython
     shell classes for matplotlib support.
 
     Given Python's MRO, this should be used as the FIRST class in the
     inheritance hierarchy, so that it overrides the relevant methods."""
     
     def _matplotlib_config(self,name,user_ns,user_global_ns=None):
         """Return items needed to setup the user's shell with matplotlib"""
 
         # Initialize matplotlib to interactive mode always
         import matplotlib
         from matplotlib import backends
         matplotlib.interactive(True)
 
         def use(arg):
             """IPython wrapper for matplotlib's backend switcher.
 
             In interactive use, we can not allow switching to a different
             interactive backend, since thread conflicts will most likely crash
             the python interpreter.  This routine does a safety check first,
             and refuses to perform a dangerous switch.  It still allows
             switching to non-interactive backends."""
 
             if arg in backends.interactive_bk and arg != self.mpl_backend:
                 m=('invalid matplotlib backend switch.\n'
                    'This script attempted to switch to the interactive '
                    'backend: `%s`\n'
                    'Your current choice of interactive backend is: `%s`\n\n'
                    'Switching interactive matplotlib backends at runtime\n'
                    'would crash the python interpreter, '
                    'and IPython has blocked it.\n\n'
                    'You need to either change your choice of matplotlib backend\n'
                    'by editing your .matplotlibrc file, or run this script as a \n'
                    'standalone file from the command line, not using IPython.\n' %
                    (arg,self.mpl_backend) )
                 raise RuntimeError, m
             else:
                 self.mpl_use(arg)
                 self.mpl_use._called = True
         
         self.matplotlib = matplotlib
         self.mpl_backend = matplotlib.rcParams['backend']
 
         # we also need to block switching of interactive backends by use()
         self.mpl_use = matplotlib.use
         self.mpl_use._called = False
         # overwrite the original matplotlib.use with our wrapper
         matplotlib.use = use
 
         # This must be imported last in the matplotlib series, after
         # backend/interactivity choices have been made
         import matplotlib.pylab as pylab
         self.pylab = pylab
 
         self.pylab.show._needmain = False
         # We need to detect at runtime whether show() is called by the user.
         # For this, we wrap it into a decorator which adds a 'called' flag.
         self.pylab.draw_if_interactive = flag_calls(self.pylab.draw_if_interactive)
 
         # Build a user namespace initialized with matplotlib/matlab features.
         user_ns, user_global_ns = IPython.ipapi.make_user_namespaces(user_ns,
             user_global_ns)
 
         # Import numpy as np/pyplot as plt are conventions we're trying to
         # somewhat standardize on.  Making them available to users by default
         # will greatly help this. 
         exec ("import numpy\n"
               "import numpy as np\n"
               "import matplotlib\n"
               "import matplotlib.pylab as pylab\n"
               "try:\n"
               "    import matplotlib.pyplot as plt\n"
               "except ImportError:\n"
               "    pass\n"
               ) in user_ns
         
         # Build matplotlib info banner
         b="""
   Welcome to pylab, a matplotlib-based Python environment.
   For more information, type 'help(pylab)'.
 """
         return user_ns,user_global_ns,b
 
     def mplot_exec(self,fname,*where,**kw):
         """Execute a matplotlib script.
 
         This is a call to execfile(), but wrapped in safeties to properly
         handle interactive rendering and backend switching."""
 
         #print '*** Matplotlib runner ***' # dbg
         # turn off rendering until end of script
         isInteractive = self.matplotlib.rcParams['interactive']
         self.matplotlib.interactive(False)
         self.safe_execfile(fname,*where,**kw)
         self.matplotlib.interactive(isInteractive)
         # make rendering call now, if the user tried to do it
         if self.pylab.draw_if_interactive.called:
             self.pylab.draw()
             self.pylab.draw_if_interactive.called = False
                 
         # if a backend switch was performed, reverse it now
         if self.mpl_use._called:
             self.matplotlib.rcParams['backend'] = self.mpl_backend
 
     @testdec.skip_doctest
     def magic_run(self,parameter_s=''):
         Magic.magic_run(self,parameter_s,runner=self.mplot_exec)
 
     # Fix the docstring so users see the original as well
     magic_run.__doc__ = "%s\n%s" % (Magic.magic_run.__doc__,
                                     "\n        *** Modified %run for Matplotlib,"
                                     " with proper interactive handling ***")
 
 # Now we provide 2 versions of a matplotlib-aware IPython base shells, single
 # and multithreaded.  Note that these are meant for internal use, the IPShell*
 # classes below are the ones meant for public consumption.
 
 class MatplotlibShell(MatplotlibShellBase,InteractiveShell):
     """Single-threaded shell with matplotlib support."""
 
     def __init__(self,name,usage=None,rc=Struct(opts=None,args=None),
                  user_ns=None,user_global_ns=None,**kw):
         user_ns,user_global_ns,b2 = self._matplotlib_config(name,user_ns,user_global_ns)
         InteractiveShell.__init__(self,name,usage,rc,user_ns,user_global_ns,
                                   banner2=b2,**kw)
 
 class MatplotlibMTShell(MatplotlibShellBase,MTInteractiveShell):
     """Multi-threaded shell with matplotlib support."""
 
     def __init__(self,name,usage=None,rc=Struct(opts=None,args=None),
                  user_ns=None,user_global_ns=None, **kw):
         user_ns,user_global_ns,b2 = self._matplotlib_config(name,user_ns,user_global_ns)
         MTInteractiveShell.__init__(self,name,usage,rc,user_ns,user_global_ns,
                                     banner2=b2,**kw)
 
 #-----------------------------------------------------------------------------
 # Utility functions for the different GUI enabled IPShell* classes.
 
 def get_tk():
     """Tries to import Tkinter and returns a withdrawn Tkinter root
     window.  If Tkinter is already imported or not available, this
     returns None.  This function calls `hijack_tk` underneath.
     """
     if not USE_TK or sys.modules.has_key('Tkinter'):
         return None
     else:
         try:
             import Tkinter
         except ImportError:
             return None
         else:
             hijack_tk()
             r = Tkinter.Tk()
             r.withdraw()
             return r
 
 def hijack_tk():
     """Modifies Tkinter's mainloop with a dummy so when a module calls
     mainloop, it does not block.
 
     """
     def misc_mainloop(self, n=0):
         pass
     def tkinter_mainloop(n=0):
         pass
     
     import Tkinter
     Tkinter.Misc.mainloop = misc_mainloop
     Tkinter.mainloop = tkinter_mainloop
 
 def update_tk(tk):
     """Updates the Tkinter event loop.  This is typically called from
     the respective WX or GTK mainloops.
     """    
     if tk:
         tk.update()
 
 def hijack_wx():
     """Modifies wxPython's MainLoop with a dummy so user code does not
     block IPython.  The hijacked mainloop function is returned.
     """    
     def dummy_mainloop(*args, **kw):
         pass
 
     try:
         import wx
     except ImportError:
         # For very old versions of WX
         import wxPython as wx
         
     ver = wx.__version__
     orig_mainloop = None
     if ver[:3] >= '2.5':
         import wx
         if hasattr(wx, '_core_'): core = getattr(wx, '_core_')
         elif hasattr(wx, '_core'): core = getattr(wx, '_core')
         else: raise AttributeError('Could not find wx core module')
         orig_mainloop = core.PyApp_MainLoop
         core.PyApp_MainLoop = dummy_mainloop
     elif ver[:3] == '2.4':
         orig_mainloop = wx.wxc.wxPyApp_MainLoop
         wx.wxc.wxPyApp_MainLoop = dummy_mainloop
     else:
         warn("Unable to find either wxPython version 2.4 or >= 2.5.")
     return orig_mainloop
 
 def hijack_gtk():
     """Modifies pyGTK's mainloop with a dummy so user code does not
     block IPython.  This function returns the original `gtk.mainloop`
     function that has been hijacked.
     """    
     def dummy_mainloop(*args, **kw):
         pass
     import gtk
     if gtk.pygtk_version >= (2,4,0): orig_mainloop = gtk.main
     else:                            orig_mainloop = gtk.mainloop
     gtk.mainloop = dummy_mainloop
     gtk.main = dummy_mainloop
     return orig_mainloop
 
 def hijack_qt():
     """Modifies PyQt's mainloop with a dummy so user code does not 
     block IPython.  This function returns the original 
     `qt.qApp.exec_loop` function that has been hijacked.
     """    
     def dummy_mainloop(*args, **kw):
         pass
     import qt
     orig_mainloop = qt.qApp.exec_loop
     qt.qApp.exec_loop = dummy_mainloop
     qt.QApplication.exec_loop = dummy_mainloop
     return orig_mainloop
 
 def hijack_qt4():
     """Modifies PyQt4's mainloop with a dummy so user code does not
     block IPython.  This function returns the original 
     `QtGui.qApp.exec_` function that has been hijacked.
     """    
     def dummy_mainloop(*args, **kw):
         pass
     from PyQt4 import QtGui, QtCore
     orig_mainloop = QtGui.qApp.exec_
     QtGui.qApp.exec_ = dummy_mainloop
     QtGui.QApplication.exec_ = dummy_mainloop
     QtCore.QCoreApplication.exec_ = dummy_mainloop
     return orig_mainloop
 
 #-----------------------------------------------------------------------------
 # The IPShell* classes below are the ones meant to be run by external code as
 # IPython instances.  Note that unless a specific threading strategy is
 # desired, the factory function start() below should be used instead (it
 # selects the proper threaded class).
 
 class IPThread(threading.Thread):
     def run(self):
         self.IP.mainloop(self._banner)
         self.IP.kill()
 
 class IPShellGTK(IPThread):
     """Run a gtk mainloop() in a separate thread.
     
     Python commands can be passed to the thread where they will be executed.
     This is implemented by periodically checking for passed code using a
     GTK timeout callback."""
     
     TIMEOUT = 100 # Millisecond interval between timeouts.
 
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,
                  debug=1,shell_class=MTInteractiveShell):
 
         import gtk
-        # Check for set_interactive, coming up in new pygtk.
-        # Disable it so that this code works, but notify 
-        # the user that he has a better option as well.
-        # XXX TODO better support when set_interactive is released
-        try:
-            gtk.set_interactive(False)
-            print "Your PyGtk has set_interactive(), so you can use the"
-            print "more stable single-threaded Gtk mode."
-            print "See https://bugs.launchpad.net/ipython/+bug/270856"
-        except AttributeError:
-            pass
+        ## # Check for set_interactive, coming up in new pygtk.
+        ## # Disable it so that this code works, but notify 
+        ## # the user that he has a better option as well.
+        ## # XXX TODO better support when set_interactive is released
+        ## try:
+        ##     gtk.set_interactive(False)
+        ##     print "Your PyGtk has set_interactive(), so you can use the"
+        ##     print "more stable single-threaded Gtk mode."
+        ##     print "See https://bugs.launchpad.net/ipython/+bug/270856"
+        ## except AttributeError:
+        ##     pass
         
         self.gtk = gtk
         self.gtk_mainloop = hijack_gtk()
 
         # Allows us to use both Tk and GTK.
         self.tk = get_tk()
         
         if gtk.pygtk_version >= (2,4,0): mainquit = self.gtk.main_quit
         else:                            mainquit = self.gtk.mainquit
 
         self.IP = make_IPython(argv,user_ns=user_ns,
                                user_global_ns=user_global_ns,
                                debug=debug,
                                shell_class=shell_class,
                                on_kill=[mainquit])
 
         # HACK: slot for banner in self; it will be passed to the mainloop
         # method only and .run() needs it.  The actual value will be set by
         # .mainloop().
         self._banner = None 
 
         threading.Thread.__init__(self)
 
     def mainloop(self,sys_exit=0,banner=None):
 
         self._banner = banner
         
         if self.gtk.pygtk_version >= (2,4,0):
             import gobject
             gobject.idle_add(self.on_timer)
         else:
             self.gtk.idle_add(self.on_timer)
 
         if sys.platform != 'win32':
             try:
                 if self.gtk.gtk_version[0] >= 2:
                     self.gtk.gdk.threads_init()
             except AttributeError:
                 pass
             except RuntimeError:
                 error('Your pyGTK likely has not been compiled with '
                       'threading support.\n'
                       'The exception printout is below.\n'
                       'You can either rebuild pyGTK with threads, or '
                       'try using \n'
                       'matplotlib with a different backend (like Tk or WX).\n'
                       'Note that matplotlib will most likely not work in its '
                       'current state!')
                 self.IP.InteractiveTB()
 
         self.start()
         self.gtk.gdk.threads_enter()
         self.gtk_mainloop()
         self.gtk.gdk.threads_leave()
         self.join()
 
     def on_timer(self):
         """Called when GTK is idle.
 
         Must return True always, otherwise GTK stops calling it"""
         
         update_tk(self.tk)
         self.IP.runcode()
         time.sleep(0.01)
         return True
 
 
 class IPShellWX(IPThread):
     """Run a wx mainloop() in a separate thread.
     
     Python commands can be passed to the thread where they will be executed.
     This is implemented by periodically checking for passed code using a
     GTK timeout callback."""
     
     TIMEOUT = 100 # Millisecond interval between timeouts.
 
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,
                  debug=1,shell_class=MTInteractiveShell):
 
         self.IP = make_IPython(argv,user_ns=user_ns,
                                user_global_ns=user_global_ns,
                                debug=debug,
                                shell_class=shell_class,
                                on_kill=[self.wxexit])
 
         wantedwxversion=self.IP.rc.wxversion
         if wantedwxversion!="0":
             try:
                 import wxversion
             except ImportError:
                 error('The wxversion module is needed for WX version selection')
             else:
                 try:
                     wxversion.select(wantedwxversion)
                 except:
                     self.IP.InteractiveTB()
                     error('Requested wxPython version %s could not be loaded' %
                                                                wantedwxversion)
 
         import wx
 
         threading.Thread.__init__(self)
         self.wx = wx
         self.wx_mainloop = hijack_wx()
 
         # Allows us to use both Tk and GTK.
         self.tk = get_tk()
         
         # HACK: slot for banner in self; it will be passed to the mainloop
         # method only and .run() needs it.  The actual value will be set by
         # .mainloop().
         self._banner = None 
 
         self.app = None
 
     def wxexit(self, *args):
         if self.app is not None:
             self.app.agent.timer.Stop()
             self.app.ExitMainLoop()
 
     def mainloop(self,sys_exit=0,banner=None):
 
         self._banner = banner
         
         self.start()
 
         class TimerAgent(self.wx.MiniFrame):
             wx = self.wx
             IP = self.IP
             tk = self.tk
             def __init__(self, parent, interval):
                 style = self.wx.DEFAULT_FRAME_STYLE | self.wx.TINY_CAPTION_HORIZ
                 self.wx.MiniFrame.__init__(self, parent, -1, ' ', pos=(200, 200),
                                              size=(100, 100),style=style)
                 self.Show(False)
                 self.interval = interval
                 self.timerId = self.wx.NewId()                                
 
             def StartWork(self):
                 self.timer = self.wx.Timer(self, self.timerId)
                 self.wx.EVT_TIMER(self,  self.timerId, self.OnTimer)
                 self.timer.Start(self.interval)
 
             def OnTimer(self, event):
                 update_tk(self.tk)
                 self.IP.runcode()
 
         class App(self.wx.App):
             wx = self.wx
             TIMEOUT = self.TIMEOUT
             def OnInit(self):
                 'Create the main window and insert the custom frame'
                 self.agent = TimerAgent(None, self.TIMEOUT)
                 self.agent.Show(False)
                 self.agent.StartWork()
                 return True
 
         self.app = App(redirect=False)
         self.wx_mainloop(self.app)
         self.join()
 
 
 class IPShellQt(IPThread):
     """Run a Qt event loop in a separate thread.
     
     Python commands can be passed to the thread where they will be executed.
     This is implemented by periodically checking for passed code using a
     Qt timer / slot."""
     
     TIMEOUT = 100 # Millisecond interval between timeouts.
 
     def __init__(self, argv=None, user_ns=None, user_global_ns=None,
                  debug=0, shell_class=MTInteractiveShell):
 
         import qt
 
         self.exec_loop = hijack_qt()
 
         # Allows us to use both Tk and QT.
         self.tk = get_tk()
 
         self.IP = make_IPython(argv,
                                user_ns=user_ns,
                                user_global_ns=user_global_ns,
                                debug=debug,
                                shell_class=shell_class,
                                on_kill=[qt.qApp.exit])
 
         # HACK: slot for banner in self; it will be passed to the mainloop
         # method only and .run() needs it.  The actual value will be set by
         # .mainloop().
         self._banner = None 
         
         threading.Thread.__init__(self)
 
     def mainloop(self, sys_exit=0, banner=None):
 
         import qt
 
         self._banner = banner
 
         if qt.QApplication.startingUp():
             a = qt.QApplication(sys.argv)
 
         self.timer = qt.QTimer()
         qt.QObject.connect(self.timer,
                            qt.SIGNAL('timeout()'),
                            self.on_timer)
 
         self.start()
         self.timer.start(self.TIMEOUT, True)
         while True:
             if self.IP._kill: break
             self.exec_loop()
         self.join()
 
     def on_timer(self):
         update_tk(self.tk)
         result = self.IP.runcode()
         self.timer.start(self.TIMEOUT, True)
         return result
 
 
 class IPShellQt4(IPThread):
     """Run a Qt event loop in a separate thread.
 
     Python commands can be passed to the thread where they will be executed.
     This is implemented by periodically checking for passed code using a
     Qt timer / slot."""
 
     TIMEOUT = 100 # Millisecond interval between timeouts.
 
     def __init__(self, argv=None, user_ns=None, user_global_ns=None,
                  debug=0, shell_class=MTInteractiveShell):
 
         from PyQt4 import QtCore, QtGui
 
         try:
             # present in PyQt4-4.2.1 or later
             QtCore.pyqtRemoveInputHook()
         except AttributeError:
             pass
 
         if QtCore.PYQT_VERSION_STR == '4.3':
             warn('''PyQt4 version 4.3 detected.
 If you experience repeated threading warnings, please update PyQt4.
 ''')
 
         self.exec_ = hijack_qt4()
 
         # Allows us to use both Tk and QT.
         self.tk = get_tk()
 
         self.IP = make_IPython(argv,
                                user_ns=user_ns,
                                user_global_ns=user_global_ns,
                                debug=debug,
                                shell_class=shell_class,
                                on_kill=[QtGui.qApp.exit])
 
         # HACK: slot for banner in self; it will be passed to the mainloop
         # method only and .run() needs it.  The actual value will be set by
         # .mainloop().
         self._banner = None
 
         threading.Thread.__init__(self)
 
     def mainloop(self, sys_exit=0, banner=None):
 
         from PyQt4 import QtCore, QtGui
 
         self._banner = banner
 
         if QtGui.QApplication.startingUp():
             a = QtGui.QApplication(sys.argv)
 
         self.timer = QtCore.QTimer()
         QtCore.QObject.connect(self.timer,
                                QtCore.SIGNAL('timeout()'),
                                self.on_timer)
 
         self.start()
         self.timer.start(self.TIMEOUT)
         while True:
             if self.IP._kill: break
             self.exec_()
         self.join()
 
     def on_timer(self):
         update_tk(self.tk)
         result = self.IP.runcode()
         self.timer.start(self.TIMEOUT)
         return result
 
 
 # A set of matplotlib public IPython shell classes, for single-threaded (Tk*
 # and FLTK*) and multithreaded (GTK*, WX* and Qt*) backends to use.
 def _load_pylab(user_ns):
     """Allow users to disable pulling all of pylab into the top-level
     namespace.
 
     This little utility must be called AFTER the actual ipython instance is
     running, since only then will the options file have been fully parsed."""
     
     ip = IPython.ipapi.get()
     if ip.options.pylab_import_all:
         ip.ex("from matplotlib.pylab import *")
         ip.IP.user_config_ns.update(ip.user_ns)
         
 
 class IPShellMatplotlib(IPShell):
     """Subclass IPShell with MatplotlibShell as the internal shell.
 
     Single-threaded class, meant for the Tk* and FLTK* backends.
 
     Having this on a separate class simplifies the external driver code."""
     
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
         IPShell.__init__(self,argv,user_ns,user_global_ns,debug,
                          shell_class=MatplotlibShell)
         _load_pylab(self.IP.user_ns)
 
 class IPShellMatplotlibGTK(IPShellGTK):
     """Subclass IPShellGTK with MatplotlibMTShell as the internal shell.
 
     Multi-threaded class, meant for the GTK* backends."""
     
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
         IPShellGTK.__init__(self,argv,user_ns,user_global_ns,debug,
                             shell_class=MatplotlibMTShell)
         _load_pylab(self.IP.user_ns)
 
 class IPShellMatplotlibWX(IPShellWX):
     """Subclass IPShellWX with MatplotlibMTShell as the internal shell.
 
     Multi-threaded class, meant for the WX* backends."""
     
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
         IPShellWX.__init__(self,argv,user_ns,user_global_ns,debug,
                            shell_class=MatplotlibMTShell)
         _load_pylab(self.IP.user_ns)
 
 class IPShellMatplotlibQt(IPShellQt):
     """Subclass IPShellQt with MatplotlibMTShell as the internal shell.
 
     Multi-threaded class, meant for the Qt* backends."""
     
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
         IPShellQt.__init__(self,argv,user_ns,user_global_ns,debug,
                            shell_class=MatplotlibMTShell)
         _load_pylab(self.IP.user_ns)
 
 class IPShellMatplotlibQt4(IPShellQt4):
     """Subclass IPShellQt4 with MatplotlibMTShell as the internal shell.
 
     Multi-threaded class, meant for the Qt4* backends."""
 
     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
         IPShellQt4.__init__(self,argv,user_ns,user_global_ns,debug,
                            shell_class=MatplotlibMTShell)
         _load_pylab(self.IP.user_ns)
 
 #-----------------------------------------------------------------------------
 # Factory functions to actually start the proper thread-aware shell
 
+def check_gtk(mode):
+    import gtk
+    if hasattr(gtk,'set_interactive'):
+        gtk.set_interactive(False)
+        return 'tkthread'
+    else:
+        return mode
+
+
 def _select_shell(argv):
     """Select a shell from the given argv vector.
 
     This function implements the threading selection policy, allowing runtime
     control of the threading mode, both for general users and for matplotlib.
 
     Return:
       Shell class to be instantiated for runtime operation.
     """
     
     global USE_TK
 
     mpl_shell = {'gthread' : IPShellMatplotlibGTK,
                  'wthread' : IPShellMatplotlibWX,
                  'qthread' : IPShellMatplotlibQt,
                  'q4thread' : IPShellMatplotlibQt4,
                  'tkthread' : IPShellMatplotlib,  # Tk is built-in
                  }
 
     th_shell = {'gthread' : IPShellGTK,
                 'wthread' : IPShellWX,
                 'qthread' : IPShellQt,
                 'q4thread' : IPShellQt4,
                 'tkthread' : IPShell, # Tk is built-in
                 }
 
     backends = {'gthread' : 'GTKAgg',
                 'wthread' : 'WXAgg',
                 'qthread' : 'QtAgg',
                 'q4thread' :'Qt4Agg',
                 'tkthread' :'TkAgg',
                 }
 
     all_opts = set(['tk','pylab','gthread','qthread','q4thread','wthread',
                     'tkthread'])
     user_opts = set([s.replace('-','') for s in argv[:3]])
     special_opts = user_opts & all_opts            
 
     if 'tk' in special_opts:
         USE_TK = True
         special_opts.remove('tk')
 
     if 'pylab' in special_opts:
 
         try:
             import matplotlib
         except ImportError:
             error('matplotlib could NOT be imported!  Starting normal IPython.')
             return IPShell
         
         special_opts.remove('pylab')
         # If there's any option left, it means the user wants to force the
         # threading backend, else it's auto-selected from the rc file
         if special_opts:
             th_mode = special_opts.pop()
             matplotlib.rcParams['backend'] = backends[th_mode]
         else:
             backend = matplotlib.rcParams['backend']
             if backend.startswith('GTK'):
                 th_mode = 'gthread'
             elif backend.startswith('WX'):
                 th_mode = 'wthread'
             elif backend.startswith('Qt4'):
                 th_mode = 'q4thread'
             elif backend.startswith('Qt'):
                 th_mode = 'qthread'
             else:
                 # Any other backend, use plain Tk
                 th_mode = 'tkthread'
+
+            # New versions of pygtk don't need the brittle threaded support.
+            th_mode = check_gtk(th_mode)
                 
         return mpl_shell[th_mode]
     else:
         # No pylab requested, just plain threads
         try:
             th_mode = special_opts.pop()
         except KeyError:
             th_mode = 'tkthread'
+
+        # New versions of pygtk don't need the brittle threaded support.
+        th_mode = check_gtk(th_mode)
         return th_shell[th_mode]
 
 
 # This is the one which should be called by external code.
 def start(user_ns = None):
     """Return a running shell instance, dealing with threading options.
 
     This is a factory function which will instantiate the proper IPython shell
     based on the user's threading choice.  Such a selector is needed because
     different GUI toolkits require different thread handling details."""
 
     shell = _select_shell(sys.argv)
     return shell(user_ns = user_ns)
 
 # Some aliases for backwards compatibility
 IPythonShell = IPShell
 IPythonShellEmbed = IPShellEmbed
 #************************ End of file <Shell.py> ***************************

docs/sphinxext/ipython_directive.py

@@ -1,605 +1,613 b''
 # -*- coding: utf-8 -*-
 """Sphinx directive to support embedded IPython code.
 
 This directive allows pasting of entire interactive IPython sessions, prompts
 and all, and their code will actually get re-executed at doc build time, with
 all prompts renumbered sequentially.
 
 To enable this directive, simply list it in your Sphinx ``conf.py`` file
 (making sure the directory where you placed it is visible to sphinx, as is
 needed for all Sphinx directives).
 
 By default this directive assumes that your prompts are unchanged IPython ones,
 but this can be customized.  For example, the following code in your Sphinx
 config file will configure this directive for the following input/output
 prompts ``Yade [1]:`` and ``-> [1]:``::
 
  import ipython_directive as id
  id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
  id.rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
  id.fmtin ='Yade [%d]:'
  id.fmtout=' ->  [%d]:'
 
  id.rc_override=dict(
    prompt_in1="Yade [\#]:",
    prompt_in2="     .\D..",
    prompt_out=" ->  [\#]:"
  )
+ id.reconfig_shell()
 
  import ipython_console_highlighting as ich
  ich.IPythonConsoleLexer.input_prompt=
     re.compile("(Yade \[[0-9]+\]: )|(   \.\.\.+:)")
  ich.IPythonConsoleLexer.output_prompt=
     re.compile("(( ->  )|(Out)\[[0-9]+\]: )|(   \.\.\.+:)")
  ich.IPythonConsoleLexer.continue_prompt=re.compile("   \.\.\.+:")
 
 
 ToDo
 ----
 
 - Turn the ad-hoc test() function into a real test suite.
 - Break up ipython-specific functionality from matplotlib stuff into better
   separated code.
 - Make sure %bookmarks used internally are removed on exit.
 
 
 Authors
 -------
 
 - John D Hunter: orignal author.
 - Fernando Perez: refactoring, documentation, cleanups.
 - VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generatlizations.
 """
 
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 
 # Stdlib
 import cStringIO
 import imp
 import os
 import re
 import shutil
 import sys
 import warnings
 
 # To keep compatibility with various python versions
 try:
     from hashlib import md5
 except ImportError:
     from md5 import md5
 
 # Third-party
 import matplotlib
 import sphinx
 from docutils.parsers.rst import directives
 
 matplotlib.use('Agg')
 
 # Our own
 import IPython
 from IPython.Shell import MatplotlibShell
 
 #-----------------------------------------------------------------------------
 # Globals
 #-----------------------------------------------------------------------------
 
 sphinx_version = sphinx.__version__.split(".")
 # The split is necessary for sphinx beta versions where the string is
 # '6b1'
 sphinx_version = tuple([int(re.split('[a-z]', x)[0])
                         for x in sphinx_version[:2]])
 
 COMMENT, INPUT, OUTPUT =  range(3)
 rc_override = {}
 rgxin = re.compile('In \[(\d+)\]:\s?(.*)\s*')
 rgxout = re.compile('Out\[(\d+)\]:\s?(.*)\s*')
 fmtin = 'In [%d]:'
 fmtout = 'Out[%d]:'
 
 #-----------------------------------------------------------------------------
 # Functions and class declarations
 #-----------------------------------------------------------------------------
 def block_parser(part):
     """
     part is a string of ipython text, comprised of at most one
     input, one ouput, comments, and blank lines.  The block parser
     parses the text into a list of::
 
       blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...]
 
     where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and
     data is, depending on the type of token::
 
       COMMENT : the comment string
 
       INPUT: the (DECORATOR, INPUT_LINE, REST) where
          DECORATOR: the input decorator (or None)
          INPUT_LINE: the input as string (possibly multi-line)
          REST : any stdout generated by the input line (not OUTPUT)
 
 
       OUTPUT: the output string, possibly multi-line
     """
 
     block = []
     lines = part.split('\n')
     N = len(lines)
     i = 0
     decorator = None
     while 1:
 
         if i==N:
             # nothing left to parse -- the last line
             break
 
         line = lines[i]
         i += 1
         line_stripped = line.strip()
         if line_stripped.startswith('#'):
             block.append((COMMENT, line))
             continue
 
         if line_stripped.startswith('@'):
             # we're assuming at most one decorator -- may need to
             # rethink
             decorator = line_stripped
             continue
 
         # does this look like an input line?
         matchin = rgxin.match(line)
         if matchin:
             lineno, inputline = int(matchin.group(1)), matchin.group(2)
 
             # the ....: continuation string
             continuation = '   %s:'%''.join(['.']*(len(str(lineno))+2))
             Nc = len(continuation)
             # input lines can continue on for more than one line, if
             # we have a '\' line continuation char or a function call
             # echo line 'print'.  The input line can only be
             # terminated by the end of the block or an output line, so
             # we parse out the rest of the input line if it is
             # multiline as well as any echo text
 
             rest = []
             while i<N:
 
                 # look ahead; if the next line is blank, or a comment, or
                 # an output line, we're done
 
                 nextline = lines[i]
                 matchout = rgxout.match(nextline)
                 #print "nextline=%s, continuation=%s, starts=%s"%(nextline, continuation, nextline.startswith(continuation))
                 if matchout or nextline.startswith('#'):
                     break
                 elif nextline.startswith(continuation):
                     inputline += '\n' + nextline[Nc:]
                 else:
                     rest.append(nextline)
                 i+= 1
 
             block.append((INPUT, (decorator, inputline, '\n'.join(rest))))
             continue
 
         # if it looks like an output line grab all the text to the end
         # of the block
         matchout = rgxout.match(line)
         if matchout:
             lineno, output = int(matchout.group(1)), matchout.group(2)
             if i<N-1:
                 output = '\n'.join([output] + lines[i:])
 
             block.append((OUTPUT, output))
             break
 
     return block
 
 
 class EmbeddedSphinxShell(object):
     """An embedded IPython instance to run inside Sphinx"""
 
     def __init__(self):
 
         self.cout = cStringIO.StringIO()
 
         IPython.Shell.Term.cout = self.cout
         IPython.Shell.Term.cerr = self.cout
         argv = ['-autocall', '0']
         self.user_ns = {}
         self.user_glocal_ns = {}
 
         self.IP = IPython.ipmaker.make_IPython(
             argv, self.user_ns, self.user_glocal_ns, embedded=True,
             #shell_class=IPython.Shell.InteractiveShell,
             shell_class=MatplotlibShell,
-            rc_override = dict(colors = 'NoColor'), **rc_override)
+            rc_override = dict(colors = 'NoColor', **rc_override))
 
         self.input = ''
         self.output = ''
 
         self.is_verbatim = False
         self.is_doctest = False
         self.is_suppress = False
 
         # on the first call to the savefig decorator, we'll import
         # pyplot as plt so we can make a call to the plt.gcf().savefig
         self._pyplot_imported = False
 
         # we need bookmark the current dir first so we can save
         # relative to it
         self.process_input_line('bookmark ipy_basedir')
         self.cout.seek(0)
         self.cout.truncate(0)
 
     def process_input_line(self, line):
         """process the input, capturing stdout"""
         #print "input='%s'"%self.input
         stdout = sys.stdout
         sys.stdout = self.cout
         #self.IP.resetbuffer()
         self.IP.push(self.IP.prefilter(line, 0))
         #self.IP.runlines(line)
         sys.stdout = stdout
 
     # Callbacks for each type of token
     def process_input(self, data, input_prompt, lineno):
         """Process data block for INPUT token."""
         decorator, input, rest = data
         image_file = None
         #print 'INPUT:', data
         is_verbatim = decorator=='@verbatim' or self.is_verbatim
         is_doctest = decorator=='@doctest' or self.is_doctest
         is_suppress = decorator=='@suppress' or self.is_suppress
         is_savefig = decorator is not None and \
                      decorator.startswith('@savefig')
 
         input_lines = input.split('\n')
 
         continuation = '   %s:'%''.join(['.']*(len(str(lineno))+2))
         Nc = len(continuation)
 
         if is_savefig:
             saveargs = decorator.split(' ')
             filename = saveargs[1]
             outfile = os.path.join('_static/%s'%filename)
             # build out an image directive like
             # .. image:: somefile.png
             #    :width 4in
             #
             # from an input like
             # savefig somefile.png width=4in
             imagerows = ['.. image:: %s'%outfile]
 
             for kwarg in saveargs[2:]:
                 arg, val = kwarg.split('=')
                 arg = arg.strip()
                 val = val.strip()
                 imagerows.append('   :%s: %s'%(arg, val))
 
             image_file = outfile
             image_directive = '\n'.join(imagerows)
 
         # TODO: can we get "rest" from ipython
         #self.process_input_line('\n'.join(input_lines))
 
         ret = []
         is_semicolon = False
 
         for i, line in enumerate(input_lines):
             if line.endswith(';'):
                 is_semicolon = True
 
             if i==0:
                 # process the first input line
                 if is_verbatim:
                     self.process_input_line('')
                 else:
                     # only submit the line in non-verbatim mode
                     self.process_input_line(line)
                 formatted_line = '%s %s'%(input_prompt, line)
             else:
                 # process a continuation line
                 if not is_verbatim:
                     self.process_input_line(line)
 
                 formatted_line = '%s %s'%(continuation, line)
 
             if not is_suppress:
                 ret.append(formatted_line)
 
         if not is_suppress:
             if len(rest.strip()):
                 if is_verbatim:
                     # the "rest" is the standard output of the
                     # input, which needs to be added in
                     # verbatim mode
                     ret.append(rest)
 
         self.cout.seek(0)
         output = self.cout.read()
         if not is_suppress and not is_semicolon:
             ret.append(output)
 
         self.cout.truncate(0)
         return ret, input_lines, output, is_doctest, image_file
         #print 'OUTPUT', output  # dbg
 
     def process_output(self, data, output_prompt,
                        input_lines, output, is_doctest, image_file):
         """Process data block for OUTPUT token."""
         if is_doctest:
             submitted = data.strip()
             found = output
             if found is not None:
                 ind = found.find(output_prompt)
                 if ind<0:
                     raise RuntimeError('output prompt="%s" does not match out line=%s'%(output_prompt, found))
                 found = found[len(output_prompt):].strip()
 
                 if found!=submitted:
                     raise RuntimeError('doctest failure for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted))
                 #print 'doctest PASSED for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted)
 
     def process_comment(self, data):
         """Process data block for COMMENT token."""
         if not self.is_suppress:
             return [data]
 
     def process_block(self, block):
         """
         process block from the block_parser and return a list of processed lines
         """
 
         ret = []
         output = None
         input_lines = None
 
         m = rgxin.match(str(self.IP.outputcache.prompt1).strip())
         lineno = int(m.group(1))
 
         input_prompt = fmtin%lineno
         output_prompt = fmtout%lineno
         image_file = None
         image_directive = None
         # XXX - This needs a second refactor.  There's too much state being
         # held globally, which makes for a very awkward interface and large,
         # hard to test functions.  I've already broken this up at least into
         # three separate processors to isolate the logic better, but this only
         # serves to highlight the coupling.  Next we need to clean it up...
         for token, data in block:
             if token==COMMENT:
                 out_data = self.process_comment(data)
             elif token==INPUT:
                 out_data, input_lines, output, is_doctest, image_file= \
                           self.process_input(data, input_prompt, lineno)
             elif token==OUTPUT:
                 out_data = \
                     self.process_output(data, output_prompt,
                                         input_lines, output, is_doctest,
                                         image_file)
             if out_data:
                 ret.extend(out_data)
 
         if image_file is not None:
             self.ensure_pyplot()
             command = 'plt.gcf().savefig("%s")'%image_file
             #print 'SAVEFIG', command  # dbg
             self.process_input_line('bookmark ipy_thisdir')
             self.process_input_line('cd -b ipy_basedir')
             self.process_input_line(command)
             self.process_input_line('cd -b ipy_thisdir')
             self.cout.seek(0)
             self.cout.truncate(0)
         return ret, image_directive
 
     def ensure_pyplot(self):
         if self._pyplot_imported:
             return
         self.process_input_line('import matplotlib.pyplot as plt')
 
 # A global instance used below. XXX: not sure why this can't be created inside
 # ipython_directive itself.
 shell = EmbeddedSphinxShell()
 
+def reconfig_shell():
+    """Called after setting module-level variables to re-instantiate
+    with the set values (since shell is instantiated first at import-time
+    when module variables have default values)"""
+    global shell
+    shell = EmbeddedSphinxShell()
+
 
 def ipython_directive(name, arguments, options, content, lineno,
                       content_offset, block_text, state, state_machine,
                       ):
 
     debug = ipython_directive.DEBUG
     shell.is_suppress = options.has_key('suppress')
     shell.is_doctest = options.has_key('doctest')
     shell.is_verbatim = options.has_key('verbatim')
 
     #print 'ipy', shell.is_suppress, options
     parts = '\n'.join(content).split('\n\n')
     lines = ['.. sourcecode:: ipython', '']
 
     figures = []
     for part in parts:
         block = block_parser(part)
 
         if len(block):
             rows, figure = shell.process_block(block)
             for row in rows:
                 lines.extend(['    %s'%line for line in row.split('\n')])
 
             if figure is not None:
                 figures.append(figure)
 
     for figure in figures:
         lines.append('')
         lines.extend(figure.split('\n'))
         lines.append('')
 
     #print lines
     if len(lines)>2:
         if debug:
             print '\n'.join(lines)
         else:
             #print 'INSERTING %d lines'%len(lines)
             state_machine.insert_input(
                 lines, state_machine.input_lines.source(0))
 
     return []
 
 ipython_directive.DEBUG = False
 
 # Enable as a proper Sphinx directive
 def setup(app):
     setup.app = app
     options = {'suppress': directives.flag,
                'doctest': directives.flag,
                'verbatim': directives.flag,
                }
 
     app.add_directive('ipython', ipython_directive, True, (0, 2, 0), **options)
 
 
 # Simple smoke test, needs to be converted to a proper automatic test.
 def test():
 
     examples = [
         r"""
 In [9]: pwd
 Out[9]: '/home/jdhunter/py4science/book'
 
 In [10]: cd bookdata/
 /home/jdhunter/py4science/book/bookdata
 
 In [2]: from pylab import *
 
 In [2]: ion()
 
 In [3]: im = imread('stinkbug.png')
 
 @savefig mystinkbug.png width=4in
 In [4]: imshow(im)
 Out[4]: <matplotlib.image.AxesImage object at 0x39ea850>
         
 """,
         r"""
 
 In [1]: x = 'hello world'
 
 # string methods can be
 # used to alter the string
 @doctest
 In [2]: x.upper()
 Out[2]: 'HELLO WORLD'
 
 @verbatim
 In [3]: x.st<TAB>
 x.startswith  x.strip
 """,
     r"""
 
 In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\
    .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv'
 
 In [131]: print url.split('&')
 ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv']
 
 In [60]: import urllib
 
 """,
     r"""\
 
 In [133]: import numpy.random
 
 @suppress
 In [134]: numpy.random.seed(2358)
 
 @doctest
 In [135]: np.random.rand(10,2)
 Out[135]:
 array([[ 0.64524308,  0.59943846],
        [ 0.47102322,  0.8715456 ],
        [ 0.29370834,  0.74776844],
        [ 0.99539577,  0.1313423 ],
        [ 0.16250302,  0.21103583],
        [ 0.81626524,  0.1312433 ],
        [ 0.67338089,  0.72302393],
        [ 0.7566368 ,  0.07033696],
        [ 0.22591016,  0.77731835],
        [ 0.0072729 ,  0.34273127]])
 
 """,
 
     r"""
 In [106]: print x
 jdh
 
 In [109]: for i in range(10):
    .....:     print i
    .....:
    .....:
 0
 1
 2
 3
 4
 5
 6
 7
 8
 9
 
 
 """,
 
         r"""
 
 In [144]: from pylab import *
 
 In [145]: ion()
 
 # use a semicolon to suppress the output
 @savefig test_hist.png width=4in
 In [151]: hist(np.random.randn(10000), 100);
 
 
 @savefig test_plot.png width=4in
 In [151]: plot(np.random.randn(10000), 'o');
    """,
 
         r"""
 # use a semicolon to suppress the output
 In [151]: plt.clf()
 
 @savefig plot_simple.png width=4in
 In [151]: plot([1,2,3])
 
 @savefig hist_simple.png width=4in
 In [151]: hist(np.random.randn(10000), 100);
 
 """,
      r"""
 # update the current fig
 In [151]: ylabel('number')
 
 In [152]: title('normal distribution')
 
 
 @savefig hist_with_text.png
 In [153]: grid(True)
 
         """,
     ]
 
 
     ipython_directive.DEBUG = True
     #options = dict(suppress=True)
     options = dict()
     for example in examples:
         content = example.split('\n')
         ipython_directive('debug', arguments=None, options=options,
                           content=content, lineno=0,
                           content_offset=None, block_text=None,
                           state=None, state_machine=None,
                           )
 
 # Run test suite as a script
 if __name__=='__main__':
     test()