make hiding of initial namespace optional

It is by design that names loaded by startup files, etc.
are hidden from things like `%who`.

But this behavior is pretty surprising, especially since

    ipython -i script.py

and

    %run -i script.py

have different behaviors with respect to the hidden namespace.

Since the current behavior was added at the request of @fperez,
I left the default behavior unchanged,
but added a flag to disable hiding initial variables.

IPython/core/shellapp.py

@@ -1,410 +1,416 b''
 # encoding: utf-8
 """
 A mixin for :class:`~IPython.core.application.Application` classes that
 launch InteractiveShell instances, load extensions, etc.
 
 Authors
 -------
 
 * Min Ragan-Kelley
 """
 
 #-----------------------------------------------------------------------------
 #  Copyright (C) 2008-2011  The IPython Development Team
 #
 #  Distributed under the terms of the BSD License.  The full license is in
 #  the file COPYING, distributed as part of this software.
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 
 from __future__ import absolute_import
 from __future__ import print_function
 
 import glob
 import os
 import sys
 
 from IPython.config.application import boolean_flag
 from IPython.config.configurable import Configurable
 from IPython.config.loader import Config
 from IPython.core import pylabtools
 from IPython.utils import py3compat
 from IPython.utils.contexts import preserve_keys
 from IPython.utils.path import filefind
 from IPython.utils.traitlets import (
     Unicode, Instance, List, Bool, CaselessStrEnum, Dict
 )
 from IPython.lib.inputhook import guis
 
 #-----------------------------------------------------------------------------
 # Aliases and Flags
 #-----------------------------------------------------------------------------
 
 gui_keys = tuple(sorted([ key for key in guis if key is not None ]))
 
 backend_keys = sorted(pylabtools.backends.keys())
 backend_keys.insert(0, 'auto')
 
 shell_flags = {}
 
 addflag = lambda *args: shell_flags.update(boolean_flag(*args))
 addflag('autoindent', 'InteractiveShell.autoindent',
         'Turn on autoindenting.', 'Turn off autoindenting.'
 )
 addflag('automagic', 'InteractiveShell.automagic',
         """Turn on the auto calling of magic commands. Type %%magic at the
         IPython  prompt  for  more information.""",
         'Turn off the auto calling of magic commands.'
 )
 addflag('pdb', 'InteractiveShell.pdb',
     "Enable auto calling the pdb debugger after every exception.",
     "Disable auto calling the pdb debugger after every exception."
 )
 # pydb flag doesn't do any config, as core.debugger switches on import,
 # which is before parsing.  This just allows the flag to be passed.
 shell_flags.update(dict(
     pydb = ({},
         """Use the third party 'pydb' package as debugger, instead of pdb.
         Requires that pydb is installed."""
     )
 ))
 addflag('pprint', 'PlainTextFormatter.pprint',
     "Enable auto pretty printing of results.",
     "Disable auto pretty printing of results."
 )
 addflag('color-info', 'InteractiveShell.color_info',
     """IPython can display information about objects via a set of func-
     tions, and optionally can use colors for this, syntax highlighting
     source code and various other elements.  However, because this
     information is passed through a pager (like 'less') and many pagers get
     confused with color codes, this option is off by default.  You can test
     it and turn it on permanently in your ipython_config.py file if it
     works for you.  Test it and turn it on permanently if it works with
     your system.  The magic function %%color_info allows you to toggle this
     interactively for testing.""",
     "Disable using colors for info related things."
 )
 addflag('deep-reload', 'InteractiveShell.deep_reload',
     """Enable deep (recursive) reloading by default. IPython can use the
     deep_reload module which reloads changes in modules recursively (it
     replaces the reload() function, so you don't need to change anything to
     use it). deep_reload() forces a full reload of modules whose code may
     have changed, which the default reload() function does not.  When
     deep_reload is off, IPython will use the normal reload(), but
     deep_reload will still be available as dreload(). This feature is off
     by default [which means that you have both normal reload() and
     dreload()].""",
     "Disable deep (recursive) reloading by default."
 )
 nosep_config = Config()
 nosep_config.InteractiveShell.separate_in = ''
 nosep_config.InteractiveShell.separate_out = ''
 nosep_config.InteractiveShell.separate_out2 = ''
 
 shell_flags['nosep']=(nosep_config, "Eliminate all spacing between prompts.")
 shell_flags['pylab'] = (
     {'InteractiveShellApp' : {'pylab' : 'auto'}},
     """Pre-load matplotlib and numpy for interactive use with
     the default matplotlib backend."""
 )
 shell_flags['matplotlib'] = (
     {'InteractiveShellApp' : {'matplotlib' : 'auto'}},
     """Configure matplotlib for interactive use with
     the default matplotlib backend."""
 )
 
 # it's possible we don't want short aliases for *all* of these:
 shell_aliases = dict(
     autocall='InteractiveShell.autocall',
     colors='InteractiveShell.colors',
     logfile='InteractiveShell.logfile',
     logappend='InteractiveShell.logappend',
     c='InteractiveShellApp.code_to_run',
     m='InteractiveShellApp.module_to_run',
     ext='InteractiveShellApp.extra_extension',
     gui='InteractiveShellApp.gui',
     pylab='InteractiveShellApp.pylab',
     matplotlib='InteractiveShellApp.matplotlib',
 )
 shell_aliases['cache-size'] = 'InteractiveShell.cache_size'
 
 #-----------------------------------------------------------------------------
 # Main classes and functions
 #-----------------------------------------------------------------------------
 
 class InteractiveShellApp(Configurable):
     """A Mixin for applications that start InteractiveShell instances.
     
     Provides configurables for loading extensions and executing files
     as part of configuring a Shell environment.
 
     The following methods should be called by the :meth:`initialize` method
     of the subclass:
 
       - :meth:`init_path`
       - :meth:`init_shell` (to be implemented by the subclass)
       - :meth:`init_gui_pylab`
       - :meth:`init_extensions`
       - :meth:`init_code`
     """
     extensions = List(Unicode, config=True,
         help="A list of dotted module names of IPython extensions to load."
     )
     extra_extension = Unicode('', config=True,
         help="dotted module name of an IPython extension to load."
     )
     def _extra_extension_changed(self, name, old, new):
         if new:
             # add to self.extensions
             self.extensions.append(new)
     
     # Extensions that are always loaded (not configurable)
     default_extensions = List(Unicode, [u'storemagic'], config=False)
+    
+    hide_initial_ns = Bool(True, config=True,
+        help="""Should variables loaded at startup (by startup files, exec_lines, etc.)
+        be hidden from tools like %who?"""
+    )
 
     exec_files = List(Unicode, config=True,
         help="""List of files to run at IPython startup."""
     )
     file_to_run = Unicode('', config=True,
         help="""A file to be run""")
 
     exec_lines = List(Unicode, config=True,
         help="""lines of code to run at IPython startup."""
     )
     code_to_run = Unicode('', config=True,
         help="Execute the given command string."
     )
     module_to_run = Unicode('', config=True,
         help="Run the module as a script."
     )
     gui = CaselessStrEnum(gui_keys, config=True,
         help="Enable GUI event loop integration with any of {0}.".format(gui_keys)
     )
     matplotlib = CaselessStrEnum(backend_keys,
         config=True,
         help="""Configure matplotlib for interactive use with
         the default matplotlib backend."""
     )
     pylab = CaselessStrEnum(backend_keys,
         config=True,
         help="""Pre-load matplotlib and numpy for interactive use,
         selecting a particular matplotlib backend and loop integration.
         """
     )
     pylab_import_all = Bool(True, config=True,
         help="""If true, IPython will populate the user namespace with numpy, pylab, etc.
         and an ``import *`` is done from numpy and pylab, when using pylab mode.
         
         When False, pylab mode should not import any names into the user namespace.
         """
     )
     shell = Instance('IPython.core.interactiveshell.InteractiveShellABC')
     
     user_ns = Instance(dict, args=None, allow_none=True)
     def _user_ns_changed(self, name, old, new):
         if self.shell is not None:
             self.shell.user_ns = new
             self.shell.init_user_ns()
 
     def init_path(self):
         """Add current working directory, '', to sys.path"""
         if sys.path[0] != '':
             sys.path.insert(0, '')
 
     def init_shell(self):
         raise NotImplementedError("Override in subclasses")
 
     def init_gui_pylab(self):
         """Enable GUI event loop integration, taking pylab into account."""
         enable = False
         shell = self.shell
         if self.pylab:
             enable = lambda key: shell.enable_pylab(key, import_all=self.pylab_import_all)
             key = self.pylab
         elif self.matplotlib:
             enable = shell.enable_matplotlib
             key = self.matplotlib
         elif self.gui:
             enable = shell.enable_gui
             key = self.gui
         
         if not enable:
             return
         
         try:
             r = enable(key)
         except ImportError:
             self.log.warn("Eventloop or matplotlib integration failed. Is matplotlib installed?")
             self.shell.showtraceback()
             return
         except Exception:
             self.log.warn("GUI event loop or pylab initialization failed")
             self.shell.showtraceback()
             return
             
         if isinstance(r, tuple):
             gui, backend = r[:2]
             self.log.info("Enabling GUI event loop integration, "
                       "eventloop=%s, matplotlib=%s", gui, backend)
             if key == "auto":
                 print("Using matplotlib backend: %s" % backend)
         else:
             gui = r
             self.log.info("Enabling GUI event loop integration, "
                       "eventloop=%s", gui)
 
     def init_extensions(self):
         """Load all IPython extensions in IPythonApp.extensions.
 
         This uses the :meth:`ExtensionManager.load_extensions` to load all
         the extensions listed in ``self.extensions``.
         """
         try:
             self.log.debug("Loading IPython extensions...")
             extensions = self.default_extensions + self.extensions
             for ext in extensions:
                 try:
                     self.log.info("Loading IPython extension: %s" % ext)
                     self.shell.extension_manager.load_extension(ext)
                 except:
                     self.log.warn("Error in loading extension: %s" % ext +
                         "\nCheck your config files in %s" % self.profile_dir.location
                     )
                     self.shell.showtraceback()
         except:
             self.log.warn("Unknown error in loading extensions:")
             self.shell.showtraceback()
 
     def init_code(self):
         """run the pre-flight code, specified via exec_lines"""
         self._run_startup_files()
         self._run_exec_lines()
         self._run_exec_files()
         self._run_cmd_line_code()
         self._run_module()
         
         # flush output, so itwon't be attached to the first cell
         sys.stdout.flush()
         sys.stderr.flush()
         
         # Hide variables defined here from %who etc.
-        self.shell.user_ns_hidden.update(self.shell.user_ns)
+        if self.hide_initial_ns:
+            self.shell.user_ns_hidden.update(self.shell.user_ns)
 
     def _run_exec_lines(self):
         """Run lines of code in IPythonApp.exec_lines in the user's namespace."""
         if not self.exec_lines:
             return
         try:
             self.log.debug("Running code from IPythonApp.exec_lines...")
             for line in self.exec_lines:
                 try:
                     self.log.info("Running code in user namespace: %s" %
                                   line)
                     self.shell.run_cell(line, store_history=False)
                 except:
                     self.log.warn("Error in executing line in user "
                                   "namespace: %s" % line)
                     self.shell.showtraceback()
         except:
             self.log.warn("Unknown error in handling IPythonApp.exec_lines:")
             self.shell.showtraceback()
 
     def _exec_file(self, fname):
         try:
             full_filename = filefind(fname, [u'.', self.ipython_dir])
         except IOError as e:
             self.log.warn("File not found: %r"%fname)
             return
         # Make sure that the running script gets a proper sys.argv as if it
         # were run from a system shell.
         save_argv = sys.argv
         sys.argv = [full_filename] + self.extra_args[1:]
         # protect sys.argv from potential unicode strings on Python 2:
         if not py3compat.PY3:
             sys.argv = [ py3compat.cast_bytes(a) for a in sys.argv ]
         try:
             if os.path.isfile(full_filename):
                 self.log.info("Running file in user namespace: %s" %
                               full_filename)
                 # Ensure that __file__ is always defined to match Python
                 # behavior.
                 with preserve_keys(self.shell.user_ns, '__file__'):
                     self.shell.user_ns['__file__'] = fname
                     if full_filename.endswith('.ipy'):
                         self.shell.safe_execfile_ipy(full_filename)
                     else:
                         # default to python, even without extension
                         self.shell.safe_execfile(full_filename,
                                                  self.shell.user_ns)
         finally:
             sys.argv = save_argv
 
     def _run_startup_files(self):
         """Run files from profile startup directory"""
         startup_dir = self.profile_dir.startup_dir
         startup_files = []
         if os.environ.get('PYTHONSTARTUP', False):
             startup_files.append(os.environ['PYTHONSTARTUP'])
         startup_files += glob.glob(os.path.join(startup_dir, '*.py'))
         startup_files += glob.glob(os.path.join(startup_dir, '*.ipy'))
         if not startup_files:
             return
         
         self.log.debug("Running startup files from %s...", startup_dir)
         try:
             for fname in sorted(startup_files):
                 self._exec_file(fname)
         except:
             self.log.warn("Unknown error in handling startup files:")
             self.shell.showtraceback()
 
     def _run_exec_files(self):
         """Run files from IPythonApp.exec_files"""
         if not self.exec_files:
             return
 
         self.log.debug("Running files in IPythonApp.exec_files...")
         try:
             for fname in self.exec_files:
                 self._exec_file(fname)
         except:
             self.log.warn("Unknown error in handling IPythonApp.exec_files:")
             self.shell.showtraceback()
 
     def _run_cmd_line_code(self):
         """Run code or file specified at the command-line"""
         if self.code_to_run:
             line = self.code_to_run
             try:
                 self.log.info("Running code given at command line (c=): %s" %
                               line)
                 self.shell.run_cell(line, store_history=False)
             except:
                 self.log.warn("Error in executing line in user namespace: %s" %
                               line)
                 self.shell.showtraceback()
 
         # Like Python itself, ignore the second if the first of these is present
         elif self.file_to_run:
             fname = self.file_to_run
             try:
                 self._exec_file(fname)
             except:
                 self.log.warn("Error in executing file in user namespace: %s" %
                               fname)
                 self.shell.showtraceback()
 
     def _run_module(self):
         """Run module specified at the command-line."""
         if self.module_to_run:
             # Make sure that the module gets a proper sys.argv as if it were
             # run using `python -m`.
             save_argv = sys.argv
             sys.argv = [sys.executable] + self.extra_args
             try:
                 self.shell.safe_run_module(self.module_to_run,
                                            self.shell.user_ns)
             finally:
                 sys.argv = save_argv