Backport PR #10644: system-wide startup files and env config

- adds `{sys.prefix}/etc/ipython` to config-file path, which is commonly used for Jupyter applications in envs
- support startup files in system-wide config directories (e.g. `/etc/ipython/startup`, now `{sys.prefix}/etc/ipython/startup`)

docs/source/whatsnew/pr/env-config.rst

@@ -0,0 +1,5 b''
+
+- IPython now looks for config files in ``{sys.prefix}/etc/ipython``
+  for environment-specific configuration.
+- Startup files can be found in ``/etc/ipython/startup`` or ``{sys.prefix}/etc/ipython/startup``
+  in addition to the profile directory, for system-wide or env-specific startup files.

IPython/core/application.py

@@ -1,458 +1,467 b''
 # encoding: utf-8
 """
 An application for IPython.
 
 All top-level applications should use the classes in this module for
 handling configuration and creating configurables.
 
 The job of an :class:`Application` is to create the master configuration
 object and then create the configurable objects, passing the config to them.
 """
 
 # Copyright (c) IPython Development Team.
 # Distributed under the terms of the Modified BSD License.
 
 import atexit
 from copy import deepcopy
 import glob
 import logging
 import os
 import shutil
 import sys
 
 from traitlets.config.application import Application, catch_config_error
 from traitlets.config.loader import ConfigFileNotFound, PyFileConfigLoader
 from IPython.core import release, crashhandler
 from IPython.core.profiledir import ProfileDir, ProfileDirError
 from IPython.paths import get_ipython_dir, get_ipython_package_dir
 from IPython.utils.path import ensure_dir_exists
 from IPython.utils import py3compat
 from traitlets import (
     List, Unicode, Type, Bool, Dict, Set, Instance, Undefined,
     default, observe,
 )
 
 if os.name == 'nt':
     programdata = os.environ.get('PROGRAMDATA', None)
     if programdata:
         SYSTEM_CONFIG_DIRS = [os.path.join(programdata, 'ipython')]
     else:  # PROGRAMDATA is not defined by default on XP.
         SYSTEM_CONFIG_DIRS = []
 else:
     SYSTEM_CONFIG_DIRS = [
         "/usr/local/etc/ipython",
         "/etc/ipython",
     ]
 
+
+ENV_CONFIG_DIRS = []
+_env_config_dir = os.path.join(sys.prefix, 'etc', 'ipython')
+if _env_config_dir not in SYSTEM_CONFIG_DIRS:
+    # only add ENV_CONFIG if sys.prefix is not already included
+    ENV_CONFIG_DIRS.append(_env_config_dir)
+
+
 _envvar = os.environ.get('IPYTHON_SUPPRESS_CONFIG_ERRORS')
 if _envvar in {None, ''}:
     IPYTHON_SUPPRESS_CONFIG_ERRORS = None
 else:
     if _envvar.lower() in {'1','true'}:
         IPYTHON_SUPPRESS_CONFIG_ERRORS = True
     elif _envvar.lower() in {'0','false'} :
         IPYTHON_SUPPRESS_CONFIG_ERRORS = False
     else:
         sys.exit("Unsupported value for environment variable: 'IPYTHON_SUPPRESS_CONFIG_ERRORS' is set to '%s' which is none of  {'0', '1', 'false', 'true', ''}."% _envvar )
 
 # aliases and flags
 
 base_aliases = {
     'profile-dir' : 'ProfileDir.location',
     'profile' : 'BaseIPythonApplication.profile',
     'ipython-dir' : 'BaseIPythonApplication.ipython_dir',
     'log-level' : 'Application.log_level',
     'config' : 'BaseIPythonApplication.extra_config_file',
 }
 
 base_flags = dict(
     debug = ({'Application' : {'log_level' : logging.DEBUG}},
             "set log level to logging.DEBUG (maximize logging output)"),
     quiet = ({'Application' : {'log_level' : logging.CRITICAL}},
             "set log level to logging.CRITICAL (minimize logging output)"),
     init = ({'BaseIPythonApplication' : {
                     'copy_config_files' : True,
                     'auto_create' : True}
             }, """Initialize profile with default config files.  This is equivalent
             to running `ipython profile create <profile>` prior to startup.
             """)
 )
 
 class ProfileAwareConfigLoader(PyFileConfigLoader):
     """A Python file config loader that is aware of IPython profiles."""
     def load_subconfig(self, fname, path=None, profile=None):
         if profile is not None:
             try:
                 profile_dir = ProfileDir.find_profile_dir_by_name(
                         get_ipython_dir(),
                         profile,
                 )
             except ProfileDirError:
                 return
             path = profile_dir.location
         return super(ProfileAwareConfigLoader, self).load_subconfig(fname, path=path)
 
 class BaseIPythonApplication(Application):
 
     name = Unicode(u'ipython')
     description = Unicode(u'IPython: an enhanced interactive Python shell.')
     version = Unicode(release.version)
 
     aliases = Dict(base_aliases)
     flags = Dict(base_flags)
     classes = List([ProfileDir])
     
     # enable `load_subconfig('cfg.py', profile='name')`
     python_config_loader_class = ProfileAwareConfigLoader
 
     # Track whether the config_file has changed,
     # because some logic happens only if we aren't using the default.
     config_file_specified = Set()
 
     config_file_name = Unicode()
     @default('config_file_name')
     def _config_file_name_default(self):
         return self.name.replace('-','_') + u'_config.py'
     @observe('config_file_name')
     def _config_file_name_changed(self, change):
         if change['new'] != change['old']:
             self.config_file_specified.add(change['new'])
 
     # The directory that contains IPython's builtin profiles.
     builtin_profile_dir = Unicode(
         os.path.join(get_ipython_package_dir(), u'config', u'profile', u'default')
     )
     
     config_file_paths = List(Unicode())
     @default('config_file_paths')
     def _config_file_paths_default(self):
         return [py3compat.getcwd()]
 
     extra_config_file = Unicode(
     help="""Path to an extra config file to load.
     
     If specified, load this config file in addition to any other IPython config.
     """).tag(config=True)
     @observe('extra_config_file')
     def _extra_config_file_changed(self, change):
         old = change['old']
         new = change['new']
         try:
             self.config_files.remove(old)
         except ValueError:
             pass
         self.config_file_specified.add(new)
         self.config_files.append(new)
 
     profile = Unicode(u'default',
         help="""The IPython profile to use."""
     ).tag(config=True)
     
     @observe('profile')
     def _profile_changed(self, change):
         self.builtin_profile_dir = os.path.join(
                 get_ipython_package_dir(), u'config', u'profile', change['new']
         )
 
     ipython_dir = Unicode(
         help="""
         The name of the IPython directory. This directory is used for logging
         configuration (through profiles), history storage, etc. The default
         is usually $HOME/.ipython. This option can also be specified through
         the environment variable IPYTHONDIR.
         """
     ).tag(config=True)
     @default('ipython_dir')
     def _ipython_dir_default(self):
         d = get_ipython_dir()
         self._ipython_dir_changed({
             'name': 'ipython_dir',
             'old': d,
             'new': d,
         })
         return d
     
     _in_init_profile_dir = False
     profile_dir = Instance(ProfileDir, allow_none=True)
     @default('profile_dir')
     def _profile_dir_default(self):
         # avoid recursion
         if self._in_init_profile_dir:
             return
         # profile_dir requested early, force initialization
         self.init_profile_dir()
         return self.profile_dir
 
     overwrite = Bool(False,
         help="""Whether to overwrite existing config files when copying"""
     ).tag(config=True)
     auto_create = Bool(False,
         help="""Whether to create profile dir if it doesn't exist"""
     ).tag(config=True)
 
     config_files = List(Unicode())
     @default('config_files')
     def _config_files_default(self):
         return [self.config_file_name]
 
     copy_config_files = Bool(False,
         help="""Whether to install the default config files into the profile dir.
         If a new profile is being created, and IPython contains config files for that
         profile, then they will be staged into the new directory.  Otherwise,
         default config files will be automatically generated.
         """).tag(config=True)
     
     verbose_crash = Bool(False,
         help="""Create a massive crash report when IPython encounters what may be an
         internal error.  The default is to append a short message to the
         usual traceback""").tag(config=True)
 
     # The class to use as the crash handler.
     crash_handler_class = Type(crashhandler.CrashHandler)
 
     @catch_config_error
     def __init__(self, **kwargs):
         super(BaseIPythonApplication, self).__init__(**kwargs)
         # ensure current working directory exists
         try:
             py3compat.getcwd()
         except:
             # exit if cwd doesn't exist
             self.log.error("Current working directory doesn't exist.")
             self.exit(1)
 
     #-------------------------------------------------------------------------
     # Various stages of Application creation
     #-------------------------------------------------------------------------
     
     deprecated_subcommands = {}
     
     def initialize_subcommand(self, subc, argv=None):
         if subc in self.deprecated_subcommands:
             self.log.warning("Subcommand `ipython {sub}` is deprecated and will be removed "
                              "in future versions.".format(sub=subc))
             self.log.warning("You likely want to use `jupyter {sub}` in the "
                              "future".format(sub=subc))
         return super(BaseIPythonApplication, self).initialize_subcommand(subc, argv)
 
     def init_crash_handler(self):
         """Create a crash handler, typically setting sys.excepthook to it."""
         self.crash_handler = self.crash_handler_class(self)
         sys.excepthook = self.excepthook
         def unset_crashhandler():
             sys.excepthook = sys.__excepthook__
         atexit.register(unset_crashhandler)
     
     def excepthook(self, etype, evalue, tb):
         """this is sys.excepthook after init_crashhandler
         
         set self.verbose_crash=True to use our full crashhandler, instead of
         a regular traceback with a short message (crash_handler_lite)
         """
         
         if self.verbose_crash:
             return self.crash_handler(etype, evalue, tb)
         else:
             return crashhandler.crash_handler_lite(etype, evalue, tb)
 
     @observe('ipython_dir')
     def _ipython_dir_changed(self, change):
         old = change['old']
         new = change['new']
         if old is not Undefined:
             str_old = py3compat.cast_bytes_py2(os.path.abspath(old),
                 sys.getfilesystemencoding()
             )
             if str_old in sys.path:
                 sys.path.remove(str_old)
         str_path = py3compat.cast_bytes_py2(os.path.abspath(new),
             sys.getfilesystemencoding()
         )
         sys.path.append(str_path)
         ensure_dir_exists(new)
         readme = os.path.join(new, 'README')
         readme_src = os.path.join(get_ipython_package_dir(), u'config', u'profile', 'README')
         if not os.path.exists(readme) and os.path.exists(readme_src):
             shutil.copy(readme_src, readme)
         for d in ('extensions', 'nbextensions'):
             path = os.path.join(new, d)
             try:
                 ensure_dir_exists(path)
             except OSError as e:
                 # this will not be EEXIST
                 self.log.error("couldn't create path %s: %s", path, e)
         self.log.debug("IPYTHONDIR set to: %s" % new)
 
     def load_config_file(self, suppress_errors=IPYTHON_SUPPRESS_CONFIG_ERRORS):
         """Load the config file.
 
         By default, errors in loading config are handled, and a warning
         printed on screen. For testing, the suppress_errors option is set
         to False, so errors will make tests fail.
 
         `supress_errors` default value is to be `None` in which case the
         behavior default to the one of `traitlets.Application`.
 
         The default value can be set :
            - to `False` by setting 'IPYTHON_SUPPRESS_CONFIG_ERRORS' environment variable to '0', or 'false' (case insensitive).
            - to `True` by setting 'IPYTHON_SUPPRESS_CONFIG_ERRORS' environment variable to '1' or 'true' (case insensitive).
            - to `None` by setting 'IPYTHON_SUPPRESS_CONFIG_ERRORS' environment variable to '' (empty string) or leaving it unset.
 
         Any other value are invalid, and will make IPython exit with a non-zero return code.
         """
 
 
         self.log.debug("Searching path %s for config files", self.config_file_paths)
         base_config = 'ipython_config.py'
         self.log.debug("Attempting to load config file: %s" %
                        base_config)
         try:
             if suppress_errors is not None:
                 old_value = Application.raise_config_file_errors
                 Application.raise_config_file_errors = not suppress_errors;
             Application.load_config_file(
                 self,
                 base_config,
                 path=self.config_file_paths
             )
         except ConfigFileNotFound:
             # ignore errors loading parent
             self.log.debug("Config file %s not found", base_config)
             pass
         if suppress_errors is not None:
             Application.raise_config_file_errors = old_value
         
         for config_file_name in self.config_files:
             if not config_file_name or config_file_name == base_config:
                 continue
             self.log.debug("Attempting to load config file: %s" %
                            self.config_file_name)
             try:
                 Application.load_config_file(
                     self,
                     config_file_name,
                     path=self.config_file_paths
                 )
             except ConfigFileNotFound:
                 # Only warn if the default config file was NOT being used.
                 if config_file_name in self.config_file_specified:
                     msg = self.log.warning
                 else:
                     msg = self.log.debug
                 msg("Config file not found, skipping: %s", config_file_name)
             except Exception:
                 # For testing purposes.
                 if not suppress_errors:
                     raise
                 self.log.warning("Error loading config file: %s" %
                               self.config_file_name, exc_info=True)
 
     def init_profile_dir(self):
         """initialize the profile dir"""
         self._in_init_profile_dir = True
         if self.profile_dir is not None:
             # already ran
             return
         if 'ProfileDir.location' not in self.config:
             # location not specified, find by profile name
             try:
                 p = ProfileDir.find_profile_dir_by_name(self.ipython_dir, self.profile, self.config)
             except ProfileDirError:
                 # not found, maybe create it (always create default profile)
                 if self.auto_create or self.profile == 'default':
                     try:
                         p = ProfileDir.create_profile_dir_by_name(self.ipython_dir, self.profile, self.config)
                     except ProfileDirError:
                         self.log.fatal("Could not create profile: %r"%self.profile)
                         self.exit(1)
                     else:
                         self.log.info("Created profile dir: %r"%p.location)
                 else:
                     self.log.fatal("Profile %r not found."%self.profile)
                     self.exit(1)
             else:
                 self.log.debug("Using existing profile dir: %r"%p.location)
         else:
             location = self.config.ProfileDir.location
             # location is fully specified
             try:
                 p = ProfileDir.find_profile_dir(location, self.config)
             except ProfileDirError:
                 # not found, maybe create it
                 if self.auto_create:
                     try:
                         p = ProfileDir.create_profile_dir(location, self.config)
                     except ProfileDirError:
                         self.log.fatal("Could not create profile directory: %r"%location)
                         self.exit(1)
                     else:
                         self.log.debug("Creating new profile dir: %r"%location)
                 else:
                     self.log.fatal("Profile directory %r not found."%location)
                     self.exit(1)
             else:
                 self.log.info("Using existing profile dir: %r"%location)
             # if profile_dir is specified explicitly, set profile name
             dir_name = os.path.basename(p.location)
             if dir_name.startswith('profile_'):
                 self.profile = dir_name[8:]
 
         self.profile_dir = p
         self.config_file_paths.append(p.location)
         self._in_init_profile_dir = False
 
     def init_config_files(self):
         """[optionally] copy default config files into profile dir."""
+        self.config_file_paths.extend(ENV_CONFIG_DIRS)
         self.config_file_paths.extend(SYSTEM_CONFIG_DIRS)
         # copy config files
         path = self.builtin_profile_dir
         if self.copy_config_files:
             src = self.profile
 
             cfg = self.config_file_name
             if path and os.path.exists(os.path.join(path, cfg)):
                 self.log.warning("Staging %r from %s into %r [overwrite=%s]"%(
                         cfg, src, self.profile_dir.location, self.overwrite)
                 )
                 self.profile_dir.copy_config_file(cfg, path=path, overwrite=self.overwrite)
             else:
                 self.stage_default_config_file()
         else:
             # Still stage *bundled* config files, but not generated ones
             # This is necessary for `ipython profile=sympy` to load the profile
             # on the first go
             files = glob.glob(os.path.join(path, '*.py'))
             for fullpath in files:
                 cfg = os.path.basename(fullpath)
                 if self.profile_dir.copy_config_file(cfg, path=path, overwrite=False):
                     # file was copied
                     self.log.warning("Staging bundled %s from %s into %r"%(
                             cfg, self.profile, self.profile_dir.location)
                     )
 
 
     def stage_default_config_file(self):
         """auto generate default config file, and stage it into the profile."""
         s = self.generate_config_file()
         fname = os.path.join(self.profile_dir.location, self.config_file_name)
         if self.overwrite or not os.path.exists(fname):
             self.log.warning("Generating default config file: %r"%(fname))
             with open(fname, 'w') as f:
                 f.write(s)
 
     @catch_config_error
     def initialize(self, argv=None):
         # don't hook up crash handler before parsing command-line
         self.parse_command_line(argv)
         self.init_crash_handler()
         if self.subapp is not None:
             # stop here if subapp is taking over
             return
         # save a copy of CLI config to re-load after config files
         # so that it has highest priority
         cl_config = deepcopy(self.config)
         self.init_profile_dir()
         self.init_config_files()
         self.load_config_file()
         # enforce cl-opts override configfile opts:
         self.update_config(cl_config)

IPython/core/shellapp.py

@@ -1,411 +1,415 b''
 # encoding: utf-8
 """
 A mixin for :class:`~IPython.core.application.Application` classes that
 launch InteractiveShell instances, load extensions, etc.
 """
 
 # Copyright (c) IPython Development Team.
 # Distributed under the terms of the Modified BSD License.
 
 from __future__ import absolute_import
 from __future__ import print_function
 
 import glob
+from itertools import chain
 import os
 import sys
 
 from traitlets.config.application import boolean_flag
 from traitlets.config.configurable import Configurable
 from traitlets.config.loader import Config
+from IPython.core.application import SYSTEM_CONFIG_DIRS, ENV_CONFIG_DIRS
 from IPython.core import pylabtools
 from IPython.utils import py3compat
 from IPython.utils.contexts import preserve_keys
 from IPython.utils.path import filefind
 from traitlets import (
     Unicode, Instance, List, Bool, CaselessStrEnum, observe,
 )
 from IPython.terminal import pt_inputhooks
 
 #-----------------------------------------------------------------------------
 # Aliases and Flags
 #-----------------------------------------------------------------------------
 
 gui_keys = tuple(sorted(pt_inputhooks.backends) + sorted(pt_inputhooks.aliases))
 
 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."
 )
 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 functions,
     and optionally can use colors for this, syntax highlighting
     source code and various other elements. This is on by default, but can cause
     problems with some pagers. If you see such problems, you can disable the
     colours.""",
     "Disable using colors for info related things."
 )
 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(),
         help="A list of dotted module names of IPython extensions to load."
     ).tag(config=True)
     extra_extension = Unicode('',
         help="dotted module name of an IPython extension to load."
     ).tag(config=True)
 
     reraise_ipython_extension_failures = Bool(False,
         help="Reraise exceptions encountered loading IPython extensions?",
     ).tag(config=True)
 
     # Extensions that are always loaded (not configurable)
     default_extensions = List(Unicode(), [u'storemagic']).tag(config=False)
 
     hide_initial_ns = Bool(True,
         help="""Should variables loaded at startup (by startup files, exec_lines, etc.)
         be hidden from tools like %who?"""
     ).tag(config=True)
 
     exec_files = List(Unicode(),
         help="""List of files to run at IPython startup."""
     ).tag(config=True)
     exec_PYTHONSTARTUP = Bool(True,
         help="""Run the file referenced by the PYTHONSTARTUP environment
         variable at IPython startup."""
     ).tag(config=True)
     file_to_run = Unicode('',
         help="""A file to be run""").tag(config=True)
 
     exec_lines = List(Unicode(),
         help="""lines of code to run at IPython startup."""
     ).tag(config=True)
     code_to_run = Unicode('',
         help="Execute the given command string."
     ).tag(config=True)
     module_to_run = Unicode('',
         help="Run the module as a script."
     ).tag(config=True)
     gui = CaselessStrEnum(gui_keys, allow_none=True,
         help="Enable GUI event loop integration with any of {0}.".format(gui_keys)
     ).tag(config=True)
     matplotlib = CaselessStrEnum(backend_keys, allow_none=True,
         help="""Configure matplotlib for interactive use with
         the default matplotlib backend."""
     ).tag(config=True)
     pylab = CaselessStrEnum(backend_keys, allow_none=True,
         help="""Pre-load matplotlib and numpy for interactive use,
         selecting a particular matplotlib backend and loop integration.
         """
     ).tag(config=True)
     pylab_import_all = Bool(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.
         """
     ).tag(config=True)
     shell = Instance('IPython.core.interactiveshell.InteractiveShellABC',
                      allow_none=True)
     # whether interact-loop should start
     interact = Bool(True)
 
     user_ns = Instance(dict, args=None, allow_none=True)
     @observe('user_ns')
     def _user_ns_changed(self, change):
         if self.shell is not None:
             self.shell.user_ns = change['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.warning("Eventloop or matplotlib integration failed. Is matplotlib installed?")
             self.shell.showtraceback()
             return
         except Exception:
             self.log.warning("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
             if self.extra_extension:
                 extensions.append(self.extra_extension)
             for ext in extensions:
                 try:
                     self.log.info("Loading IPython extension: %s" % ext)
                     self.shell.extension_manager.load_extension(ext)
                 except:
                     if self.reraise_ipython_extension_failures:
                         raise
                     msg = ("Error in loading extension: {ext}\n"
                            "Check your config files in {location}".format(
                                ext=ext,
                                location=self.profile_dir.location
                            ))
                     self.log.warning(msg, exc_info=True)
         except:
             if self.reraise_ipython_extension_failures:
                 raise
             self.log.warning("Unknown error in loading extensions:", exc_info=True)
 
     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()
 
         # Hide variables defined here from %who etc.
         if self.hide_initial_ns:
             self.shell.user_ns_hidden.update(self.shell.user_ns)
 
         # command-line execution (ipython -i script.py, ipython -m module)
         # should *not* be excluded from %whos
         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()
 
     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.warning("Error in executing line in user "
                                   "namespace: %s" % line)
                     self.shell.showtraceback()
         except:
             self.log.warning("Unknown error in handling IPythonApp.exec_lines:")
             self.shell.showtraceback()
 
     def _exec_file(self, fname, shell_futures=False):
         try:
             full_filename = filefind(fname, [u'.', self.ipython_dir])
         except IOError:
             self.log.warning("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,
                                                      shell_futures=shell_futures)
                     else:
                         # default to python, even without extension
                         self.shell.safe_execfile(full_filename,
                                                  self.shell.user_ns,
                                                  shell_futures=shell_futures,
                                                  raise_exceptions=True)
         finally:
             sys.argv = save_argv
 
     def _run_startup_files(self):
         """Run files from profile startup directory"""
-        startup_dir = self.profile_dir.startup_dir
+        startup_dirs = [self.profile_dir.startup_dir] + [
+            os.path.join(p, 'startup') for p in chain(ENV_CONFIG_DIRS, SYSTEM_CONFIG_DIRS)
+        ]
         startup_files = []
 
         if self.exec_PYTHONSTARTUP and os.environ.get('PYTHONSTARTUP', False) and \
                 not (self.file_to_run or self.code_to_run or self.module_to_run):
             python_startup = os.environ['PYTHONSTARTUP']
             self.log.debug("Running PYTHONSTARTUP file %s...", python_startup)
             try:
                 self._exec_file(python_startup)
             except:
                 self.log.warning("Unknown error in handling PYTHONSTARTUP file %s:", python_startup)
                 self.shell.showtraceback()
-
-        startup_files += glob.glob(os.path.join(startup_dir, '*.py'))
-        startup_files += glob.glob(os.path.join(startup_dir, '*.ipy'))
+        for startup_dir in startup_dirs[::-1]:
+            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.warning("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.warning("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.warning("Error in executing line in user namespace: %s" %
                               line)
                 self.shell.showtraceback()
                 if not self.interact:
                     self.exit(1)
 
         # Like Python itself, ignore the second if the first of these is present
         elif self.file_to_run:
             fname = self.file_to_run
             if os.path.isdir(fname):
                 fname = os.path.join(fname, "__main__.py")
             try:
                 self._exec_file(fname, shell_futures=True)
             except:
                 self.shell.showtraceback(tb_offset=4)
                 if not self.interact:
                     self.exit(1)
 
     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