Don't rely upon traitlets copying self.config

when saving CLI config to reload later for highest priority.

traitlets 4.1-4.2.1 don't copy self.config in update_config (rightly so),
so when saving CLI config for later re-loading, make sure it's a copy so it doesn't get changed by further loading.

IPython/core/application.py

@@ -1,455 +1,458 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",
     ]
 
 _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(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
-        cl_config = self.config
+        # 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/tests/test_application.py

@@ -1,50 +1,74 b''
 # coding: utf-8
 """Tests for IPython.core.application"""
 
 import os
 import tempfile
 
+import nose.tools as nt
+
+from traitlets import Unicode
+
 from IPython.core.application import BaseIPythonApplication
 from IPython.testing import decorators as dec
 from IPython.utils import py3compat
+from IPython.utils.tempdir import TemporaryDirectory
+
 
 @dec.onlyif_unicode_paths
 def test_unicode_cwd():
     """Check that IPython starts with non-ascii characters in the path."""
     wd = tempfile.mkdtemp(suffix=u"€")
     
     old_wd = py3compat.getcwd()
     os.chdir(wd)
     #raise Exception(repr(py3compat.getcwd()))
     try:
         app = BaseIPythonApplication()
         # The lines below are copied from Application.initialize()
         app.init_profile_dir()
         app.init_config_files()
         app.load_config_file(suppress_errors=False)
     finally:
         os.chdir(old_wd)
 
 @dec.onlyif_unicode_paths
 def test_unicode_ipdir():
     """Check that IPython starts with non-ascii characters in the IP dir."""
     ipdir = tempfile.mkdtemp(suffix=u"€")
     
     # Create the config file, so it tries to load it.
     with open(os.path.join(ipdir, 'ipython_config.py'), "w") as f:
         pass
     
     old_ipdir1 = os.environ.pop("IPYTHONDIR", None)
     old_ipdir2 = os.environ.pop("IPYTHON_DIR", None)
     os.environ["IPYTHONDIR"] = py3compat.unicode_to_str(ipdir, "utf-8")
     try:
         app = BaseIPythonApplication()
         # The lines below are copied from Application.initialize()
         app.init_profile_dir()
         app.init_config_files()
         app.load_config_file(suppress_errors=False)
     finally:
         if old_ipdir1:
             os.environ["IPYTHONDIR"] = old_ipdir1
         if old_ipdir2:
             os.environ["IPYTHONDIR"] = old_ipdir2
+
+def test_cli_priority():
+    with TemporaryDirectory() as td:
+
+        class TestApp(BaseIPythonApplication):
+            test = Unicode().tag(config=True)
+
+        # Create the config file, so it tries to load it.
+        with open(os.path.join(td, 'ipython_config.py'), "w") as f:
+            f.write("c.TestApp.test = 'config file'")
+
+        app = TestApp()
+        app.initialize(['--profile-dir', td])
+        nt.assert_equal(app.test, 'config file')
+        app = TestApp()
+        app.initialize(['--profile-dir', td, '--TestApp.test=cli'])
+        nt.assert_equal(app.test, 'cli')
+