Tidy up a few more warnings from Sphinx

docs/source/development/gitwash/development_workflow.rst

@@ -1,233 +1,232 b''
 .. _development-workflow:
 
 ====================
 Development workflow
 ====================
 
 You already have your own forked copy of the ipython_ repository, by
 following :ref:`forking`, :ref:`set-up-fork`, and you have configured
 git_ by following :ref:`configure-git`.
 
 Workflow summary
 ================
 
 * Keep your ``master`` branch clean of edits that have not been merged
   to the main ipython_ development repo.  Your ``master`` then will follow
   the main ipython_ repository.
 * Start a new *feature branch* for each set of edits that you do.
 * If you can avoid it, try not to merge other branches into your feature
   branch while you are working.
 * Ask for review!
 
 This way of working really helps to keep work well organized, and in
 keeping history as clear as possible.
 
 See - for example - `linux git workflow`_. 
 
 Making a new feature branch
 ===========================
 
 ::
 
    git branch my-new-feature
    git checkout my-new-feature
 
 Generally, you will want to keep this also on your public github_ fork
 of ipython_.  To do this, you `git push`_ this new branch up to your github_
 repo.  Generally (if you followed the instructions in these pages, and
 by default), git will have a link to your github_ repo, called
 ``origin``.  You push up to your own repo on github_ with::
 
    git push origin my-new-feature
 
 From now on git_ will know that ``my-new-feature`` is related to the
 ``my-new-feature`` branch in the github_ repo.
 
 The editing workflow
 ====================
 
 Overview
 --------
 
 ::
 
    # hack hack
    git add my_new_file
    git commit -am 'NF - some message'
    git push
 
 In more detail
 --------------
 
 #. Make some changes
 #. See which files have changed with ``git status`` (see `git status`_).
    You'll see a listing like this one::
 
      # On branch ny-new-feature
      # Changed but not updated:
      #   (use "git add <file>..." to update what will be committed)
      #   (use "git checkout -- <file>..." to discard changes in working directory)
      #
      #	modified:   README
      #
      # Untracked files:
      #   (use "git add <file>..." to include in what will be committed)
      #
      #	INSTALL
      no changes added to commit (use "git add" and/or "git commit -a")
 
 #. Check what the actual changes are with ``git diff`` (`git diff`_).
 #. Add any new files to version control ``git add new_file_name`` (see
    `git add`_). 
 #. To commit all modified files into the local copy of your repo,, do
    ``git commit -am 'A commit message'``.  Note the ``-am`` options to
    ``commit``. The ``m`` flag just signals that you're going to type a
    message on the command line.  The ``a`` flag - you can just take on
    faith - or see `why the -a flag?`_. See also the `git commit`_ manual
    page.
 #. To push the changes up to your forked repo on github_, do a ``git
    push`` (see `git push`). 
 
 Asking for code review
 ======================
 
 #. Go to your repo URL - e.g. ``http://github.com/your-user-name/ipython``.
 #. Click on the *Branch list* button:
 
    .. image:: branch_list.png
 
 #. Click on the *Compare* button for your feature branch - here ``my-new-feature``:
 
    .. image:: branch_list_compare.png
 
 #. If asked, select the *base* and *comparison* branch names you want to
    compare.  Usually these will be ``master`` and ``my-new-feature``
    (where that is your feature branch name).
 #. At this point you should get a nice summary of the changes.  Copy the
    URL for this, and post it to the `ipython mailing list`_, asking for
    review.  The URL will look something like:
    ``http://github.com/your-user-name/ipython/compare/master...my-new-feature``.
    There's an example at
    http://github.com/matthew-brett/nipy/compare/master...find-install-data
    See: http://github.com/blog/612-introducing-github-compare-view for
    more detail.
 
 The generated comparison, is between your feature branch
 ``my-new-feature``, and the place in ``master`` from which you branched
 ``my-new-feature``.  In other words, you can keep updating ``master``
 without interfering with the output from the comparison.  More detail?
-Note the three dots in the URL above (``master...my-new-feature``) and
-see :ref:`dot2-dot3`.
+Note the three dots in the URL above (``master...my-new-feature``).
 
 Asking for your changes to be merged with the main repo
 =======================================================
 
 When you are ready to ask for the merge of your code:
 
 #. Go to the URL of your forked repo, say
    ``http://github.com/your-user-name/ipython.git``.
 #. Click on the 'Pull request' button:
 
    .. image:: pull_button.png
 
    Enter a message; we suggest you select only ``ipython`` as the
    recipient.  The message will go to the `ipython mailing list`_.  Please
    feel free to add others from the list as you like.
 
 Merging from trunk
 ==================
 
 This updates your code from the upstream `ipython github`_  repo. 
 
 Overview
 --------
 
 ::
 
    # go to your master branch
    git checkout master
    # pull changes from github
    git fetch upstream
    # merge from upstream
    git merge upstream/master
 
 In detail
 ---------
 
 We suggest that you do this only for your ``master`` branch, and leave
 your 'feature' branches unmerged, to keep their history as clean as
 possible.  This makes code review easier::
 
    git checkout master
 
 Make sure you have done :ref:`linking-to-upstream`.
 
 Merge the upstream code into your current development by first pulling
 the upstream repo to a copy on your local machine::
 
    git fetch upstream
 
 then merging into your current branch::
 
    git merge upstream/master
 
 Deleting a branch on github_
 ============================
 
 ::
 
    git checkout master
    # delete branch locally
    git branch -D my-unwanted-branch
    # delete branch on github
    git push origin :my-unwanted-branch
 
 (Note the colon ``:`` before ``test-branch``.  See also:
 http://github.com/guides/remove-a-remote-branch
 
 Several people sharing a single repository
 ==========================================
 
 If you want to work on some stuff with other people, where you are all
 committing into the same repository, or even the same branch, then just
 share it via github_.
 
 First fork ipython into your account, as from :ref:`forking`.
 
 Then, go to your forked repository github page, say
 ``http://github.com/your-user-name/ipython``
 
 Click on the 'Admin' button, and add anyone else to the repo as a
 collaborator:
 
    .. image:: pull_button.png
 
 Now all those people can do::
 
     git clone [e-mail]:your-user-name/ipython.git
 
 Remember that links starting with ``git@`` use the ssh protocol and are
 read-write; links starting with ``git://`` are read-only.
 
 Your collaborators can then commit directly into that repo with the
 usual::
 
      git commit -am 'ENH - much better code'
      git push origin master # pushes directly into your repo
 
 Exploring your repository
 =========================
 
 To see a graphical representation of the repository branches and
 commits::
 
    gitk --all
 
 To see a linear list of commits for this branch::
 
    git log
 
 You can also look at the `network graph visualizer`_ for your github_
 repo.
 
 .. include:: git_links.txt

docs/source/development/index.rst

@@ -1,28 +1,29 b''
 .. _developer_guide:
 
 =========================
 IPython developer's guide
 =========================
 
 This are two categories of developer focused documentation:
 
 1. Documentation for developers of *IPython itself*.
 2. Documentation for developers of third party tools and libraries
    that use IPython.
 
 This part of our documentation only contains information in the second category.
 
 Developers interested in working on IPython itself should consult
 our `developer information <https://github.com/ipython/ipython/wiki/Dev:-Index>`_ 
 on the IPython GitHub wiki.
 
 .. toctree::
    :maxdepth: 1
 
  
    gitwash/index
    messaging
    parallel_messages
    parallel_connections
    pycompat
    config
+   inputhook_app

docs/source/whatsnew/version0.11.rst

@@ -1,765 +1,765 b''
 =============
  0.11 Series
 =============
 
 Release 0.11
 ============
 
 IPython 0.11 is a *major* overhaul of IPython, two years in the making.  Most
 of the code base has been rewritten or at least reorganized, breaking backward
 compatibility with several APIs in previous versions.  It is the first major
 release in two years, and probably the most significant change to IPython since
 its inception.  We plan to have a relatively quick succession of releases, as
 people discover new bugs and regressions.  Once we iron out any significant
 bugs in this process and settle down the new APIs, this series will become
 IPython 1.0.  We encourage feedback now on the core APIs, which we hope to
 maintain stable during the 1.0 series.
 
 Since the internal APIs have changed so much, projects using IPython as a
 library (as opposed to end-users of the application) are the most likely to
 encounter regressions or changes that break their existing use patterns.  We
 will make every effort to provide updated versions of the APIs to facilitate
 the transition, and we encourage you to contact us on the `development mailing
 list`__ with questions and feedback.
 
 .. __: http://mail.scipy.org/mailman/listinfo/ipython-dev
 
 Chris Fonnesbeck recently wrote an `excellent post`__ that highlights some of
 our major new features, with examples and screenshots.  We encourage you to
 read it as it provides an illustrated, high-level overview complementing the
 detailed feature breakdown in this document.
 
 .. __: http://fonnesbeck.calepin.co/innovations-in-ipython.html
 
 A quick summary of the major changes (see below for details):
 
 * **Standalone Qt console**: a new rich console has been added to IPython,
   started with `ipython qtconsole`.  In this application we have tried to
   retain the feel of a terminal for fast and efficient workflows, while adding
   many features that a line-oriented terminal simply can not support, such as
   inline figures, full multiline editing with syntax highlighting, graphical
   tooltips for function calls and much more.  This development was sponsored by
   `Enthought Inc.`__. See :ref:`below <qtconsole_011>` for details.
 
 .. __: http://enthought.com
 
 * **High-level parallel computing with ZeroMQ**. Using the same architecture
   that our Qt console is based on, we have completely rewritten our high-level
   parallel computing machinery that in prior versions used the Twisted
   networking framework.  While this change will require users to update their
   codes, the improvements in performance, memory control and internal
   consistency across our codebase convinced us it was a price worth paying.  We
   have tried to explain how to best proceed with this update, and will be happy
   to answer questions that may arise.  A full tutorial describing these
   features `was presented at SciPy'11`__, more details :ref:`below
   <parallel_011>`.
 
 .. __: http://minrk.github.com/scipy-tutorial-2011
 
 * **New model for GUI/plotting support in the terminal**.  Now instead of the
   various `-Xthread` flags we had before, GUI support is provided without the
   use of any threads, by directly integrating GUI event loops with Python's
   `PyOS_InputHook` API.  A new command-line flag `--gui` controls GUI support,
   and it can also be enabled after IPython startup via the new `%gui` magic.
   This requires some changes if you want to execute GUI-using scripts inside
   IPython, see :ref:`the GUI support section <gui_support>` for more details.
 
 * **A two-process architecture.** The Qt console is the first use of a new
   model that splits IPython between a kernel process where code is executed and
   a client that handles user interaction.  We plan on also providing terminal
   and web-browser based clients using this infrastructure in future releases.
   This model allows multiple clients to interact with an IPython process
   through a :ref:`well-documented messaging protocol <messaging>` using the
   ZeroMQ networking library.
 
 * **Refactoring.** the entire codebase has been refactored, in order to make it
   more modular and easier to contribute to.  IPython has traditionally been a
   hard project to participate because the old codebase was very monolithic.  We
   hope this (ongoing) restructuring will make it easier for new developers to
   join us.
 
 * **Vim integration**. Vim can be configured to seamlessly control an IPython
   kernel, see the files in :file:`docs/examples/vim` for the full details.
   This work was done by Paul Ivanov, who prepared a nice `video
   demonstration`__ of the features it provides.
 
 .. __: http://pirsquared.org/blog/2011/07/28/vim-ipython/
   
 * **Integration into Microsoft Visual Studio**. Thanks to the work of the
   Microsoft `Python Tools for Visual Studio`__ team, this version of IPython
   has been integrated into Microsoft Visual Studio's Python tools open source
   plug-in.  `Details below`_
 
 .. __: http://pytools.codeplex.com
 .. _details below: ms_visual_studio_011_
 
 * **Improved unicode support**. We closed many bugs related to unicode input.
 
 * **Python 3**. IPython now runs on Python 3.x. See :ref:`python3_011` for
   details.
 
 * **New profile model**. Profiles are now directories that contain all relevant
   information for that session, and thus better isolate IPython use-cases.
 
 * **SQLite storage for history**. All history is now stored in a SQLite
   database, providing support for multiple simultaneous sessions that won't
   clobber each other as well as the ability to perform queries on all stored
   data.
 
 * **New configuration system**. All parts of IPython are now configured via a
   mechanism inspired by the Enthought Traits library.  Any configurable element
   can have its attributes set either via files that now use real Python syntax
   or from the command-line.
 
 * **Pasting of code with prompts**. IPython now intelligently strips out input
   prompts , be they plain Python ones (``>>>`` and ``...``) or IPython ones
   (``In [N]:`` and ``...:``).  More details :ref:`here <pasting_with_prompts>`.
   
 
 Authors and support
 -------------------
 
 Over 60 separate authors have contributed to this release, see :ref:`below
 <credits_011>` for a full list.  In particular, we want to highlight the
 extremely active participation of two new core team members: Evan Patterson
 implemented the Qt console, and Thomas Kluyver started with our Python 3 port
 and by now has made major contributions to just about every area of IPython.
 
 We are also grateful for the support we have received during this development
 cycle from several institutions:
 
 - `Enthought Inc`__ funded the development of our new Qt console, an effort that
   required developing major pieces of underlying infrastructure, which now
   power not only the Qt console but also our new parallel machinery.  We'd like
   to thank Eric Jones and Travis Oliphant for their support, as well as Ilan
   Schnell for his tireless work integrating and testing IPython in the
   `Enthought Python Distribution`_.
 
 .. __: http://enthought.com
 .. _Enthought Python Distribution: http://www.enthought.com/products/epd.php
 
 - Nipy/NIH: funding via the `NiPy project`__ (NIH grant 5R01MH081909-02) helped
   us jumpstart the development of this series by restructuring the entire
   codebase two years ago in a way that would make modular development and
   testing more approachable.  Without this initial groundwork, all the new
   features we have added would have been impossible to develop.
 
 .. __: http://nipy.org
 
 - Sage/NSF: funding via the grant `Sage: Unifying Mathematical Software for
   Scientists, Engineers, and Mathematicians`__ (NSF grant DMS-1015114)
   supported a meeting in spring 2011 of several of the core IPython developers
   where major progress was made integrating the last key pieces leading to this
   release.
 
 .. __: http://modular.math.washington.edu/grants/compmath09
 
 - Microsoft's team working on `Python Tools for Visual Studio`__ developed the 
   integraton of IPython into the Python plugin for Visual Studio 2010.
 
 .. __: http://pytools.codeplex.com
 
 - Google Summer of Code: in 2010, we had two students developing prototypes of
   the new machinery that is now maturing in this release: `Omar Zapata`_ and
   `Gerardo Gutiérrez`_.
 
 .. _Omar Zapata: http://ipythonzmq.blogspot.com/2010/08/ipython-zmq-status.html
 .. _Gerardo Gutiérrez: http://ipythonqt.blogspot.com/2010/04/ipython-qt-interface-gsoc-2010-proposal.html>
 
 
 Development summary: moving to Git and Github
 ---------------------------------------------
 
 In April 2010, after `one breakage too many with bzr`__, we decided to move our
 entire development process to Git and Github.com.  This has proven to be one of
 the best decisions in the project's history, as the combination of git and
 github have made us far, far more productive than we could be with our previous
 tools.  We first converted our bzr repo to a git one without losing history,
 and a few weeks later ported all open Launchpad bugs to github issues with
 their comments mostly intact (modulo some formatting changes).  This ensured a
 smooth transition where no development history or submitted bugs were lost.
 Feel free to use our little Launchpad to Github issues `porting script`_ if you
 need to make a similar transition.
 
 .. __: http://mail.scipy.org/pipermail/ipython-dev/2010-April/005944.html
 .. _porting script: https://gist.github.com/835577
 
 These simple statistics show how much work has been done on the new release, by
 comparing the current code to the last point it had in common with the 0.10
 series.  A huge diff and ~2200 commits make up this cycle::
 
     git diff $(git merge-base 0.10.2 HEAD)  | wc -l
     288019
 
     git log $(git merge-base 0.10.2 HEAD)..HEAD --oneline | wc -l
     2200
 
 Since our move to github, 511 issues were closed, 226 of which were pull
 requests and 285 regular issues (:ref:`a full list with links
 <issues_list_011>` is available for those interested in the details).  Github's
 pull requests are a fantastic mechanism for reviewing code and building a
 shared ownership of the project, and we are making enthusiastic use of it.
 
 .. Note::
 
    This undercounts the number of issues closed in this development cycle,
    since we only moved to github for issue tracking in May 2010, but we have no
    way of collecting statistics on the number of issues closed in the old
    Launchpad bug tracker prior to that.
 
    
 .. _qtconsole_011:
 
 Qt Console
 ----------
 
 IPython now ships with a Qt application that feels very much like a terminal,
 but is in fact a rich GUI that runs an IPython client but supports inline
 figures, saving sessions to PDF and HTML, multiline editing with syntax
 highlighting, graphical calltips and much more:
 
 .. figure:: ../_images/qtconsole.png
     :width: 400px
     :alt: IPython Qt console with embedded plots
     :align: center
     :target: ../_images/qtconsole.png
 
     The Qt console for IPython, using inline matplotlib plots.
 
 We hope that many projects will embed this widget, which we've kept
 deliberately very lightweight, into their own environments.  In the future we
 may also offer a slightly more featureful application (with menus and other GUI
 elements), but we remain committed to always shipping this easy to embed
 widget.
 
 See the :ref:`Qt console section <qtconsole>` of the docs for a detailed
 description of the console's features and use.
 
 
 .. _parallel_011:
 
 High-level parallel computing with ZeroMQ
 -----------------------------------------
 
 We have completely rewritten the Twisted-based code for high-level parallel
 computing to work atop our new ZeroMQ architecture.  While we realize this will
 break compatibility for a number of users, we hope to make the transition as
 easy as possible with our docs, and we are convinced the change is worth it.
 ZeroMQ provides us with much tighter control over memory, higher performance,
 and its communications are impervious to the Python Global Interpreter Lock
 because they take place in a system-level C++ thread.  The impact of the GIL in
 our previous code was something we could simply not work around, given that
 Twisted is itself a Python library.  So while Twisted is a very capable
 framework, we think ZeroMQ fits our needs much better and we hope you will find
 the change to be a significant improvement in the long run.
 
 Our manual contains :ref:`a full description of how to use IPython for parallel
 computing <parallel_overview>`, and the `tutorial`__ presented by Min
 Ragan-Kelley at the SciPy 2011 conference provides a hands-on complement to the
 reference docs.
 
 .. __: http://minrk.github.com/scipy-tutorial-2011
 
 
 Refactoring
 -----------
 
 As of this release, a signifiant portion of IPython has been refactored.  This
 refactoring is founded on a number of new abstractions.  The main new classes
 that implement these abstractions are:
 
 * :class:`IPython.utils.traitlets.HasTraits`.
 * :class:`IPython.config.configurable.Configurable`.
 * :class:`IPython.config.application.Application`.
 * :class:`IPython.config.loader.ConfigLoader`.
 * :class:`IPython.config.loader.Config`
 
 We are still in the process of writing developer focused documentation about
 these classes, but for now our :ref:`configuration documentation
 <config_overview>` contains a high level overview of the concepts that these
 classes express.
 
 The biggest user-visible change is likely the move to using the config system
 to determine the command-line arguments for IPython applications. The benefit
 of this is that *all* configurable values in IPython are exposed on the
 command-line, but the syntax for specifying values has changed. The gist is
 that assigning values is pure Python assignment.  Simple flags exist for
 commonly used options, these are always prefixed with '--'.
 
 The IPython command-line help has the details of all the options (via
 ``ipythyon --help``), but a simple example should clarify things; the ``pylab``
 flag can be used to start in pylab mode with the qt4 backend::
 
   ipython --pylab=qt
 
 which is equivalent to using the fully qualified form::
 
   ipython --TerminalIPythonApp.pylab=qt
 
 The long-form options can be listed via ``ipython --help-all``.
 
 
 ZeroMQ architecture
 -------------------
 
 There is a new GUI framework for IPython, based on a client-server model in
 which multiple clients can communicate with one IPython kernel, using the
 ZeroMQ messaging framework. There is already a Qt console client, which can
 be started by calling ``ipython qtconsole``. The protocol is :ref:`documented
 <messaging>`.
 
 The parallel computing framework has also been rewritten using ZMQ. The
 protocol is described :ref:`here <parallel_messages>`, and the code is in the
 new :mod:`IPython.parallel` module.
 
 .. _python3_011:
 
 Python 3 support
 ----------------
 
 A Python 3 version of IPython has been prepared. For the time being, this is
 maintained separately and updated from the main codebase. Its code can be found
 `here <https://github.com/ipython/ipython-py3k>`_. The parallel computing
 components are not perfect on Python3, but most functionality appears to be
 working.  As this work is evolving quickly, the best place to find updated
 information about it is our `Python 3 wiki page`__.
 
 .. __: http://wiki.ipython.org/index.php?title=Python_3
 
 
 Unicode
 -------
 
 Entering non-ascii characters in unicode literals (``u"€ø"``) now works
 properly on all platforms. However, entering these in byte/string literals
 (``"€ø"``) will not work as expected on Windows (or any platform where the
 terminal encoding is not UTF-8, as it typically is for Linux & Mac OS X). You
 can use escape sequences (``"\xe9\x82"``) to get bytes above 128, or use
 unicode literals and encode them. This is a limitation of Python 2 which we
 cannot easily work around.
 
 .. _ms_visual_studio_011:
 
 Integration with Microsoft Visual Studio
 ----------------------------------------
 
 IPython can be used as the interactive shell in the `Python plugin for
 Microsoft Visual Studio`__, as seen here:
 
 .. figure:: ../_images/ms_visual_studio.png
     :width: 500px
     :alt: IPython console embedded in Microsoft Visual Studio.
     :align: center
     :target: ../_images/ms_visual_studio.png
 
     IPython console embedded in Microsoft Visual Studio.
 
 The Microsoft team developing this currently has a release candidate out using
 IPython 0.11. We will continue to collaborate with them to ensure that as they
 approach their final release date, the integration with IPython remains smooth.
 We'd like to thank Dino Viehland and Shahrokh Mortazavi for the work they have
 done towards this feature, as well as Wenming Ye for his support of our WinHPC
 capabilities.
 
 .. __: http://pytools.codeplex.com
 
 
 Additional new features
 -----------------------
 
 * Added ``Bytes`` traitlet, removing ``Str``.  All 'string' traitlets should
   either be ``Unicode`` if a real string, or ``Bytes`` if a C-string. This
   removes ambiguity and helps the Python 3 transition.
 
 * New magic ``%loadpy`` loads a python file from disk or web URL into
   the current input buffer.
 
 * New magic ``%pastebin`` for sharing code via the 'Lodge it' pastebin.
 
 * New magic ``%precision`` for controlling float and numpy pretty printing.
 
 * IPython applications initiate logging, so any object can gain access to
   a the logger of the currently running Application with:
 
 .. sourcecode:: python
 
     from IPython.config.application import Application
     logger = Application.instance().log
 
 * You can now get help on an object halfway through typing a command. For
   instance, typing ``a = zip?`` shows the details of :func:`zip`. It also
   leaves the command at the next prompt so you can carry on with it.
 
 * The input history is now written to an SQLite database. The API for
   retrieving items from the history has also been redesigned.
 
 * The :mod:`IPython.extensions.pretty` extension has been moved out of
   quarantine and fully updated to the new extension API.
 
 * New magics for loading/unloading/reloading extensions have been added:
   ``%load_ext``, ``%unload_ext`` and ``%reload_ext``.
 
 * The configuration system and configuration files are brand new. See the
   configuration system :ref:`documentation <config_index>` for more details.
 
 * The :class:`~IPython.core.interactiveshell.InteractiveShell` class is now a
   :class:`~IPython.config.configurable.Configurable` subclass and has traitlets
   that determine the defaults and runtime environment. The ``__init__`` method
   has also been refactored so this class can be instantiated and run without
   the old :mod:`ipmaker` module.
 
 * The methods of :class:`~IPython.core.interactiveshell.InteractiveShell` have
   been organized into sections to make it easier to turn more sections
   of functionality into components.
 
 * The embedded shell has been refactored into a truly standalone subclass of
   :class:`InteractiveShell` called :class:`InteractiveShellEmbed`.  All
   embedding logic has been taken out of the base class and put into the 
   embedded subclass.
 
 * Added methods of :class:`~IPython.core.interactiveshell.InteractiveShell` to
   help it cleanup after itself. The :meth:`cleanup` method controls this. We
   couldn't do this in :meth:`__del__` because we have cycles in our object
   graph that prevent it from being called.
 
 * Created a new module :mod:`IPython.utils.importstring` for resolving
   strings like ``foo.bar.Bar`` to the actual class.
 
 * Completely refactored the :mod:`IPython.core.prefilter` module into
   :class:`~IPython.config.configurable.Configurable` subclasses. Added a new
   layer into the prefilter system, called "transformations" that all new
   prefilter logic should use (rather than the older "checker/handler"
   approach).
 
 * Aliases are now components (:mod:`IPython.core.alias`).
 
 * New top level :func:`~IPython.frontend.terminal.embed.embed` function that can
   be called to embed IPython at any place in user's code. On the first call it
   will create an :class:`~IPython.frontend.terminal.embed.InteractiveShellEmbed`
   instance and call it. In later calls, it just calls the previously created
   :class:`~IPython.frontend.terminal.embed.InteractiveShellEmbed`.
 
 * Created a configuration system (:mod:`IPython.config.configurable`) that is
   based on :mod:`IPython.utils.traitlets`. Configurables are arranged into a
   runtime containment tree (not inheritance) that i) automatically propagates
   configuration information and ii) allows singletons to discover each other in
   a loosely coupled manner. In the future all parts of IPython will be
   subclasses of :class:`~IPython.config.configurable.Configurable`. All IPython
   developers should become familiar with the config system.
 
 * Created a new :class:`~IPython.config.loader.Config` for holding
   configuration information. This is a dict like class with a few extras: i)
   it supports attribute style access, ii) it has a merge function that merges
   two :class:`~IPython.config.loader.Config` instances recursively and iii) it
   will automatically create sub-:class:`~IPython.config.loader.Config`
   instances for attributes that start with an uppercase character.
 
 * Created new configuration loaders in :mod:`IPython.config.loader`. These
   loaders provide a unified loading interface for all configuration
   information including command line arguments and configuration files. We
   have two default implementations based on :mod:`argparse` and plain python
   files.  These are used to implement the new configuration system.
 
 * Created a top-level :class:`Application` class in
   :mod:`IPython.core.application` that is designed to encapsulate the starting
   of any basic Python program. An application loads and merges all the
   configuration objects, constructs the main application, configures and
   initiates logging, and creates and configures any :class:`Configurable`
   instances and then starts the application running. An extended
   :class:`BaseIPythonApplication` class adds logic for handling the
   IPython directory as well as profiles, and all IPython entry points
   extend it.
 
 * The :class:`Type` and :class:`Instance` traitlets now handle classes given
   as strings, like ``foo.bar.Bar``. This is needed for forward declarations.
   But, this was implemented in a careful way so that string to class
   resolution is done at a single point, when the parent
   :class:`~IPython.utils.traitlets.HasTraitlets` is instantiated.
 
 * :mod:`IPython.utils.ipstruct` has been refactored to be a subclass of 
   dict.  It also now has full docstrings and doctests.
 
 * Created a Traits like implementation in :mod:`IPython.utils.traitlets`.  This
   is a pure Python, lightweight version of a library that is similar to
   Enthought's Traits project, but has no dependencies on Enthought's code.  We
   are using this for validation, defaults and notification in our new component
   system.  Although it is not 100% API compatible with Enthought's Traits, we
   plan on moving in this direction so that eventually our implementation could
   be replaced by a (yet to exist) pure Python version of Enthought Traits.
 
 * Added a new module :mod:`IPython.lib.inputhook` to manage the integration
   with GUI event loops using `PyOS_InputHook`.  See the docstrings in this
   module or the main IPython docs for details.
 
 * For users, GUI event loop integration is now handled through the new
   :command:`%gui` magic command.  Type ``%gui?`` at an IPython prompt for
   documentation.
 
 * For developers :mod:`IPython.lib.inputhook` provides a simple interface
   for managing the event loops in their interactive GUI applications.
   Examples can be found in our :file:`examples/lib` directory.
 
 Backwards incompatible changes
 ------------------------------
 
 * The Twisted-based :mod:`IPython.kernel` has been removed, and completely
   rewritten as :mod:`IPython.parallel`, using ZeroMQ.
 
 * Profiles are now directories. Instead of a profile being a single config file,
   profiles are now self-contained directories. By default, profiles get their
   own IPython history, log files, and everything. To create a new profile, do
   ``ipython profile create <name>``.
 
 * All IPython applications have been rewritten to use
   :class:`~IPython.config.loader.KeyValueConfigLoader`. This means that
   command-line options have changed. Now, all configurable values are accessible
   from the command-line with the same syntax as in a configuration file.
 
 * The command line options ``-wthread``, ``-qthread`` and
   ``-gthread`` have been removed. Use ``--gui=wx``, ``--gui=qt``, ``--gui=gtk``
   instead.
 
 * The extension loading functions have been renamed to
   :func:`load_ipython_extension` and :func:`unload_ipython_extension`.
 
 * :class:`~IPython.core.interactiveshell.InteractiveShell` no longer takes an
   ``embedded`` argument. Instead just use the
   :class:`~IPython.core.interactiveshell.InteractiveShellEmbed` class.
 
 * ``__IPYTHON__`` is no longer injected into ``__builtin__``.
 
 * :meth:`Struct.__init__` no longer takes `None` as its first argument.  It
   must be a :class:`dict` or :class:`Struct`.
 
 * :meth:`~IPython.core.interactiveshell.InteractiveShell.ipmagic` has been
   renamed :meth:`~IPython.core.interactiveshell.InteractiveShell.magic.`
 
 * The functions :func:`ipmagic` and :func:`ipalias` have been removed from
   :mod:`__builtins__`.
 
 * The references to the global
   :class:`~IPython.core.interactivehell.InteractiveShell` instance (``_ip``, and
   ``__IP``) have been removed from the user's namespace. They are replaced by a
   new function called :func:`get_ipython` that returns the current
   :class:`~IPython.core.interactiveshell.InteractiveShell` instance. This
   function is injected into the user's namespace and is now the main way of
   accessing the running IPython.
 
 * Old style configuration files :file:`ipythonrc` and :file:`ipy_user_conf.py`
   are no longer supported. Users should migrate there configuration files to
-  the new format described :doc:`here <config/intro>` and
+  the new format described :doc:`here </config/intro>` and
   :ref:`here <config_overview>`.
 
 * The old IPython extension API that relied on :func:`ipapi` has been
   completely removed. The new extension API is described :ref:`here
   <extensions_overview>`.
 
 * Support for ``qt3`` has been dropped.  Users who need this should use
   previous versions of IPython.
 
 * Removed :mod:`shellglobals` as it was obsolete.
 
 * Removed all the threaded shells in :mod:`IPython.core.shell`. These are no
   longer needed because of the new capabilities in
   :mod:`IPython.lib.inputhook`.
 
 * New top-level sub-packages have been created: :mod:`IPython.core`, 
   :mod:`IPython.lib`, :mod:`IPython.utils`, :mod:`IPython.deathrow`,
   :mod:`IPython.quarantine`.  All existing top-level modules have been
   moved to appropriate sub-packages.  All internal import statements
   have been updated and tests have been added.  The build system (setup.py
   and friends) have been updated. See :doc:`/api/index` for details of these
   new sub-packages.
 
 * :mod:`IPython.ipapi` has been moved to :mod:`IPython.core.ipapi`.
   :mod:`IPython.Shell` and :mod:`IPython.iplib` have been split and removed as
   part of the refactor.
 
 * :mod:`Extensions` has been moved to :mod:`extensions` and all existing
   extensions have been moved to either :mod:`IPython.quarantine` or
   :mod:`IPython.deathrow`. :mod:`IPython.quarantine` contains modules that we
   plan on keeping but that need to be updated. :mod:`IPython.deathrow` contains
   modules that are either dead or that should be maintained as third party
   libraries.
 
 * Previous IPython GUIs in :mod:`IPython.frontend` and :mod:`IPython.gui` are
   likely broken, and have been removed to :mod:`IPython.deathrow` because of the
   refactoring in the core. With proper updates, these should still work.
 
 
 Known Regressions
 -----------------
 
 We do our best to improve IPython, but there are some known regressions in 0.11
 relative to 0.10.2.  First of all, there are features that have yet to be
 ported to the new APIs, and in order to ensure that all of the installed code
 runs for our users, we have moved them to two separate directories in the
 source distribution, `quarantine` and `deathrow`.  Finally, we have some other
 miscellaneous regressions that we hope to fix as soon as possible.  We now
 describe all of these in more detail.
 
 Quarantine
 ~~~~~~~~~~
 
 These are tools and extensions that we consider relatively easy to update to
 the new classes and APIs, but that we simply haven't had time for.  Any user
 who is interested in one of these is encouraged to help us by porting it and
 submitting a pull request on our `development site`_.
 
 .. _development site: http://github.com/ipython/ipython
 
 Currently, the quarantine directory contains::
 
     clearcmd.py            ipy_fsops.py            ipy_signals.py
     envpersist.py          ipy_gnuglobal.py        ipy_synchronize_with.py
     ext_rescapture.py      ipy_greedycompleter.py  ipy_system_conf.py
     InterpreterExec.py     ipy_jot.py              ipy_which.py
     ipy_app_completers.py  ipy_lookfor.py          ipy_winpdb.py
     ipy_autoreload.py      ipy_profile_doctest.py  ipy_workdir.py
     ipy_completers.py      ipy_pydb.py             jobctrl.py
     ipy_editors.py         ipy_rehashdir.py        ledit.py
     ipy_exportdb.py        ipy_render.py           pspersistence.py
     ipy_extutil.py         ipy_server.py           win32clip.py
 
 Deathrow
 ~~~~~~~~
 
 These packages may be harder to update or make most sense as third-party
 libraries.  Some of them are completely obsolete and have been already replaced
 by better functionality (we simply haven't had the time to carefully weed them
 out so they are kept here for now). Others simply require fixes to code that
 the current core team may not be familiar with.  If a tool you were used to is
 included here, we encourage you to contact the dev list and we can discuss
 whether it makes sense to keep it in IPython (if it can be maintained).
 
 Currently, the deathrow directory contains::
 
     astyle.py              ipy_defaults.py          ipy_vimserver.py
     dtutils.py             ipy_kitcfg.py            numeric_formats.py
     Gnuplot2.py            ipy_legacy.py            numutils.py
     GnuplotInteractive.py  ipy_p4.py                outputtrap.py
     GnuplotRuntime.py      ipy_profile_none.py      PhysicalQInput.py
     ibrowse.py             ipy_profile_numpy.py     PhysicalQInteractive.py
     igrid.py               ipy_profile_scipy.py     quitter.py*
     ipipe.py               ipy_profile_sh.py        scitedirector.py
     iplib.py               ipy_profile_zope.py      Shell.py
     ipy_constants.py       ipy_traits_completer.py  twshell.py
 
 
 Other regressions
 ~~~~~~~~~~~~~~~~~
 
 * The machinery that adds functionality to the 'sh' profile for using IPython
   as your system shell has not been updated to use the new APIs.  As a result,
   only the aesthetic (prompt) changes are still implemented. We intend to fix
   this by 0.12.  Tracked as issue 547_.
 
 .. _547: https://github.com/ipython/ipython/issues/547
 
 * The installation of scripts on Windows was broken without setuptools, so we
   now depend on setuptools on Windows.  We hope to fix setuptools-less
   installation, and then remove the setuptools dependency.  Issue 539_.
 
 .. _539: https://github.com/ipython/ipython/issues/539
 
 * The directory history `_dh` is not saved between sessions.  Issue 634_.
 
 .. _634: https://github.com/ipython/ipython/issues/634
 
 
 Removed Features
 ----------------
 
 As part of the updating of IPython, we have removed a few features for the
 purposes of cleaning up the codebase and interfaces.  These removals are
 permanent, but for any item listed below, equivalent functionality is
 available.
 
 * The magics Exit and Quit have been dropped as ways to exit IPython. Instead,
   the lowercase forms of both work either as a bare name (``exit``) or a
   function call (``exit()``).  You can assign these to other names using
   exec_lines in the config file.
 
 
 .. _credits_011:
 
 Credits
 -------
 
 Many users and developers contributed code, features, bug reports and ideas to
 this release.  Please do not hesitate in contacting us if we've failed to
 acknowledge your contribution here.  In particular, for this release we have
 contribution from the following people, a mix of new and regular names (in
 alphabetical order by first name):
 
 * Aenugu Sai Kiran Reddy <saikrn08-at-gmail.com>
 * andy wilson <wilson.andrew.j+github-at-gmail.com>
 * Antonio Cuni <antocuni>
 * Barry Wark <barrywark-at-gmail.com>
 * Beetoju Anuradha <anu.beethoju-at-gmail.com>
 * Benjamin Ragan-Kelley <minrk-at-Mercury.local>
 * Brad Reisfeld
 * Brian E. Granger <ellisonbg-at-gmail.com>
 * Christoph Gohlke <cgohlke-at-uci.edu>
 * Cody Precord
 * dan.milstein
 * Darren Dale <dsdale24-at-gmail.com>
 * Dav Clark <davclark-at-berkeley.edu>
 * David Warde-Farley <wardefar-at-iro.umontreal.ca>
 * epatters <ejpatters-at-gmail.com>
 * epatters <epatters-at-caltech.edu>
 * epatters <epatters-at-enthought.com>
 * Eric Firing <efiring-at-hawaii.edu>
 * Erik Tollerud <erik.tollerud-at-gmail.com>
 * Evan Patterson <epatters-at-enthought.com>
 * Fernando Perez <Fernando.Perez-at-berkeley.edu>
 * Gael Varoquaux <gael.varoquaux-at-normalesup.org>
 * Gerardo <muzgash-at-Muzpelheim>
 * Jason Grout <jason.grout-at-drake.edu>
 * John Hunter <jdh2358-at-gmail.com>
 * Jens Hedegaard Nielsen <jenshnielsen-at-gmail.com>
 * Johann Cohen-Tanugi <johann.cohentanugi-at-gmail.com>
 * Jörgen Stenarson <jorgen.stenarson-at-bostream.nu>
 * Justin Riley <justin.t.riley-at-gmail.com>
 * Kiorky
 * Laurent Dufrechou <laurent.dufrechou-at-gmail.com>
 * Luis Pedro Coelho <lpc-at-cmu.edu>
 * Mani chandra <mchandra-at-iitk.ac.in>
 * Mark E. Smith
 * Mark Voorhies <mark.voorhies-at-ucsf.edu>
 * Martin Spacek <git-at-mspacek.mm.st>
 * Michael Droettboom <mdroe-at-stsci.edu>
 * MinRK <benjaminrk-at-gmail.com>
 * muzuiget <muzuiget-at-gmail.com>
 * Nick Tarleton <nick-at-quixey.com>
 * Nicolas Rougier <Nicolas.rougier-at-inria.fr>
 * Omar Andres Zapata Mesa <andresete.chaos-at-gmail.com>
 * Paul Ivanov <pivanov314-at-gmail.com>
 * Pauli Virtanen <pauli.virtanen-at-iki.fi>
 * Prabhu Ramachandran
 * Ramana <sramana9-at-gmail.com>
 * Robert Kern <robert.kern-at-gmail.com>
 * Sathesh Chandra <satheshchandra88-at-gmail.com>
 * Satrajit Ghosh <satra-at-mit.edu>
 * Sebastian Busch
 * Skipper Seabold <jsseabold-at-gmail.com>
 * Stefan van der Walt <bzr-at-mentat.za.net>
 * Stephan Peijnik <debian-at-sp.or.at>
 * Steven Bethard
 * Thomas Kluyver <takowl-at-gmail.com>
 * Thomas Spura <tomspur-at-fedoraproject.org>
 * Tom Fetherston <tfetherston-at-aol.com>
 * Tom MacWright
 * tzanko
 * vankayala sowjanya <hai.sowjanya-at-gmail.com>
 * Vivian De Smedt <vds2212-at-VIVIAN>
 * Ville M. Vainio <vivainio-at-gmail.com>
 * Vishal Vatsa <vishal.vatsa-at-gmail.com>
 * Vishnu S G <sgvishnu777-at-gmail.com>
 * Walter Doerwald <walter-at-livinglogic.de>
 
 .. note::
 
     This list was generated with the output of
     ``git log dev-0.11 HEAD --format='* %aN <%aE>' | sed 's/@/\-at\-/' | sed 's/<>//' | sort -u``
     after some cleanup.  If you should be on this list, please add yourself.