docs/source/whatsnew/version0.13.rst

=============
 0.13 Series
=============

Release 0.13
============

IPython 0.13 contains several major new features, as well as a large amount of
bug and regression fixes.  The previous version (0.12) was released on December
19 2011, and in this development cycle we had:

- ~6 months of work.
- 373 pull requests merged.
- 742 issues closed (non-pull requests).
- contributions from 62 authors.
- 1760 commits.
- a diff of 114226 lines.

The amount of work included in this release is so large, that we can only cover
here the main highlights; please see our :ref:`detailed release statistics
<issues_list_013>` for links to every issue and pull request closed on GitHub
as well as a full list of individual contributors.


Major Notebook improvements: new user interface and more
--------------------------------------------------------

The IPython Notebook, which has proven since its release to be wildly popular,
has seen a massive amount of work in this release cycle, leading to a
significantly improved user experience as well as many new features.

The first user-visible change is a reorganization of the user interface; the
left panel has been removed and was replaced by a real menu system and a
toolbar with icons.  Both the toolbar and the header above the menu can be
collapsed to leave an unobstructed working area:

.. image:: ../_images/ipy_013_notebook_spectrogram.png
    :width: 460px
    :alt: New user interface for Notebook
    :align: center
    :target: ../_images/ipy_013_notebook_spectrogram.png

The notebook handles very long outputs much better than before (this was a
serious usability issue when running processes that generated massive amounts
of output).  Now, in the presence of outputs longer than ~100 lines, the
notebook will automatically collapse to a scrollable area and the entire left
part of this area controls the display: one click in this area will expand the
output region completely, and a double-click will hide it completely.  This
figure shows both the scrolled and hidden modes:

.. image:: ../_images/ipy_013_notebook_long_out.png
    :width: 460px
    :alt: Scrolling and hiding of long output in the notebook.
    :align: center
    :target: ../_images/ipy_013_notebook_long_out.png

.. note::

   The auto-folding of long outputs is disabled in Firefox due to bugs in its
   scrolling behavior.  See :ghpull:`2047` for details.

Uploading notebooks to the dashboard is now easier: in addition to drag and
drop (which can be finicky sometimes), you can now click on the upload text and
use a regular file dialog box to select notebooks to upload. Furthermore, the
notebook dashboard now auto-refreshes its contents and offers buttons to shut
down any running kernels (:ghpull:`1739`):

.. image:: ../_images/ipy_013_dashboard.png
    :width: 460px
    :alt: Improved dashboard
    :align: center
    :target: ../_images/ipy_013_dashboard.png


Cluster management
~~~~~~~~~~~~~~~~~~

The notebook dashboard can now also start and stop clusters, thanks to a new
tab in the dashboard user interface:

.. image:: ../_images/ipy_013_dashboard_cluster.png
    :width: 460px
    :alt: Cluster management from the notebook dashboard
    :align: center
    :target: ../_images/ipy_013_dashboard_cluster.png

This interface allows, for each profile you have configured, to start and stop
a cluster (and optionally override the default number of engines corresponding
to that configuration).  While this hides all error reporting, once you have a
configuration that you know works smoothly, it is a very convenient interface
for controlling your parallel resources.


New notebook format
~~~~~~~~~~~~~~~~~~~

The notebooks saved now use version 3 of our format, which supports heading
levels as well as the concept of 'raw' text cells that are not rendered as
Markdown.  These will be useful with converters_ we are developing, to pass raw
markup (say LaTeX).  That conversion code is still under heavy development and
not quite ready for prime time, but we welcome help on this front so that we
can merge it for full production use as soon as possible.

.. _converters: https://github.com/ipython/nbconvert

.. note::

   v3 notebooks can *not* be read by older versions of IPython, but we provide
   a `simple script`_ that you can use in case you need to export a v3
   notebook to share with a v2 user.

.. _simple script: https://gist.github.com/1935808


JavaScript refactoring
~~~~~~~~~~~~~~~~~~~~~~
  
All the client-side JavaScript has been decoupled to ease reuse of parts of the
machinery without having to build a full-blown notebook. This will make it much
easier to communicate with an IPython kernel from existing web pages and to
integrate single cells into other sites, without loading the full notebook
document-like UI. :ghpull:`1711`.
    
This refactoring also enables the possibility of writing dynamic javascript
widgets that are returned from Python code and that present an interactive view
to the user, with callbacks in Javascript executing calls to the Kernel.  This
will enable many interactive elements to be added by users in notebooks.

An example of this capability has been provided as a proof of concept in
:file:`examples/widgets` that lets you directly communicate with one or more
parallel engines, acting as a mini-console for parallel debugging and
introspection.

    
Improved tooltips
~~~~~~~~~~~~~~~~~

The object tooltips have gained some new functionality. By pressing tab several
times, you can expand them to see more of a docstring, keep them visible as you
fill in a function's parameters, or transfer the information to the pager at the
bottom of the screen. For the details, look at the example notebook
:file:`01_notebook_introduction.ipynb`.

.. figure:: ../_images/ipy_013_notebook_tooltip.png
    :width: 460px
    :alt: Improved tooltips in the notebook.
    :align: center
    :target: ../_images/ipy_013_notebook_tooltip.png

    The new notebook tooltips.

Other improvements to the Notebook
----------------------------------

These are some other notable small improvements to the notebook, in addition to
many bug fixes and minor changes to add polish and robustness throughout:

* The notebook pager (the area at the bottom) is now resizeable by dragging its
  divider handle, a feature that had been requested many times by just about
  anyone who had used the notebook system.  :ghpull:`1705`.

* It is now possible to open notebooks directly from the command line; for
  example: ``ipython notebook path/`` will automatically set ``path/`` as the
  notebook directory, and ``ipython notebook path/foo.ipynb`` will further
  start with the ``foo.ipynb`` notebook opened.  :ghpull:`1686`.
  
* If a notebook directory is specified with ``--notebook-dir`` (or with the
  corresponding configuration flag ``NotebookManager.notebook_dir``), all
  kernels start in this directory.

* Fix codemirror clearing of cells with ``Ctrl-Z``; :ghpull:`1965`.
  
* Text (markdown) cells now line wrap correctly in the notebook, making them
  much easier to edit :ghpull:`1330`.
  
* PNG and JPEG figures returned from plots can be interactively resized in the
  notebook, by dragging them from their lower left corner. :ghpull:`1832`.

* Clear ``In []`` prompt numbers on "Clear All Output".  For more
  version-control-friendly ``.ipynb`` files, we now strip all prompt numbers
  when doing a "Clear all output".  This reduces the amount of noise in
  commit-to-commit diffs that would otherwise show the (highly variable) prompt
  number changes. :ghpull:`1621`.

* The notebook server now requires *two* consecutive ``Ctrl-C`` within 5
  seconds (or an interactive confirmation) to terminate operation.  This makes
  it less likely that you will accidentally kill a long-running server by
  typing ``Ctrl-C`` in the wrong terminal.  :ghpull:`1609`.

* Using ``Ctrl-S`` (or ``Cmd-S`` on a Mac) actually saves the notebook rather
  than providing the fairly useless browser html save dialog.  :ghpull:`1334`.
  
* Allow accessing local files from the notebook (in urls), by serving any local
  file as the url ``files/<relativepath>``.  This makes it possible to, for
  example, embed local images in a notebook.  :ghpull:`1211`.

      
Cell magics
-----------

We have completely refactored the magic system, finally moving the magic
objects to standalone, independent objects instead of being the mixin class
we'd had since the beginning of IPython (:ghpull:`1732`).  Now, a separate base
class is provided in :class:`IPython.core.magic.Magics` that users can subclass
to create their own magics.  Decorators are also provided to create magics from
simple functions without the need for object orientation.  Please see the
:ref:`magic` docs for further details.

All builtin magics now exist in a few subclasses that group together related
functionality, and the new :mod:`IPython.core.magics` package has been created
to organize this into smaller files.
    
This cleanup was the last major piece of deep refactoring needed from the
original 2001 codebase.
    
We have also introduced a new type of magic function, prefixed with `%%`
instead of `%`, which operates at the whole-cell level.  A cell magic receives
two arguments: the line it is called on (like a line magic) and the body of the
cell below it.
    
Cell magics are most natural in the notebook, but they also work in the
terminal and qt console, with the usual approach of using a blank line to
signal cell termination.
    
For example, to time the execution of several statements::

    %%timeit x = 0   # setup
    for i in range(100000):
        x += i**2

This is particularly useful to integrate code in another language, and cell
magics already exist for shell scripts, Cython, R and Octave. Using ``%%script
/usr/bin/foo``, you can run a cell in any interpreter that accepts code via
stdin.

Another handy cell magic makes it easy to write short text files: ``%%file
~/save/to/here.txt``.

The following cell magics are now included by default; all those that use
special interpreters (Perl, Ruby, bash, etc.) assume you have the requisite
interpreter installed:

* ``%%!``: run cell body with the underlying OS shell; this is similar to
  prefixing every line in the cell with ``!``.
  
* ``%%bash``: run cell body under bash.
  
* ``%%capture``: capture the output of the code in the cell (and stderr as
  well).  Useful to run codes that produce too much output that you don't even
  want scrolled.
  
* ``%%file``: save cell body as a file.
  
* ``%%perl``: run cell body using Perl.
  
* ``%%prun``: run cell body with profiler (cell extension of ``%prun``).
  
* ``%%python3``: run cell body using Python 3.
  
* ``%%ruby``: run cell body using Ruby.
  
* ``%%script``: run cell body with the script specified in the first line.
  
* ``%%sh``: run cell body using sh.
  
* ``%%sx``: run cell with system shell and capture process output (cell
  extension of ``%sx``).
  
* ``%%system``: run cell with system shell (``%%!`` is an alias to this).
  
* ``%%timeit``: time the execution of the cell (extension of ``%timeit``).

This is what some of the script-related magics look like in action:

.. image:: ../_images/ipy_013_notebook_script_cells.png
    :width: 460px
    :alt: Cluster management from the notebook dashboard
    :align: center
    :target: ../_images/ipy_013_notebook_script_cells.png
  
In addition, we have also a number of :ref:`extensions <extensions_overview>`
that provide specialized magics.  These typically require additional software
to run and must be manually loaded via ``%load_ext <extension name>``, but are
extremely useful.  The following extensions are provided:

**Cython magics** (extension :ref:`cythonmagic <extensions_cythonmagic>`)
    This extension provides magics to automatically build and compile Python
    extension modules using the Cython_ language. You must install Cython
    separately, as well as a C compiler, for this to work.  The examples
    directory in the source distribution ships with a full notebook
    demonstrating these capabilities:

.. image:: ../_images/ipy_013_notebook_cythonmagic.png
    :width: 460px
    :alt: Cython magic
    :align: center
    :target: ../_images/ipy_013_notebook_cythonmagic.png

.. _cython: http://cython.org

**Octave magics** (extension :ref:`octavemagic <extensions_octavemagic>`)
    This extension provides several magics that support calling code written in
    the Octave_ language for numerical computing.  You can execute single-lines
    or whole blocks of Octave code, capture both output and figures inline
    (just like matplotlib plots), and have variables automatically converted
    between the two languages.  To use this extension, you must have Octave
    installed as well as the oct2py_ package.  The examples
    directory in the source distribution ships with a full notebook
    demonstrating these capabilities:

.. image:: ../_images/ipy_013_notebook_octavemagic.png
    :width: 460px
    :alt: Octave magic
    :align: center
    :target: ../_images/ipy_013_notebook_octavemagic.png

.. _octave: http://www.gnu.org/software/octave
.. _oct2py: http://pypi.python.org/pypi/oct2py

**R magics** (extension :ref:`rmagic <extensions_rmagic>`)
    This extension provides several magics that support calling code written in
    the R_ language for statistical data analysis.  You can execute
    single-lines or whole blocks of R code, capture both output and figures
    inline (just like matplotlib plots), and have variables automatically
    converted between the two languages.  To use this extension, you must have
    R installed as well as the rpy2_ package that bridges Python and R.  The
    examples directory in the source distribution ships with a full notebook
    demonstrating these capabilities:

.. image:: ../_images/ipy_013_notebook_rmagic.png
    :width: 460px
    :alt: R magic
    :align: center
    :target: ../_images/ipy_013_notebook_rmagic.png

.. _R: http://www.r-project.org
.. _rpy2: http://rpy.sourceforge.net/rpy2.html


Tab completer improvements
--------------------------

Useful tab-completion based on live inspection of objects is one of the most
popular features of IPython. To make this process even more user-friendly, the
completers of both the Qt console and the Notebook have been reworked.

The Qt console comes with a new ncurses-like tab completer, activated by
default, which lets you cycle through the available completions by pressing tab,
or select a completion with the arrow keys (:ghpull:`1851`).

.. figure:: ../_images/ipy_013_qtconsole_completer.png
    :width: 460px
    :alt: ncurses-like completer, with highlighted selection.
    :align: center
    :target: ../_images/ipy_013_qtconsole_completer.png

    The new improved Qt console's ncurses-like completer allows to easily
    navigate thought long list of completions.

In the notebook, completions are now sourced both from object introspection and
analysis of surrounding code, so limited completions can be offered for
variables defined in the current cell, or while the kernel is busy 
(:ghpull:`1711`).


We have implemented a new configurable flag to control tab completion on
modules that provide the ``__all__`` attribute::

  IPCompleter.limit_to__all__= Boolean

This instructs the completer to honor ``__all__`` for the completion.
Specifically, when completing on ``object.<tab>``, if True: only those names
in ``obj.__all__`` will be included.  When False [default]: the ``__all__``
attribute is ignored. :ghpull:`1529`.


Improvements to the Qt console
------------------------------

The Qt console continues to receive improvements and refinements, despite the
fact that it is by now a fairly mature and robust component.  Lots of small
polish has gone into it, here are a few highlights:

* A number of changes were made to the underlying code for easier integration
  into other projects such as Spyder_ (:ghpull:`2007`, :ghpull:`2024`).

* Improved menus with a new Magic menu that is organized by magic groups (this
  was made possible by the reorganization of the magic system
  internals). :ghpull:`1782`.

* Allow for restarting kernels without clearing the qtconsole, while leaving a
  visible indication that the kernel has restarted. :ghpull:`1681`.
  
* Allow the native display of jpeg images in the qtconsole. :ghpull:`1643`.

.. _spyder: https://code.google.com/p/spyderlib


  
Parallel
--------

The parallel tools have been improved and fine-tuned on multiple fronts.  Now,
the creation of an :class:`IPython.parallel.Client` object automatically
activates a line and cell magic function ``px`` that sends its code to all the
engines. Further magics can be easily created with the :meth:`.Client.activate`
method, to conveniently execute code on any subset of engines. :ghpull:`1893`.

The ``%%px`` cell magic can also be given an optional targets argument, as well
as a ``--out`` argument for storing its output.

A new magic has also been added, ``%pxconfig``, that lets you configure various
defaults of the parallel magics.  As usual, type  ``%pxconfig?`` for details.

The exception reporting in parallel contexts has been improved to be easier to
read.  Now, IPython directly reports the remote exceptions without showing any
of the internal execution parts:

.. image::  ../_images/ipy_013_par_tb.png
    :width: 460px
    :alt: Improved parallel exceptions.
    :align: center
    :target: ../_images/ipy_013_par_tb.png

The parallel tools now default to using ``NoDB`` as the storage backend for
intermediate results.  This means that the default usage case will have a
significantly reduced memory footprint, though certain advanced features are
not available with this backend.  For more details, see :ref:`parallel_db`.

The parallel magics now display all output, so you can do parallel plotting or
other actions with complex display.  The ``px`` magic has now both line and cell
modes, and in cell mode finer control has been added about how to collate
output from multiple engines. :ghpull:`1768`.

There have also been incremental improvements to the SSH launchers:
    
* add to_send/fetch steps for moving connection files around.
  
* add SSHProxyEngineSetLauncher, for invoking to `ipcluster engines` on a
  remote host. This can be used to start a set of engines via PBS/SGE/MPI
  *remotely*.
    
This makes the SSHLauncher usable on machines without shared filesystems.

A number of 'sugar' methods/properties were added to AsyncResult that are
quite useful (:ghpull:`1548`) for everday work:
    
    * ``ar.wall_time`` = received - submitted
    * ``ar.serial_time`` = sum of serial computation time
    * ``ar.elapsed`` = time since submission (wall_time if done)
    * ``ar.progress`` = (int) number of sub-tasks that have completed
    * ``len(ar)`` = # of tasks
    * ``ar.wait_interactive()``: prints progress
    
Added :meth:`.Client.spin_thread` / :meth:`~.Client.stop_spin_thread` for
running spin in a background thread, to keep zmq queue clear.  This can be used
to ensure that timing information is as accurate as possible (at the cost of
having a background thread active).

Set TaskScheduler.hwm default to 1 instead of 0.  1 has more
predictable/intuitive behavior, if often slower, and thus a more logical
default.  Users whose workloads require maximum throughput and are largely
homogeneous in time per task can make the optimization themselves, but now the
behavior will be less surprising to new users. :ghpull:`1294`.


Kernel/Engine unification
-------------------------

This is mostly work 'under the hood', but it is actually a *major* achievement
for the project that has deep implications in the long term: at last, we have
unified the main object that executes as the user's interactive shell (which we
refer to as the *IPython kernel*) with the objects that run in all the worker
nodes of the parallel computing facilities (the *IPython engines*).  Ever since
the first implementation of IPython's parallel code back in 2006, we had wanted
to have these two roles be played by the same machinery, but a number of
technical reasons had prevented that from being true.

In this release we have now merged them, and this has a number of important
consequences:

* It is now possible to connect any of our clients (qtconsole or terminal
  console) to any individual parallel engine, with the *exact* behavior of
  working at a 'regular' IPython console/qtconsole.  This makes debugging,
  plotting, etc. in parallel scenarios vastly easier.

* Parallel engines can always execute arbitrary 'IPython code', that is, code
  that has magics, shell extensions, etc.  In combination with the ``%%px``
  magics, it is thus extremely natural for example to send to all engines a
  block of Cython or R code to be executed via the new Cython and R magics. For
  example, this snippet would send the R block to all active engines in a
  cluster::

    %%px
    %%R
    ... R code goes here
  
* It is possible to embed not only an interactive shell with the
  :func:`IPython.embed` call as always, but now you can also embed a *kernel*
  with :func:`IPython.embed_kernel()`.  Embedding an IPython kernel in an
  application is useful when you want to use :func:`IPython.embed` but don't
  have a terminal attached on stdin and stdout.

* The new :func:`IPython.parallel.bind_kernel` allows you to promote Engines to
  listening Kernels, and connect QtConsoles to an Engine and debug it
  directly.

In addition, having a single core object through our entire architecture also
makes the project conceptually cleaner, easier to maintain and more robust.
This took a lot of work to get in place, but we are thrilled to have this major
piece of architecture finally where we'd always wanted it to be.
  

Official Public API
-------------------

We have begun organizing our API for easier public use, with an eye towards an
official IPython 1.0 release which will firmly maintain this API compatible for
its entire lifecycle.  There is now an :mod:`IPython.display` module that
aggregates all display routines, and the :mod:`IPython.config` namespace has
all public configuration tools.  We will continue improving our public API
layout so that users only need to import names one level deeper than the main
``IPython`` package to access all public namespaces.


IPython notebook file icons
---------------------------

The directory ``docs/resources`` in the source distribution contains SVG and
PNG versions of our file icons, as well as an ``Info.plist.example`` file with
instructions to install them on Mac OSX.  This is a first draft of our icons,
and we encourage contributions from users with graphic talent to improve them
in the future:

.. image:: ../../resources/ipynb_icon_128x128.png
   :alt:  IPython notebook file icon.

	  
New top-level `locate` command
------------------------------

Add `locate` entry points; these would be useful for quickly locating IPython
directories and profiles from other (non-Python) applications. :ghpull:`1762`.
    
Examples::
    
    $> ipython locate
    /Users/me/.ipython
  
    $> ipython locate profile foo
    /Users/me/.ipython/profile_foo
  
    $> ipython locate profile
    /Users/me/.ipython/profile_default
  
    $> ipython locate profile dne
    [ProfileLocate] Profile u'dne' not found.

	
Other new features and improvements
-----------------------------------

* **%install_ext**: A new magic function to install an IPython extension from
  a URL. E.g. ``%install_ext
  https://bitbucket.org/birkenfeld/ipython-physics/raw/default/physics.py``.

* The ``%loadpy`` magic is no longer restricted to Python files, and has been
  renamed ``%load``. The old name remains as an alias.

* New command line arguments will help external programs find IPython folders:
  ``ipython locate`` finds the user's IPython directory, and ``ipython locate
  profile foo`` finds the folder for the 'foo' profile (if it exists).

* The :envvar:`IPYTHON_DIR` environment variable, introduced in the Great
  Reorganization of 0.11 and existing only in versions 0.11-0.13, has been
  deprecated. As described in :ghpull:`1167`, the complexity and confusion of
  migrating to this variable is not worth the aesthetic improvement. Please use
  the historical :envvar:`IPYTHONDIR` environment variable instead.

* The default value of *interactivity* passed from
  :meth:`~IPython.core.interactiveshell.InteractiveShell.run_cell` to
  :meth:`~IPython.core.interactiveshell.InteractiveShell.run_ast_nodes`
  is now configurable.

* New ``%alias_magic`` function to conveniently create aliases of existing
  magics, if you prefer to have shorter names for personal use.

* We ship unminified versions of the JavaScript libraries we use, to better
  comply with Debian's packaging policies.

* Simplify the information presented by ``obj?/obj??`` to eliminate a few
  redundant fields when possible.  :ghpull:`2038`.

* Improved continuous integration for IPython.  We now have automated test runs
  on `Shining Panda <https://jenkins.shiningpanda.com/ipython>`_ and `Travis-CI
  <http://travis-ci.org/#!/ipython/ipython>`_, as well as `Tox support
  <http://tox.testrun.org>`_.

* The `vim-ipython`_ functionality (externally developed) has been updated to
  the latest version.

.. _vim-ipython: https://github.com/ivanov/vim-ipython

* The ``%save`` magic now has a ``-f`` flag to force overwriting, which makes
  it much more usable in the notebook where it is not possible to reply to
  interactive questions from the kernel. :ghpull:`1937`.

* Use dvipng to format sympy.Matrix, enabling display of matrices in the Qt
  console with the sympy printing extension. :ghpull:`1861`.

* Our messaging protocol now has a reasonable test suite, helping ensure that
  we don't accidentally deviate from the spec and possibly break third-party
  applications that may have been using it.  We encourage users to contribute
  more stringent tests to this part of the test suite.  :ghpull:`1627`.

* Use LaTeX to display, on output, various built-in types with the SymPy
  printing extension. :ghpull:`1399`.

* Add Gtk3 event loop integration and example. :ghpull:`1588`.

* ``clear_output`` improvements, which allow things like progress bars and other
  simple animations to work well in the notebook (:ghpull:`1563`):
    
    * `clear_output()` clears the line, even in terminal IPython, the QtConsole
      and plain Python as well, by printing `\r` to streams.
    
    * `clear_output()` avoids the flicker in the notebook by adding a delay,
      and firing immediately upon the next actual display message.
    
    * `display_javascript` hides its `output_area` element, so using display to
      run a bunch of javascript doesn't result in ever-growing vertical space.

* Add simple support for running inside a virtualenv.  While this doesn't
  supplant proper installation (as users should do), it helps ad-hoc calling of
  IPython from inside a virtualenv. :ghpull:`1388`.

  
Major Bugs fixed
----------------

In this cycle, we have :ref:`closed over 740 issues <issues_list_013>`, but a
few major ones merit special mention:

* The ``%pastebin`` magic has been updated to point to gist.github.com, since
  unfortunately http://paste.pocoo.org has closed down. We also added a -d flag
  for the user to provide a gist description string. :ghpull:`1670`.

* Fix ``%paste`` that would reject certain valid inputs. :ghpull:`1258`.

* Fix sending and receiving of Numpy structured arrays (those with composite
  dtypes, often used as recarrays). :ghpull:`2034`.

* Reconnect when the websocket connection closes unexpectedly. :ghpull:`1577`.

* Fix truncated representation of objects in the debugger by showing at least
  80 characters' worth of information.  :ghpull:`1793`.

* Fix logger to be Unicode-aware: logging could crash ipython if there was
  unicode in the input. :ghpull:`1792`.

* Fix images missing from XML/SVG export in the Qt console. :ghpull:`1449`.

* Fix deepreload on Python 3. :ghpull:`1625`, as well as having a much cleaner
  and more robust implementation of deepreload in general. :ghpull:`1457`.


Backwards incompatible changes
------------------------------

* The exception :exc:`IPython.core.error.TryNext` previously accepted
  arguments and keyword arguments to be passed to the next implementation
  of the hook. This feature was removed as it made error message propagation
  difficult and violated the principle of loose coupling.