release notes for 3.1

docs/source/whatsnew/github-stats-3.rst

@@ -1,173 +1,220 b''
 .. _issues_list_3:
 
 Issues closed in the 3.x development cycle
 ==========================================
 
+Issues closed in 3.1
+--------------------
+
+GitHub stats for 2015/02/27 - 2015/04/03 (since 3.0)
+
+These lists are automatically generated, and may be incomplete or contain duplicates.
+
+We closed 46 issues and merged 133 pull requests.
+The full list can be seen `on GitHub <https://github.com/ipython/ipython/milestones/3.1>`_.
+
+The following 33 authors contributed 344 commits:
+
+* Abe Guerra
+* Adal Chiriliuc
+* Benjamin Ragan-Kelley
+* Brian Drawert
+* Fernando Perez
+* Gareth Elston
+* Gert-Ludwig Ingold
+* Giuseppe Venturini
+* Jakob Gager
+* Jan Schulz
+* Jason Grout
+* Jessica B. Hamrick
+* Jonathan Frederic
+* Justin Tyberg
+* Lorena Pantano
+* mashenjun
+* Mathieu
+* Matthias Bussonnier
+* Morten Enemark Lund
+* Naveen Nathan
+* Nicholas Bollweg
+* onesandzeroes
+* Patrick Snape
+* Peter Parente
+* RickWinter
+* Robert Smith
+* Ryan Nelson
+* Scott Sanderson
+* Sylvain Corlay
+* Thomas Kluyver
+* tmtabor
+* Wieland Hoffmann
+* Yuval Langer
+
+
 Issues closed in 3.0
-----------------------
+--------------------
 
 GitHub stats for 2014/04/02 - 2015/02/13 (since 2.0)
 
 These lists are automatically generated, and may be incomplete or contain duplicates.
 
 We closed 469 issues and merged 925 pull requests.
 The full list can be seen `on GitHub <https://github.com/ipython/ipython/milestones/3.0>`_.
 
 The following 155 authors contributed 5975 commits.
 
 * A.J. Holyoake
 * abalkin
 * Adam Hodgen
 * Adrian Price-Whelan
 * Amin Bandali
 * Andreas Amann
 * Andrew Dawes
 * Andrew Jesaitis
 * Andrew Payne
 * AnneTheAgile
 * Aron Ahmadia
 * Ben Duffield
 * Benjamin ABEL
 * Benjamin Ragan-Kelley
 * Benjamin Schultz
 * Björn Grüning
 * Björn Linse
 * Blake Griffith
 * Boris Egorov
 * Brian E. Granger
 * bsvh
 * Carlos Cordoba
 * Cedric GESTES
 * cel
 * chebee7i
 * Christoph Gohlke
 * CJ Carey
 * Cyrille Rossant
 * Dale Jung
 * Damián Avila
 * Damon Allen
 * Daniel B. Vasquez
 * Daniel Rocco
 * Daniel Wehner
 * Dav Clark
 * David Hirschfeld
 * David Neto
 * dexterdev
 * Dimitry Kloper
 * dongweiming
 * Doug Blank
 * drevicko
 * Dustin Rodriguez
 * Eric Firing
 * Eric Galloway
 * Erik M. Bray
 * Erik Tollerud
 * Ezequiel (Zac) Panepucci
 * Fernando Perez
 * foogunlana
 * Francisco de la Peña
 * George Titsworth
 * Gordon Ball
 * gporras
 * Grzegorz Rożniecki
 * Helen ST
 * immerrr
 * Ingolf Becker
 * Jakob Gager
 * James Goppert
 * James Porter
 * Jan Schulz
 * Jason Goad
 * Jason Gors
 * Jason Grout
 * Jason Newton
 * jdavidheiser
 * Jean-Christophe Jaskula
 * Jeff Hemmelgarn
 * Jeffrey Bush
 * Jeroen Demeyer
 * Jessica B. Hamrick
 * Jessica Frazelle
 * jhemmelg
 * Jim Garrison
 * Joel Nothman
 * Johannes Feist
 * John Stowers
 * John Zwinck
 * jonasc
 * Jonathan Frederic
 * Juergen Hasch
 * Julia Evans
 * Justyna Ilczuk
 * Jörg Dietrich
 * K.-Michael Aye
 * Kalibri
 * Kester Tong
 * Kyle Kelley
 * Kyle Rawlins
 * Lev Abalkin
 * Manuel Riel
 * Martin Bergtholdt
 * Martin Spacek
 * Mateusz Paprocki
 * Mathieu
 * Matthias Bussonnier
 * Maximilian Albert
 * mbyt
 * MechCoder
 * Mohan Raj Rajamanickam
 * mvr
 * Narahari
 * Nathan Goldbaum
 * Nathan Heijermans
 * Nathaniel J. Smith
 * ncornette
 * Nicholas Bollweg
 * Nick White
 * Nikolay Koldunov
 * Nile Geisinger
 * Olga Botvinnik
 * Osada Paranaliyanage
 * Pankaj Pandey
 * Pascal Bugnion
 * patricktokeeffe
 * Paul Ivanov
 * Peter Odding
 * Peter Parente
 * Peter Würtz
 * Phil Elson
 * Phillip Nordwall
 * Pierre Gerold
 * Pierre Haessig
 * Raffaele De Feo
 * Ramiro Gómez
 * Reggie Pierce
 * Remi Rampin
 * Renaud Richardet
 * Richard Everson
 * Scott Sanderson
 * Silvia Vinyes
 * Simon Guillot
 * Spencer Nelson
 * Stefan Zimmermann
 * Steve Chan
 * Steven Anton
 * Steven Silvester
 * sunny
 * Susan Tan
 * Sylvain Corlay
 * Tarun Gaba
 * Thomas Ballinger
 * Thomas Kluyver
 * Thomas Robitaille
 * Thomas Spura
 * Tobias Oberstein
 * Torsten Bittner
 * unknown
 * v923z
 * vaibhavsagar
 * W. Trevor King
 * weichm
 * Xiuming Chen
 * Yaroslav Halchenko
 * zah

docs/source/whatsnew/version3.rst

@@ -1,322 +1,349 b''
 ============
  3.x Series
 ============
 
+IPython 3.1
+===========
+
+Released April 3, 2015
+
+The first 3.x bugfix release, with 33 contributors and 344 commits.
+This primarily includes bugfixes to notebook layout and focus problems.
+
+
+Highlights:
+
+- Various focus jumping and scrolling fixes in the notebook.
+- Various message ordering and widget fixes in the notebook.
+- Images in markdown and output are confined to the notebook width.
+  An `.unconfined` CSS class is added to disable this behavior per-image.
+  The resize handle on output images is removed.
+- Improved ordering of tooltip content for Python functions, putting the signature at the top.
+- Fix UnicodeErrors when displaying some objects with unicode reprs on Python 2.
+- Set the kernel's working directory to the notebook directory when running ``nbconvert --execute``,
+  so that behavior matches the live notebook.
+- Allow setting custom SSL options for the tornado server with ``NotebookApp.ssl_options``,
+  and protect against POODLE with default settings by disabling SSLv3.
+- Fix memory leak in the IPython.parallel Controller on Python 3.
+
+
+See :ref:`issues_list_3` for details.
+
 
 Release 3.0
 ===========
 
 Released February 27, 2015
 
 This is a really big release. Over 150 contributors, and almost 6000 commits in a bit under a year.
 Support for languages other than Python is greatly improved,
 notebook UI has been significantly redesigned,
 and a lot of improvement has happened in the experimental interactive widgets.
 The message protocol and document format have both been updated,
 while maintaining better compatibility with previous versions than prior updates.
 The notebook webapp now enables editing of any text file, and even
 a web-based terminal (on Unix platforms).
 
 3.x will be the last monolithic release of IPython,
 as the next release cycle will see the growing project split into its Python-specific and language-agnostic components.
 Language-agnostic projects (notebook, qtconsole, etc.) will move under the umbrella of the new Project Jupyter name,
 while Python-specific projects (interactive Python shell, Python kernel, IPython.parallel)
 will remain under IPython, and be split into a few smaller packages.
 To reflect this, IPython is in a bit of a transition state.
 The logo on the notebook is now the Jupyter logo.
 When installing kernels system-wide, they go in a `jupyter` directory.
 We are going to do our best to ease this transition for users and developers.
 
 Big changes are ahead.
 
 
 Using different kernels
 -----------------------
 
 .. image:: ../_images/kernel_selector_screenshot.png
    :alt: Screenshot of 'new' dropdown showing different kernels
    :align: center
 
 You can now choose a kernel for a notebook within the user interface, rather
 than starting up a separate notebook server for each kernel you want to use. The
 syntax highlighting adapts to match the language you're working in.
 
 Information about the kernel is stored in the notebook file, so when you open a
 notebook, it will automatically start the correct kernel.
 
 It is also easier to use the Qt console and the terminal console with other
 kernels, using the --kernel flag::
 
     ipython qtconsole --kernel bash
     ipython console --kernel bash
 
     # To list available kernels
     ipython kernelspec list
 
 Kernel authors should see :ref:`kernelspecs` for how to register their kernels
 with IPython so that these mechanisms work.
 
 Typing unicode identifiers
 --------------------------
 
 .. image:: /_images/unicode_completion.png
 
 Complex expressions can be much cleaner when written with a wider choice of
 characters. Python 3 allows unicode identifiers, and IPython 3 makes it easier
 to type those, using a feature from Julia. Type a backslash followed by a LaTeX
 style short name, such as ``\alpha``. Press tab, and it will turn into α.
 
 Widget migration guide
 ----------------------
 The widget framework has a lot of backwards incompatible changes.
 For information about migrating widget notebooks and custom widgets to 3.0 refer
 to the :doc:`widget migration guide<version3_widget_migration>`.
 
 Other new features
 ------------------
 
 * :class:`~.TextWidget` and :class:`~.TextareaWidget` objects now include a
   ``placeholder`` attribute, for displaying placeholder text before the
   user has typed anything.
 
 * The :magic:`load` magic can now find the source for objects in the user namespace.
   To enable searching the namespace, use the ``-n`` option.
 
   .. sourcecode:: ipython
 
       In [1]: %load -n my_module.some_function
 
 * :class:`~.DirectView` objects have a new :meth:`~.DirectView.use_cloudpickle`
   method, which works like ``view.use_dill()``, but causes the ``cloudpickle``
   module from PiCloud's `cloud`__ library to be used rather than dill or the
   builtin pickle module.
 
   __ https://pypi.python.org/pypi/cloud
 
 * Added a .ipynb exporter to nbconvert.  It can be used by passing `--to notebook`
   as a commandline argument to nbconvert.
 
 * New nbconvert preprocessor called :class:`~.ClearOutputPreprocessor`. This
   clears the output from IPython notebooks.
 
 * New preprocessor for nbconvert that executes all the code cells in a notebook.
   To run a notebook and save its output in a new notebook::
 
       ipython nbconvert InputNotebook --ExecutePreprocessor.enabled=True --to notebook --output Executed
 
 * Consecutive stream (stdout/stderr) output is merged into a single output
   in the notebook document.
   Previously, all output messages were preserved as separate output fields in the JSON.
   Now, the same merge is applied to the stored output as the displayed output,
   improving document load time for notebooks with many small outputs.
 
 * ``NotebookApp.webapp_settings`` is deprecated and replaced with
   the more informatively named ``NotebookApp.tornado_settings``.
 
 * Using :magic:`timeit` prints warnings if there is atleast a 4x difference in timings
   between the slowest and fastest runs, since this might meant that the multiple
   runs are not independent of one another.
 
 * It's now possible to provide mechanisms to integrate IPython with other event
   loops, in addition to the ones we already support. This lets you run GUI code
   in IPython with an interactive prompt, and to embed the IPython
   kernel in GUI applications. See :doc:`/config/eventloops` for details. As part
   of this, the direct ``enable_*`` and ``disable_*`` functions for various GUIs
   in :mod:`IPython.lib.inputhook` have been deprecated in favour of
   :meth:`~.InputHookManager.enable_gui` and :meth:`~.InputHookManager.disable_gui`.
 
 * A ``ScrollManager`` was added to the notebook.  The ``ScrollManager`` controls how the notebook document is scrolled using keyboard.  Users can inherit from the ``ScrollManager`` or ``TargetScrollManager`` to customize how their notebook scrolls.  The default ``ScrollManager`` is the ``SlideScrollManager``, which tries to scroll to the nearest slide or sub-slide cell.
 
 * The function :func:`~IPython.html.widgets.interaction.interact_manual` has been
   added which behaves similarly to :func:`~IPython.html.widgets.interaction.interact`,
   but adds a button to explicitly run the interacted-with function, rather than
   doing it automatically for every change of the parameter widgets. This should
   be useful for long-running functions.
 
 * The ``%cython`` magic is now part of the Cython module. Use `%load_ext Cython` with a version of Cython >= 0.21 to have access to the magic now.
 
 * The Notebook application now offers integrated terminals on Unix platforms,
   intended for when it is used on a remote server. To enable these, install
   the ``terminado`` Python package.
 
 * The Notebook application can now edit any plain text files, via a full-page CodeMirror instance.
 
 * Setting the default highlighting language for nbconvert with the config option
   ``NbConvertBase.default_language`` is deprecated. Nbconvert now respects
   metadata stored in the :ref:`kernel spec <kernelspecs>`.
 
 * IPython can now be configured systemwide, with files in :file:`/etc/ipython`
   or :file:`/usr/local/etc/ipython` on Unix systems,
   or :file:`{%PROGRAMDATA%}\\ipython` on Windows.
 
 * Added support for configurable user-supplied `Jinja
   <http://jinja.pocoo.org/>`_ HTML templates for the notebook.  Paths to
   directories containing template files can be specified via
   ``NotebookApp.extra_template_paths``.  User-supplied template directories
   searched first by the notebook, making it possible to replace existing
   templates with your own files.
 
   For example, to replace the notebook's built-in ``error.html`` with your own,
   create a directory like ``/home/my_templates`` and put your override template
   at ``/home/my_templates/error.html``.  To start the notebook with your custom
   error page enabled, you would run::
 
       ipython notebook '--extra_template_paths=["/home/my_templates/"]'
 
   It's also possible to override a template while also `inheriting
   <http://jinja.pocoo.org/docs/dev/templates/#template-inheritance>`_ from that
   template, by prepending ``templates/`` to the ``{% extends %}`` target of
   your child template.  This is useful when you only want to override a
   specific block of a template.  For example, to add additional CSS to the
   built-in ``error.html``, you might create an override that looks like::
 
     {% extends "templates/error.html" %}
 
     {% block stylesheet %}
     {{super()}}
     <style type="text/css">
       /* My Awesome CSS */
     </style>
     {% endblock %}
 
 * Added a widget persistence API.  This allows you to persist your notebooks interactive widgets.
   Two levels of control are provided:
   1. Higher level- ``WidgetManager.set_state_callbacks`` allows you to register callbacks for loading and saving widget state.  The callbacks you register are automatically called when necessary.
   2. Lower level- the ``WidgetManager`` Javascript class now has ``get_state`` and ``set_state`` methods that allow you to get and set the state of the widget runtime.
 
   Example code for persisting your widget state to session data::
 
     %%javascript
     require(['widgets/js/manager'], function(manager) {
         manager.WidgetManager.set_state_callbacks(function() { // Load
             return JSON.parse(sessionStorage.widgets_state || '{}');
         }, function(state) { // Save
             sessionStorage.widgets_state = JSON.stringify(state);
         });
     });
 
 * Enhanced support for :magic:`env` magic.  As before, :magic:`env` with no
   arguments displays all environment variables and values.  Additionally,
   :magic:`env` can be used to get or set individual environment variables. To
   display an individual value, use the `%env var` syntax. To set a value, use
   `env var val` or `env var=val`. Python value expansion using `$` works as usual.
 
 
 Backwards incompatible changes
 ------------------------------
 
 * The :ref:`message protocol <messaging>` has been updated from version 4 to version 5.
   Adapters are included, so IPython frontends can still talk to kernels that
   implement protocol version 4.
 
 * The :ref:`notebook format <nbformat>` has been updated from version 3 to version 4.
   Read-only support for v4 notebooks has been backported to IPython 2.4.
   Notable changes:
   
   * heading cells are removed in favor or markdown headings
   * notebook outputs and output messages are more consistent with each other
   * use :func:`IPython.nbformat.read` and :func:`~IPython.nbformat.write`
     to read and write notebook files
     instead of the deprecated :mod:`IPython.nbformat.current` APIs.
 
   You can downgrade a notebook to v3 via ``nbconvert``::
   
       ipython nbconvert --to notebook --nbformat 3 <notebook>
   
   which will create :file:`notebook.v3.ipynb`, a copy of the notebook in v3 format.
 
 * :func:`IPython.core.oinspect.getsource` call specification has changed:
 
   * `oname` keyword argument has been added for property source formatting
   * `is_binary` keyword argument has been dropped, passing ``True`` had
     previously short-circuited the function to return ``None`` unconditionally
 
 * Removed the octavemagic extension: it is now available as ``oct2py.ipython``.
 
 * Creating PDFs with LaTeX no longer uses a post processor.
   Use `nbconvert --to pdf` instead of `nbconvert --to latex --post pdf`.
 
 * Used https://github.com/jdfreder/bootstrap2to3 to migrate the Notebook to Bootstrap 3.
 
   Additional changes:
 
   - Set `.tab-content .row` `0px;` left and right margin (bootstrap default is `-15px;`)
   - Removed `height: @btn_mini_height;` from `.list_header>div, .list_item>div` in `tree.less`
   - Set `#header` div `margin-bottom: 0px;`
   - Set `#menus` to `float: left;`
   - Set `#maintoolbar .navbar-text` to `float: none;`
   - Added no-padding convenience class.
   - Set border of #maintoolbar to 0px
 
 * Accessing the `container` DOM object when displaying javascript has been
   deprecated in IPython 2.0 in favor of accessing `element`. Starting with
   IPython 3.0 trying to access `container` will raise an error in browser
   javascript console.
 
 * ``IPython.utils.py3compat.open`` was removed: :func:`io.open` provides all
   the same functionality.
 
 * The NotebookManager and ``/api/notebooks`` service has been replaced by
   a more generic ContentsManager and ``/api/contents`` service,
   which supports all kinds of files.
 * The Dashboard now lists all files, not just notebooks and directories.
 * The ``--script`` hook for saving notebooks to Python scripts is removed,
   use :samp:`ipython nbconvert --to python {notebook}` instead.
 
 * The ``rmagic`` extension is deprecated, as it is now part of rpy2. See
   :mod:`rpy2.ipython.rmagic`.
 
 * :meth:`~.KernelManager.start_kernel` and :meth:`~.KernelManager.format_kernel_cmd`
   no longer accept a ``executable`` parameter. Use the kernelspec machinery instead.
 
 * The widget classes have been renamed from `*Widget` to `*`.  The old names are
   still functional, but are deprecated.  i.e. `IntSliderWidget` has been renamed
   to `IntSlider`.
 * The ContainerWidget was renamed to Box and no longer defaults as a flexible
   box in the web browser.  A new FlexBox widget was added, which allows you to
   use the flexible box model.
 
 * The notebook now uses a single websocket at `/kernels/<kernel-id>/channels` instead of separate
   `/kernels/<kernel-id>/{shell|iopub|stdin}` channels. Messages on each channel are identified by a
   `channel` key in the message dict, for both send and recv.
 
 
 Content Security Policy
 ```````````````````````
 
 The Content Security Policy is a web standard for adding a layer of security to
 detect and mitigate certain classes of attacks, including Cross Site Scripting
 (XSS) and data injection attacks. This was introduced into the notebook to
 ensure that the IPython Notebook and its APIs (by default) can only be embedded
 in an iframe on the same origin.
 
 Override ``headers['Content-Security-Policy']`` within your notebook
 configuration to extend for alternate domains and security settings.::
 
     c.NotebookApp.tornado_settings = {
         'headers': {
             'Content-Security-Policy': "frame-ancestors 'self'"
         }
     }
 
 Example policies::
 
     Content-Security-Policy: default-src 'self' https://*.jupyter.org
 
 Matches embeddings on any subdomain of jupyter.org, so long as they are served
 over SSL.
 
 There is a `report-uri <https://developer.mozilla.org/en-US/docs/Web/Security/CSP/CSP_policy_directives#report-uri>`_ endpoint available for logging CSP violations, located at
 ``/api/security/csp-report``. To use it, set ``report-uri`` as part of the CSP::
 
     c.NotebookApp.tornado_settings = {
         'headers': {
             'Content-Security-Policy': "frame-ancestors 'self'; report-uri /api/security/csp-report"
         }
     }
 
 It simply provides the CSP report as a warning in IPython's logs. The default
 CSP sets this report-uri relative to the ``base_url`` (not shown above).
 
 For a more thorough and accurate guide on Content Security Policies, check out
 `MDN's Using Content Security Policy <https://developer.mozilla.org/en-US/docs/Web/Security/CSP/Using_Content_Security_Policy>`_ for more examples.