Merge pull request #9668 from Carreau/more-docs

One more pass on the docs.

docs/source/conf.py

@@ -1,284 +1,284 b''
 # -*- coding: utf-8 -*-
 #
 # IPython documentation build configuration file.
 
 # NOTE: This file has been edited manually from the auto-generated one from
 # sphinx.  Do NOT delete and re-generate.  If any changes from sphinx are
 # needed, generate a scratch one and merge by hand any new fields needed.
 
 #
 # This file is execfile()d with the current directory set to its containing dir.
 #
 # The contents of this file are pickled, so don't put values in the namespace
 # that aren't pickleable (module imports are okay, they're removed automatically).
 #
 # All configuration values have a default value; values that are commented out
 # serve to show the default value.
 
 import sys, os
 
 ON_RTD = os.environ.get('READTHEDOCS', None) == 'True'
 
 if ON_RTD:
     # Mock the presence of matplotlib, which we don't have on RTD
     # see
     # http://read-the-docs.readthedocs.io/en/latest/faq.html
     tags.add('rtd')
 
     # RTD doesn't use the Makefile, so re-run autogen_{things}.py here.
     for name in ('config', 'api', 'magics'):
         fname = 'autogen_{}.py'.format(name)
         fpath = os.path.abspath(os.path.join('..', fname))
         with open(fpath) as f:
             exec(compile(f.read(), fname, 'exec'), {
                 '__file__': fpath,
                 '__name__': '__main__',
             })
 else:
     import sphinx_rtd_theme
     html_theme = "sphinx_rtd_theme"
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # If your extensions are in another directory, add it here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../sphinxext'))
 
 # We load the ipython release info into a dict by explicit execution
 iprelease = {}
 exec(compile(open('../../IPython/core/release.py').read(), '../../IPython/core/release.py', 'exec'),iprelease)
 
 # General configuration
 # ---------------------
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
     'matplotlib.sphinxext.mathmpl',
     'matplotlib.sphinxext.only_directives',
     'matplotlib.sphinxext.plot_directive',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.doctest',
     'sphinx.ext.inheritance_diagram',
     'sphinx.ext.intersphinx',
     'IPython.sphinxext.ipython_console_highlighting',
     'IPython.sphinxext.ipython_directive',
     'sphinx.ext.napoleon',  # to preprocess docstrings
     'github',  # for easy GitHub links
     'magics',
 ]
 
 if ON_RTD:
     # Remove extensions not currently supported on RTD
     extensions.remove('matplotlib.sphinxext.only_directives')
     extensions.remove('matplotlib.sphinxext.mathmpl')
     extensions.remove('matplotlib.sphinxext.plot_directive')
     extensions.remove('IPython.sphinxext.ipython_directive')
     extensions.remove('IPython.sphinxext.ipython_console_highlighting')
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # The suffix of source filenames.
 source_suffix = '.rst'
 
 def is_stable(extra):
     for ext in {'dev', 'b', 'rc'}:
         if ext in extra:
             return False
     return True
 
 if is_stable(iprelease['_version_extra']):
     tags.add('ipystable')
 else:
     tags.add('ipydev')
     rst_prolog = """
     .. warning::
 
         This documentation is for a development version of IPython. There may be
         significant differences from the latest stable release.
 
     """
 
 # The master toctree document.
 master_doc = 'index'
 
 # General substitutions.
 project = 'IPython'
 copyright = 'The IPython Development Team'
 
 # ghissue config
 github_project_url = "https://github.com/ipython/ipython"
 
 # numpydoc config
 numpydoc_show_class_members = False # Otherwise Sphinx emits thousands of warnings
 numpydoc_class_members_toctree = False
 
 # The default replacements for |version| and |release|, also used in various
 # other places throughout the built documents.
 #
 # The full version, including alpha/beta/rc tags.
 release = "%s" % iprelease['version']
 # Just the X.Y.Z part, no '-dev'
 version = iprelease['version'].split('-', 1)[0]
 
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 #today = ''
 # Else, today_fmt is used as the format for a strftime call.
 today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
 #unused_docs = []
 
 # Exclude these glob-style patterns when looking for source files. They are
 # relative to the source/ directory.
 exclude_patterns = ['whatsnew/pr']
 
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
 #add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
 #add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # Set the default role so we can use `foo` instead of ``foo``
 default_role = 'literal'
 
 # Options for HTML output
 # -----------------------
 
 # The style sheet to use for HTML and HTML Help pages. A file of that name
 # must exist either in Sphinx' static/ path, or in one of the custom paths
 # given in html_static_path.
 # html_style = 'default.css'
 
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 #html_title = None
 
 # The name of an image file (within the static path) to place at the top of
 # the sidebar.
 #html_logo = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
 # Favicon needs the directory name
 html_favicon = '_static/favicon.ico'
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
 html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
 html_additional_pages = {
     'interactive/htmlnotebook': 'notebook_redirect.html',
     'interactive/notebook': 'notebook_redirect.html',
     'interactive/nbconvert': 'notebook_redirect.html',
     'interactive/public_server': 'notebook_redirect.html',
 }
 
 # If false, no module index is generated.
 #html_use_modindex = True
 
 # If true, the reST sources are included in the HTML build as _sources/<name>.
 #html_copy_source = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
 #html_use_opensearch = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
 #html_file_suffix = ''
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'ipythondoc'
 
-intersphinx_mapping = {'python': ('http://docs.python.org/3/', None),
-                       'rpy2': ('http://rpy.sourceforge.net/rpy2/doc-2.4/html/', None),
-                       'traitlets': ('http://traitlets.readthedocs.io/en/latest/', None),
-                       'jupyterclient': ('http://jupyter-client.readthedocs.io/en/latest/', None),
-                       'ipyparallel': ('http://ipyparallel.readthedocs.io/en/latest/', None),
-                       'jupyter': ('http://jupyter.readthedocs.io/en/latest/', None),
+intersphinx_mapping = {'python': ('https://docs.python.org/3/', None),
+                       'rpy2': ('https://rpy2.readthedocs.io/en/version_2.8.x/', None),
+                       'traitlets': ('https://traitlets.readthedocs.io/en/latest/', None),
+                       'jupyterclient': ('https://jupyter-client.readthedocs.io/en/latest/', None),
+                       'ipyparallel': ('https://ipyparallel.readthedocs.io/en/latest/', None),
+                       'jupyter': ('https://jupyter.readthedocs.io/en/latest/', None),
                       }
 
 # Options for LaTeX output
 # ------------------------
 
 # The paper size ('letter' or 'a4').
 latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
 latex_font_size = '11pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class [howto/manual]).
 
 latex_documents = [
     ('index', 'ipython.tex', 'IPython Documentation',
      u"""The IPython Development Team""", 'manual', True),
     ('parallel/winhpc_index', 'winhpc_whitepaper.tex',
      'Using IPython on Windows HPC Server 2008',
      u"Brian E. Granger", 'manual', True)
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 #latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 #latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
 #latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
 #latex_appendices = []
 
 # If false, no module index is generated.
 latex_use_modindex = True
 
 
 # Options for texinfo output
 # --------------------------
 
 texinfo_documents = [
   (master_doc, 'ipython', 'IPython Documentation',
    'The IPython Development Team',
    'IPython',
    'IPython Documentation',
    'Programming',
    1),
 ]
 
 modindex_common_prefix = ['IPython.']
 
 
 # Cleanup
 # -------
 # delete release info to avoid pickling errors from sphinx
 
 del iprelease

docs/source/interactive/index.rst

@@ -1,19 +1,31 b''
 ==================================
 Using IPython for interactive work
 ==================================
 
+This section of IPython documentation walk you through most of the IPython
+functionality. You do not need to have any deep knowledge of Python to read this
+tutorial, though some section might make slightly more sens if you have already
+done some work in the REPL.
+
+.. note::
+    
+    Some part of this documentation are more than a decade old so might be out
+    of date, we welcome any report of inacuracy, and Pull Requests that make
+    that up to date.
+
 .. toctree::
    :maxdepth: 2
+   :hidden:
 
    tutorial
-   magics
    plotting
    reference
    shell
    tips
    python-ipython-diff
+   magics
 
 .. seealso::
 
     `A Qt Console for Jupyter <http://jupyter.org/qtconsole/>`__
     `The Jupyter Notebook <http://jupyter-notebook.readthedocs.io/en/latest/>`__

docs/source/interactive/magics.rst

@@ -1,5 +1,23 b''
 =======================
 Built-in magic commands
 =======================
 
+.. note::
+
+    To Jupyter users: Magics are specific to and provided by the IPython kernel.
+    Whether magics are available on a kernel is a decision that is made by
+    the kernel developer on a per-kernel basis. To work properly, Magics must
+    use a syntax element which is not valid in the underlying language. For
+    example, the IPython kernel uses the `%` syntax element for magics as `%`
+    is not a valid unary operator in Python. While, the syntax element has
+    meaning in other languages.
+
+Here is the help auto generated from the docstrings of all the available magics
+function that IPython ships with. 
+
+You can create an register your own magics with IPython. You can find many user
+defined magics on `PyPI <https://pypi.io>`_. Feel free to publish your own and
+use the ``Framework :: IPython`` trove classifier. 
+
+
 .. include:: magics-generated.txt

docs/source/interactive/plotting.rst

@@ -1,36 +1,42 b''
 .. _plotting:
 
 Plotting
 --------
 One major feature of the IPython kernel is the ability to display plots that 
 are the output of running code cells. The IPython kernel is designed to work 
 seamlessly with the matplotlib_ plotting library to provide this functionality.
 
-To set this up, before any plotting is performed you must execute the
-``%matplotlib``  :ref:`magic command <magics_explained>`. This performs the
-necessary behind-the-scenes setup for IPython to work correctly hand in hand
-with ``matplotlib``; it does *not*, however, actually execute any Python
-``import`` commands, that is, no names are added to the namespace.
+To set this up, before any plotting or import of matplotlib is performed you
+must execute the ``%matplotlib``  :ref:`magic command <magics_explained>`. This
+performs the necessary behind-the-scenes setup for IPython to work correctly
+hand in hand with ``matplotlib``; it does *not*, however, actually execute any
+Python ``import`` commands, that is, no names are added to the namespace.
 
 If the ``%matplotlib`` magic is called without an argument, the
 output of a plotting command is displayed using the default ``matplotlib``
 backend in a separate window. Alternatively, the backend can be explicitly
 requested using, for example::
 
   %matplotlib gtk
 
 A particularly interesting backend, provided by IPython, is the ``inline``
 backend.  This is available only for the Jupyter Notebook and the
 Jupyter QtConsole.  It can be invoked as follows::
 
   %matplotlib inline
 
-With this backend, the output of plotting commands is displayed *inline*
-within the notebook, directly below the code cell that produced it. The
-resulting plots will then also be stored in the notebook document.
+With this backend, the output of plotting commands is displayed *inline* within
+frontends like the Jupyter notebook, directly below the code cell that produced
+it. The resulting plots will then also be stored in the notebook document.
 
 .. seealso::
 
     `Plotting with Matplotlib`_  example notebook
 
+
+The matplotlib_ library also ships with ``%matplotlib notebook`` command that
+allows interactive figures if your environment allows it.
+
+See the matplotlib_ documentation for more information. 
+
 .. include:: ../links.txt

docs/source/interactive/reference.rst

@@ -1,1000 +1,1007 b''
 =================
 IPython reference
 =================
 
 .. _command_line_options:
 
 Command-line usage
 ==================
 
 You start IPython with the command::
 
     $ ipython [options] files
 
-If invoked with no options, it executes all the files listed in sequence
-and drops you into the interpreter while still acknowledging any options
-you may have set in your ipython_config.py. This behavior is different from
-standard Python, which when called as python -i will only execute one
-file and ignore your configuration setup.
-
-Please note that some of the configuration options are not available at
-the command line, simply because they are not practical here. Look into
-your configuration files for details on those. There are separate configuration
-files for each profile, and the files look like :file:`ipython_config.py` or
+If invoked with no options, it executes all the files listed in sequence and
+exits. If you add the ``-i`` flag, it drops you into the interpreter while still
+acknowledging any options you may have set in your ``ipython_config.py``. This
+behavior is different from standard Python, which when called as python ``-i``
+will only execute one file and ignore your configuration setup.
+
+Please note that some of the configuration options are not available at the
+command line, simply because they are not practical here. Look into your
+configuration files for details on those. There are separate configuration files
+for each profile, and the files look like :file:`ipython_config.py` or
 :file:`ipython_config_{frontendname}.py`.  Profile directories look like
-:file:`profile_{profilename}` and are typically installed in the :envvar:`IPYTHONDIR` directory,
-which defaults to :file:`$HOME/.ipython`. For Windows users, :envvar:`HOME`
-resolves to :file:`C:\\Users\\{YourUserName}` in most instances.
+:file:`profile_{profilename}` and are typically installed in the
+:envvar:`IPYTHONDIR` directory, which defaults to :file:`$HOME/.ipython`. For
+Windows users, :envvar:`HOME` resolves to :file:`C:\\Users\\{YourUserName}` in
+most instances.
 
 Command-line Options
 --------------------
 
 To see the options IPython accepts, use ``ipython --help`` (and you probably
 should run the output through a pager such as ``ipython --help | less`` for
 more convenient reading).  This shows all the options that have a single-word
 alias to control them, but IPython lets you configure all of its objects from
 the command-line by passing the full class name and a corresponding value; type
 ``ipython --help-all`` to see this full list.  For example::
 
-  ipython --matplotlib qt
+    $ ipython --help-all
+    <...snip...>
+    --matplotlib=<CaselessStrEnum> (InteractiveShellApp.matplotlib)
+        Default: None
+        Choices: ['auto', 'gtk', 'gtk3', 'inline', 'nbagg', 'notebook', 'osx', 'qt', 'qt4', 'qt5', 'tk', 'wx']
+        Configure matplotlib for interactive use with the default matplotlib
+        backend.
+    <...snip...>
+
+
+Indicate that the following::
+
+   $ ipython --matplotlib qt
+
 
 is equivalent to::
 
-  ipython --TerminalIPythonApp.matplotlib='qt'
+   $ ipython --TerminalIPythonApp.matplotlib='qt'
 
 Note that in the second form, you *must* use the equal sign, as the expression
 is evaluated as an actual Python assignment.  While in the above example the
 short form is more convenient, only the most common options have a short form,
 while any configurable variable in IPython can be set at the command-line by
 using the long form.  This long form is the same syntax used in the
 configuration files, if you want to set these options permanently.
 
 
 Interactive use
 ===============
 
 IPython is meant to work as a drop-in replacement for the standard interactive
 interpreter. As such, any code which is valid python should execute normally
 under IPython (cases where this is not true should be reported as bugs). It
 does, however, offer many features which are not available at a standard python
 prompt. What follows is a list of these.
 
 
 Caution for Windows users
 -------------------------
 
 Windows, unfortunately, uses the '\\' character as a path separator. This is a
 terrible choice, because '\\' also represents the escape character in most
 modern programming languages, including Python. For this reason, using '/'
 character is recommended if you have problems with ``\``.  However, in Windows
 commands '/' flags options, so you can not use it for the root directory. This
 means that paths beginning at the root must be typed in a contrived manner
 like: ``%copy \opt/foo/bar.txt \tmp``
 
 .. _magic:
 
 Magic command system
 --------------------
 
 IPython will treat any line whose first character is a % as a special
 call to a 'magic' function. These allow you to control the behavior of
 IPython itself, plus a lot of system-type features. They are all
 prefixed with a % character, but parameters are given without
 parentheses or quotes.
 
 Lines that begin with ``%%`` signal a *cell magic*: they take as arguments not
 only the rest of the current line, but all lines below them as well, in the
 current execution block.  Cell magics can in fact make arbitrary modifications
 to the input they receive, which need not even be valid Python code at all.
 They receive the whole block as a single string.
 
 As a line magic example, the :magic:`cd` magic works just like the OS command of
 the same name::
 
       In [8]: %cd
       /home/fperez
 
 The following uses the builtin :magic:`timeit` in cell mode::
 
   In [10]: %%timeit x = range(10000)
       ...: min(x)
       ...: max(x)
       ...:
   1000 loops, best of 3: 438 us per loop
 
 In this case, ``x = range(10000)`` is called as the line argument, and the
 block with ``min(x)`` and ``max(x)`` is called as the cell body.  The
 :magic:`timeit` magic receives both.
 
 If you have 'automagic' enabled (as it is by default), you don't need to type in
 the single ``%`` explicitly for line magics; IPython will scan its internal
 list of magic functions and call one if it exists. With automagic on you can
 then just type ``cd mydir`` to go to directory 'mydir'::
 
       In [9]: cd mydir
       /home/fperez/mydir
 
 Cell magics *always* require an explicit ``%%`` prefix, automagic
 calling only works for line magics.
 
 The automagic system has the lowest possible precedence in name searches, so
 you can freely use variables with the same names as magic commands. If a magic
 command is 'shadowed' by a variable, you will need the explicit ``%`` prefix to
 use it:
 
 .. sourcecode:: ipython
 
     In [1]: cd ipython     # %cd is called by automagic
     /home/fperez/ipython
 
     In [2]: cd=1 	   # now cd is just a variable
 
     In [3]: cd .. 	   # and doesn't work as a function anymore
     File "<ipython-input-3-9fedb3aff56c>", line 1
       cd ..
           ^
     SyntaxError: invalid syntax
 
 
     In [4]: %cd .. 	   # but %cd always works
     /home/fperez
 
     In [5]: del cd     # if you remove the cd variable, automagic works again
 
     In [6]: cd ipython
 
     /home/fperez/ipython
 
-Line magics, if they return a value, can be assigned to a variable using the syntax
-``l = %sx ls`` (which in this particular case returns the result of `ls` as a python list).
-See :ref:`below <manual_capture>` for more information.
+Line magics, if they return a value, can be assigned to a variable using the
+syntax ``l = %sx ls`` (which in this particular case returns the result of `ls`
+as a python list). See :ref:`below <manual_capture>` for more information.
 
 Type ``%magic`` for more information, including a list of all available magic
 functions at any time and their docstrings. You can also type
 ``%magic_function_name?`` (see :ref:`below <dynamic_object_info>` for
 information on the '?' system) to get information about any particular magic
 function you are interested in.
 
 The API documentation for the :mod:`IPython.core.magic` module contains the full
 docstrings of all currently available magic commands.
 
 .. seealso::
 
    :doc:`magics`
      A list of the line and cell magics available in IPython by default
 
    :ref:`defining_magics`
      How to define and register additional magic functions
 
 
 Access to the standard Python help
 ----------------------------------
 
 Simply type ``help()`` to access Python's standard help system. You can
 also type ``help(object)`` for information about a given object, or
 ``help('keyword')`` for information on a keyword. You may need to configure your
 PYTHONDOCS environment variable for this feature to work correctly.
 
 .. _dynamic_object_info:
 
 Dynamic object information
 --------------------------
 
 Typing ``?word`` or ``word?`` prints detailed information about an object. If
 certain strings in the object are too long (e.g. function signatures) they get
 snipped in the center for brevity. This system gives access variable types and
 values, docstrings, function prototypes and other useful information.
 
 If the information will not fit in the terminal, it is displayed in a pager
 (``less`` if available, otherwise a basic internal pager).
 
 Typing ``??word`` or ``word??`` gives access to the full information, including
 the source code where possible. Long strings are not snipped.
 
 The following magic functions are particularly useful for gathering
 information about your working environment:
 
     * :magic:`pdoc` **<object>**: Print (or run through a pager if too long) the
       docstring for an object. If the given object is a class, it will
       print both the class and the constructor docstrings.
     * :magic:`pdef` **<object>**: Print the call signature for any callable
       object. If the object is a class, print the constructor information.
     * :magic:`psource` **<object>**: Print (or run through a pager if too long)
       the source code for an object.
     * :magic:`pfile` **<object>**: Show the entire source file where an object was
       defined via a pager, opening it at the line where the object
       definition begins.
     * :magic:`who`/:magic:`whos`: These functions give information about identifiers
       you have defined interactively (not things you loaded or defined
       in your configuration files). %who just prints a list of
       identifiers and %whos prints a table with some basic details about
       each identifier.
 
 The dynamic object information functions (?/??, ``%pdoc``,
 ``%pfile``, ``%pdef``, ``%psource``) work on object attributes, as well as
 directly on variables. For example, after doing ``import os``, you can use
 ``os.path.abspath??``.
 
-.. _readline:
-
-Readline-based features
------------------------
-
-These features require the GNU readline library, so they won't work if your
-Python installation lacks readline support. We will first describe the default
-behavior IPython uses, and then how to change it to suit your preferences.
-
 
 Command line completion
 +++++++++++++++++++++++
 
 At any time, hitting TAB will complete any available python commands or
 variable names, and show you a list of the possible completions if
 there's no unambiguous one. It will also complete filenames in the
 current directory if no python names match what you've typed so far.
 
 
 Search command history
 ++++++++++++++++++++++
 
 IPython provides two ways for searching through previous input and thus
 reduce the need for repetitive typing:
 
    1. Start typing, and then use the up and down arrow keys (or :kbd:`Ctrl-p`
       and :kbd:`Ctrl-n`) to search through only the history items that match
       what you've typed so far.
    2. Hit :kbd:`Ctrl-r`: to open a search prompt. Begin typing and the system
       searches your history for lines that contain what you've typed so
       far, completing as much as it can.
 
 IPython will save your input history when it leaves and reload it next
 time you restart it. By default, the history file is named
 :file:`.ipython/profile_{name}/history.sqlite`.
 
 Autoindent
 ++++++++++
 
 Starting with 5.0, IPython uses `prompt_toolkit` in place of ``readline``,
 it thus can recognize lines ending in ':' and indent the next line,
 while also un-indenting automatically after 'raise' or 'return',
 and support real multi-line editing as well as syntactic coloration
 during edition.
 
 This feature does not use the ``readline`` library anymore, so it will
 not honor your :file:`~/.inputrc` configuration (or whatever
 file your :envvar:`INPUTRC` environment variable points to).
 
 In particular if you want to change the input mode to ``vi``, you will need to
 set the ``TerminalInteractiveShell.editing_mode`` configuration  option of IPython.
 
 Session logging and restoring
 -----------------------------
 
 You can log all input from a session either by starting IPython with the
 command line switch ``--logfile=foo.py`` (see :ref:`here <command_line_options>`)
 or by activating the logging at any moment with the magic function :magic:`logstart`.
 
 Log files can later be reloaded by running them as scripts and IPython
 will attempt to 'replay' the log by executing all the lines in it, thus
 restoring the state of a previous session. This feature is not quite
 perfect, but can still be useful in many cases.
 
 The log files can also be used as a way to have a permanent record of
 any code you wrote while experimenting. Log files are regular text files
 which you can later open in your favorite text editor to extract code or
 to 'clean them up' before using them to replay a session.
 
 The :magic:`logstart` function for activating logging in mid-session is used as
 follows::
 
     %logstart [log_name [log_mode]]
 
 If no name is given, it defaults to a file named 'ipython_log.py' in your
 current working directory, in 'rotate' mode (see below).
 
 '%logstart name' saves to file 'name' in 'backup' mode. It saves your
 history up to that point and then continues logging.
 
 %logstart takes a second optional parameter: logging mode. This can be
 one of (note that the modes are given unquoted):
 
     * [over:] overwrite existing log_name.
     * [backup:] rename (if exists) to log_name~ and start log_name.
     * [append:] well, that says it.
     * [rotate:] create rotating logs log_name.1~, log_name.2~, etc.
 
 The :magic:`logoff` and :magic:`logon` functions allow you to temporarily stop and
 resume logging to a file which had previously been started with
 %logstart. They will fail (with an explanation) if you try to use them
 before logging has been started.
 
 .. _system_shell_access:
 
 System shell access
 -------------------
 
-Any input line beginning with a ! character is passed verbatim (minus
-the !, of course) to the underlying operating system. For example,
+Any input line beginning with a ``!`` character is passed verbatim (minus
+the ``!``, of course) to the underlying operating system. For example,
 typing ``!ls`` will run 'ls' in the current directory.
 
 .. _manual_capture:
 
 Manual capture of command output and magic output
 -------------------------------------------------
 
 You can assign the result of a system command to a Python variable with the
 syntax ``myfiles = !ls``. Similarly, the result of a magic (as long as it returns
 a value) can be assigned to a variable.  For example, the syntax ``myfiles = %sx ls``
 is equivalent to the above system command example (the :magic:`sx` magic runs a shell command
 and captures the output).  Each of these gets machine
 readable output from stdout (e.g. without colours), and splits on newlines. To
 explicitly get this sort of output without assigning to a variable, use two
 exclamation marks (``!!ls``) or the :magic:`sx` magic command without an assignment.
 (However, ``!!`` commands cannot be assigned to a variable.)
 
 The captured list in this example has some convenience features. ``myfiles.n`` or ``myfiles.s``
 returns a string delimited by newlines or spaces, respectively. ``myfiles.p``
 produces `path objects <http://pypi.python.org/pypi/path.py>`_ from the list items.
 See :ref:`string_lists` for details.
 
 IPython also allows you to expand the value of python variables when
 making system calls. Wrap variables or expressions in {braces}::
 
     In [1]: pyvar = 'Hello world'
     In [2]: !echo "A python variable: {pyvar}"
     A python variable: Hello world
     In [3]: import math
     In [4]: x = 8
     In [5]: !echo {math.factorial(x)}
     40320
 
 For simple cases, you can alternatively prepend $ to a variable name::
 
     In [6]: !echo $sys.argv
     [/home/fperez/usr/bin/ipython]
     In [7]: !echo "A system variable: $$HOME"  # Use $$ for literal $
     A system variable: /home/fperez
 
 Note that `$$` is used to represent a literal `$`.
 
 System command aliases
 ----------------------
 
 The :magic:`alias` magic function allows you to define magic functions which are in fact
 system shell commands. These aliases can have parameters.
 
 ``%alias alias_name cmd`` defines 'alias_name' as an alias for 'cmd'
 
 Then, typing ``alias_name params`` will execute the system command 'cmd
 params' (from your underlying operating system).
 
-You can also define aliases with parameters using %s specifiers (one per
+You can also define aliases with parameters using ``%s`` specifiers (one per
 parameter). The following example defines the parts function as an
-alias to the command 'echo first %s second %s' where each %s will be
+alias to the command ``echo first %s second %s`` where each ``%s`` will be
 replaced by a positional parameter to the call to %parts::
 
     In [1]: %alias parts echo first %s second %s
     In [2]: parts A B
     first A second B
     In [3]: parts A
     ERROR: Alias <parts> requires 2 arguments, 1 given.
 
 If called with no parameters, :magic:`alias` prints the table of currently
 defined aliases.
 
 The :magic:`rehashx` magic allows you to load your entire $PATH as
 ipython aliases. See its docstring for further details.
 
 
 .. _dreload:
 
 Recursive reload
 ----------------
 
 The :mod:`IPython.lib.deepreload` module allows you to recursively reload a
 module: changes made to any of its dependencies will be reloaded without
 having to exit. To start using it, do::
 
     from IPython.lib.deepreload import reload as dreload
 
 
 Verbose and colored exception traceback printouts
 -------------------------------------------------
 
 IPython provides the option to see very detailed exception tracebacks,
 which can be especially useful when debugging large programs. You can
 run any Python file with the %run function to benefit from these
 detailed tracebacks. Furthermore, both normal and verbose tracebacks can
 be colored (if your terminal supports it) which makes them much easier
 to parse visually.
 
 See the magic :magic:`xmode` and :magic:`colors` functions for details.
 
 These features are basically a terminal version of Ka-Ping Yee's cgitb
 module, now part of the standard Python library.
 
 
 .. _input_caching:
 
 Input caching system
 --------------------
 
 IPython offers numbered prompts (In/Out) with input and output caching
 (also referred to as 'input history'). All input is saved and can be
 retrieved as variables (besides the usual arrow key recall), in
 addition to the :magic:`rep` magic command that brings a history entry
 up for editing on the next command line.
 
 The following variables always exist:
 
-* _i, _ii, _iii: store previous, next previous and next-next previous inputs.
-* In, _ih : a list of all inputs; _ih[n] is the input from line n. If you
-  overwrite In with a variable of your own, you can remake the assignment to the
-  internal list with a simple ``In=_ih``.
+* ``_i``, ``_ii``, ``_iii``: store previous, next previous and next-next
+  previous inputs.
+
+* ``In``, ``_ih`` : a list of all inputs; ``_ih[n]`` is the input from line
+  ``n``. If you overwrite In with a variable of your own, you can remake the
+  assignment to the internal list with a simple ``In=_ih``.
 
-Additionally, global variables named _i<n> are dynamically created (<n>
+Additionally, global variables named ``_i<n>`` are dynamically created (``<n>``
 being the prompt counter), so ``_i<n> == _ih[<n>] == In[<n>]``.
 
 For example, what you typed at prompt 14 is available as ``_i14``, ``_ih[14]``
 and ``In[14]``.
 
 This allows you to easily cut and paste multi line interactive prompts
 by printing them out: they print like a clean string, without prompt
 characters. You can also manipulate them like regular variables (they
 are strings), modify or exec them.
 
-You can also re-execute multiple lines of input easily by using the
-magic :magic:`rerun` or :magic:`macro` functions. The macro system also allows you to re-execute
-previous lines which include magic function calls (which require special
-processing). Type %macro? for more details on the macro system.
+You can also re-execute multiple lines of input easily by using the magic
+:magic:`rerun` or :magic:`macro` functions. The macro system also allows you to
+re-execute previous lines which include magic function calls (which require
+special processing). Type %macro? for more details on the macro system.
 
 A history function :magic:`history` allows you to see any part of your input
 history by printing a range of the _i variables.
 
 You can also search ('grep') through your history by typing
 ``%hist -g somestring``. This is handy for searching for URLs, IP addresses,
 etc. You can bring history entries listed by '%hist -g' up for editing
 with the %recall command, or run them immediately with :magic:`rerun`.
 
 .. _output_caching:
 
 Output caching system
 ---------------------
 
 For output that is returned from actions, a system similar to the input
 cache exists but using _ instead of _i. Only actions that produce a
 result (NOT assignments, for example) are cached. If you are familiar
 with Mathematica, IPython's _ variables behave exactly like
 Mathematica's % variables.
 
 The following variables always exist:
 
     * [_] (a single underscore): stores previous output, like Python's
       default interpreter.
     * [__] (two underscores): next previous.
     * [___] (three underscores): next-next previous.
 
 Additionally, global variables named _<n> are dynamically created (<n>
 being the prompt counter), such that the result of output <n> is always
 available as _<n> (don't use the angle brackets, just the number, e.g.
 ``_21``).
 
 These variables are also stored in a global dictionary (not a
 list, since it only has entries for lines which returned a result)
 available under the names _oh and Out (similar to _ih and In). So the
 output from line 12 can be obtained as ``_12``, ``Out[12]`` or ``_oh[12]``. If you
 accidentally overwrite the Out variable you can recover it by typing
 ``Out=_oh`` at the prompt.
 
 This system obviously can potentially put heavy memory demands on your
 system, since it prevents Python's garbage collector from removing any
 previously computed results. You can control how many results are kept
 in memory with the configuration option ``InteractiveShell.cache_size``.
 If you set it to 0, output caching is disabled. You can also use the :magic:`reset`
 and :magic:`xdel` magics to clear large items from memory.
 
 Directory history
 -----------------
 
 Your history of visited directories is kept in the global list _dh, and
 the magic :magic:`cd` command can be used to go to any entry in that list. The
 :magic:`dhist` command allows you to view this history. Do ``cd -<TAB>`` to
 conveniently view the directory history.
 
 
 Automatic parentheses and quotes
 --------------------------------
 
 These features were adapted from Nathan Gray's LazyPython. They are
 meant to allow less typing for common situations.
 
 Callable objects (i.e. functions, methods, etc) can be invoked like this
 (notice the commas between the arguments)::
 
     In [1]: callable_ob arg1, arg2, arg3
     ------> callable_ob(arg1, arg2, arg3)
 
 .. note::
    This feature is disabled by default. To enable it, use the ``%autocall``
    magic command. The commands below with special prefixes will always work,
    however.
 
 You can force automatic parentheses by using '/' as the first character
 of a line. For example::
 
     In [2]: /globals # becomes 'globals()'
 
 Note that the '/' MUST be the first character on the line! This won't work::
 
     In [3]: print /globals # syntax error
 
 In most cases the automatic algorithm should work, so you should rarely
 need to explicitly invoke /. One notable exception is if you are trying
 to call a function with a list of tuples as arguments (the parenthesis
 will confuse IPython)::
 
     In [4]: zip (1,2,3),(4,5,6) # won't work
 
 but this will work::
 
     In [5]: /zip (1,2,3),(4,5,6)
     ------> zip ((1,2,3),(4,5,6))
     Out[5]: [(1, 4), (2, 5), (3, 6)]
 
 IPython tells you that it has altered your command line by displaying
 the new command line preceded by ``--->``.
 
 You can force automatic quoting of a function's arguments by using ``,``
 or ``;`` as the first character of a line. For example::
 
     In [1]: ,my_function /home/me  # becomes my_function("/home/me")
 
 If you use ';' the whole argument is quoted as a single string, while ',' splits
 on whitespace::
 
     In [2]: ,my_function a b c    # becomes my_function("a","b","c")
 
     In [3]: ;my_function a b c    # becomes my_function("a b c")
 
 Note that the ',' or ';' MUST be the first character on the line! This
 won't work::
 
     In [4]: x = ,my_function /home/me # syntax error
 
 IPython as your default Python environment
 ==========================================
 
 Python honors the environment variable :envvar:`PYTHONSTARTUP` and will
 execute at startup the file referenced by this variable. If you put the
 following code at the end of that file, then IPython will be your working
 environment anytime you start Python::
 
     import os, IPython
     os.environ['PYTHONSTARTUP'] = ''  # Prevent running this again
     IPython.start_ipython()
     raise SystemExit
 
 The ``raise SystemExit`` is needed to exit Python when
 it finishes, otherwise you'll be back at the normal Python ``>>>``
 prompt.
 
 This is probably useful to developers who manage multiple Python
 versions and don't want to have correspondingly multiple IPython
 versions. Note that in this mode, there is no way to pass IPython any
 command-line options, as those are trapped first by Python itself.
 
 .. _Embedding:
 
 Embedding IPython
 =================
 
 You can start a regular IPython session with
 
 .. sourcecode:: python
 
     import IPython
     IPython.start_ipython(argv=[])
 
 at any point in your program.  This will load IPython configuration,
 startup files, and everything, just as if it were a normal IPython session.
 
 It is also possible to embed an IPython shell in a namespace in your Python code.
 This allows you to evaluate dynamically the state of your code,
 operate with your variables, analyze them, etc. Note however that
 any changes you make to values while in the shell do not propagate back
 to the running code, so it is safe to modify your values because you
 won't break your code in bizarre ways by doing so.
 
 .. note::
 
   At present, embedding IPython cannot be done from inside IPython.
   Run the code samples below outside IPython.
 
 This feature allows you to easily have a fully functional python
 environment for doing object introspection anywhere in your code with a
 simple function call. In some cases a simple print statement is enough,
 but if you need to do more detailed analysis of a code fragment this
 feature can be very valuable.
 
 It can also be useful in scientific computing situations where it is
 common to need to do some automatic, computationally intensive part and
 then stop to look at data, plots, etc.
 Opening an IPython instance will give you full access to your data and
 functions, and you can resume program execution once you are done with
 the interactive part (perhaps to stop again later, as many times as
 needed).
 
 The following code snippet is the bare minimum you need to include in
 your Python programs for this to work (detailed examples follow later)::
 
     from IPython import embed
 
     embed() # this call anywhere in your program will start IPython
 
 You can also embed an IPython *kernel*, for use with qtconsole, etc. via
 ``IPython.embed_kernel()``. This should function work the same way, but you can
 connect an external frontend (``ipython qtconsole`` or ``ipython console``),
 rather than interacting with it in the terminal.
 
 You can run embedded instances even in code which is itself being run at
 the IPython interactive prompt with '%run <filename>'. Since it's easy
 to get lost as to where you are (in your top-level IPython or in your
 embedded one), it's a good idea in such cases to set the in/out prompts
 to something different for the embedded instances. The code examples
 below illustrate this.
 
 You can also have multiple IPython instances in your program and open
 them separately, for example with different options for data
 presentation. If you close and open the same instance multiple times,
 its prompt counters simply continue from each execution to the next.
 
 Please look at the docstrings in the :mod:`~IPython.frontend.terminal.embed`
 module for more details on the use of this system.
 
 The following sample file illustrating how to use the embedding
 functionality is provided in the examples directory as embed_class_long.py.
 It should be fairly self-explanatory:
 
 .. literalinclude:: ../../../examples/Embedding/embed_class_long.py
     :language: python
 
 Once you understand how the system functions, you can use the following
 code fragments in your programs which are ready for cut and paste:
 
 .. literalinclude:: ../../../examples/Embedding/embed_class_short.py
     :language: python
 
 Using the Python debugger (pdb)
 ===============================
 
 Running entire programs via pdb
 -------------------------------
 
 pdb, the Python debugger, is a powerful interactive debugger which
 allows you to step through code, set breakpoints, watch variables,
 etc.  IPython makes it very easy to start any script under the control
 of pdb, regardless of whether you have wrapped it into a 'main()'
 function or not. For this, simply type ``%run -d myscript`` at an
 IPython prompt. See the :magic:`run` command's documentation for more details, including
 how to control where pdb will stop execution first.
 
 For more information on the use of the pdb debugger, see :ref:`debugger-commands`
 in the Python documentation.
 
 IPython extends the debugger with a few useful additions, like coloring of
 tracebacks. The debugger will adopt the color scheme selected for IPython.
 
 The ``where`` command has also been extended to take as argument the number of
 context line to show. This allows to a many line of context on shallow stack trace:
 
 .. code::
 
     In [5]: def foo(x):
     ...:     1
     ...:     2
     ...:     3
     ...:     return 1/x+foo(x-1)
     ...:     5
     ...:     6
     ...:     7
     ...:
 
     In[6]: foo(1)
     # ...
     ipdb> where 8
     <ipython-input-6-9e45007b2b59>(1)<module>()
     ----> 1 foo(1)
 
     <ipython-input-5-7baadc3d1465>(5)foo()
         1 def foo(x):
         2     1
         3     2
         4     3
     ----> 5     return 1/x+foo(x-1)
         6     5
         7     6
         8     7
 
     > <ipython-input-5-7baadc3d1465>(5)foo()
         1 def foo(x):
         2     1
         3     2
         4     3
     ----> 5     return 1/x+foo(x-1)
         6     5
         7     6
         8     7
 
 
 And less context on shallower Stack Trace:
 
 .. code::
 
     ipdb> where 1
     <ipython-input-13-afa180a57233>(1)<module>()
     ----> 1 foo(7)
 
     <ipython-input-5-7baadc3d1465>(5)foo()
     ----> 5     return 1/x+foo(x-1)
 
     <ipython-input-5-7baadc3d1465>(5)foo()
     ----> 5     return 1/x+foo(x-1)
 
     <ipython-input-5-7baadc3d1465>(5)foo()
     ----> 5     return 1/x+foo(x-1)
 
     <ipython-input-5-7baadc3d1465>(5)foo()
     ----> 5     return 1/x+foo(x-1)
 
 
 Post-mortem debugging
 ---------------------
 
 Going into a debugger when an exception occurs can be
 extremely useful in order to find the origin of subtle bugs, because pdb
 opens up at the point in your code which triggered the exception, and
 while your program is at this point 'dead', all the data is still
 available and you can walk up and down the stack frame and understand
 the origin of the problem.
 
 You can use the :magic:`debug` magic after an exception has occurred to start
 post-mortem debugging. IPython can also call debugger every time your code
 triggers an uncaught exception. This feature can be toggled with the :magic:`pdb` magic
 command, or you can start IPython with the ``--pdb`` option.
 
 For a post-mortem debugger in your programs outside IPython,
 put the following lines toward the top of your 'main' routine::
 
     import sys
     from IPython.core import ultratb
     sys.excepthook = ultratb.FormattedTB(mode='Verbose',
     color_scheme='Linux', call_pdb=1)
 
 The mode keyword can be either 'Verbose' or 'Plain', giving either very
 detailed or normal tracebacks respectively. The color_scheme keyword can
 be one of 'NoColor', 'Linux' (default) or 'LightBG'. These are the same
 options which can be set in IPython with ``--colors`` and ``--xmode``.
 
 This will give any of your programs detailed, colored tracebacks with
 automatic invocation of pdb.
 
 .. _pasting_with_prompts:
 
 Pasting of code starting with Python or IPython prompts
 =======================================================
 
 IPython is smart enough to filter out input prompts, be they plain Python ones
 (``>>>`` and ``...``) or IPython ones (``In [N]:`` and ``...:``).  You can
 therefore copy and paste from existing interactive sessions without worry.
 
 The following is a 'screenshot' of how things work, copying an example from the
 standard Python tutorial::
 
     In [1]: >>> # Fibonacci series:
 
     In [2]: ... # the sum of two elements defines the next
 
     In [3]: ... a, b = 0, 1
 
     In [4]: >>> while b < 10:
        ...:     ...     print(b)
        ...:     ...     a, b = b, a+b
        ...:
     1
     1
     2
     3
     5
     8
 
 And pasting from IPython sessions works equally well::
 
     In [1]: In [5]: def f(x):
        ...:        ...:     "A simple function"
        ...:        ...:     return x**2
        ...:    ...:
 
     In [2]: f(3)
     Out[2]: 9
 
 .. _gui_support:
 
 GUI event loop support
 ======================
 
 .. versionadded:: 0.11
     The ``%gui`` magic and :mod:`IPython.lib.inputhook`.
 
 IPython has excellent support for working interactively with Graphical User
 Interface (GUI) toolkits, such as wxPython, PyQt4/PySide, PyGTK and Tk. This is
 implemented using Python's builtin ``PyOSInputHook`` hook. This implementation
 is extremely robust compared to our previous thread-based version. The
 advantages of this are:
 
 * GUIs can be enabled and disabled dynamically at runtime.
 * The active GUI can be switched dynamically at runtime.
 * In some cases, multiple GUIs can run simultaneously with no problems.
 * There is a developer API in :mod:`IPython.lib.inputhook` for customizing
   all of these things.
 
 For users, enabling GUI event loop integration is simple.  You simple use the
 :magic:`gui` magic as follows::
 
     %gui [GUINAME]
 
 With no arguments, ``%gui`` removes all GUI support.  Valid ``GUINAME``
 arguments are ``wx``, ``qt``, ``gtk`` and ``tk``.
 
 Thus, to use wxPython interactively and create a running :class:`wx.App`
 object, do::
 
     %gui wx
 
 You can also start IPython with an event loop set up using the `--gui`
 flag::
 
     $ ipython --gui=qt
 
 For information on IPython's matplotlib_ integration (and the ``matplotlib``
 mode) see :ref:`this section <matplotlib_support>`.
 
 For developers that want to use IPython's GUI event loop integration in the
 form of a library, these capabilities are exposed in library form in the
 :mod:`IPython.lib.inputhook` and :mod:`IPython.lib.guisupport` modules.
 Interested developers should see the module docstrings for more information,
 but there are a few points that should be mentioned here.
 
 First, the ``PyOSInputHook`` approach only works in command line settings
 where readline is activated.  The integration with various eventloops
 is handled somewhat differently (and more simply) when using the standalone
 kernel, as in the qtconsole and notebook.
 
 Second, when using the ``PyOSInputHook`` approach, a GUI application should
 *not* start its event loop. Instead all of this is handled by the
 ``PyOSInputHook``. This means that applications that are meant to be used both
 in IPython and as standalone apps need to have special code to detects how the
 application is being run. We highly recommend using IPython's support for this.
 Since the details vary slightly between toolkits, we point you to the various
 examples in our source directory :file:`examples/Embedding` that demonstrate
 these capabilities.
 
 Third, unlike previous versions of IPython, we no longer "hijack" (replace
 them with no-ops) the event loops. This is done to allow applications that
 actually need to run the real event loops to do so. This is often needed to
 process pending events at critical points.
 
 Finally, we also have a number of examples in our source directory
 :file:`examples/Embedding` that demonstrate these capabilities.
 
 PyQt and PySide
 ---------------
 
 .. attempt at explanation of the complete mess that is Qt support
 
 When you use ``--gui=qt`` or ``--matplotlib=qt``, IPython can work with either
 PyQt4 or PySide.  There are three options for configuration here, because
 PyQt4 has two APIs for QString and QVariant: v1, which is the default on
 Python 2, and the more natural v2, which is the only API supported by PySide.
 v2 is also the default for PyQt4 on Python 3.  IPython's code for the QtConsole
 uses v2, but you can still use any interface in your code, since the
 Qt frontend is in a different process.
 
 The default will be to import PyQt4 without configuration of the APIs, thus
 matching what most applications would expect. It will fall back to PySide if
 PyQt4 is unavailable.
 
 If specified, IPython will respect the environment variable ``QT_API`` used
 by ETS.  ETS 4.0 also works with both PyQt4 and PySide, but it requires
 PyQt4 to use its v2 API.  So if ``QT_API=pyside`` PySide will be used,
 and if ``QT_API=pyqt`` then PyQt4 will be used *with the v2 API* for
 QString and QVariant, so ETS codes like MayaVi will also work with IPython.
 
 If you launch IPython in matplotlib mode with ``ipython --matplotlib=qt``,
 then IPython will ask matplotlib which Qt library to use (only if QT_API is
 *not set*), via the 'backend.qt4' rcParam.  If matplotlib is version 1.0.1 or
 older, then IPython will always use PyQt4 without setting the v2 APIs, since
 neither v2 PyQt nor PySide work.
 
 .. warning::
 
     Note that this means for ETS 4 to work with PyQt4, ``QT_API`` *must* be set
     to work with IPython's qt integration, because otherwise PyQt4 will be
     loaded in an incompatible mode.
 
     It also means that you must *not* have ``QT_API`` set if you want to
     use ``--gui=qt`` with code that requires PyQt4 API v1.
 
 
 .. _matplotlib_support:
 
 Plotting with matplotlib
 ========================
 
 matplotlib_ provides high quality 2D and 3D plotting for Python. matplotlib_
 can produce plots on screen using a variety of GUI toolkits, including Tk,
 PyGTK, PyQt4 and wxPython. It also provides a number of commands useful for
 scientific computing, all with a syntax compatible with that of the popular
 Matlab program.
 
 To start IPython with matplotlib support, use the ``--matplotlib`` switch. If
 IPython is already running, you can run the :magic:`matplotlib` magic.  If no
 arguments are given, IPython will automatically detect your choice of
 matplotlib backend.  You can also request a specific backend with
 ``%matplotlib backend``, where ``backend`` must be one of: 'tk', 'qt', 'wx',
 'gtk', 'osx'.  In the web notebook and Qt console, 'inline' is also a valid
 backend value, which produces static figures inlined inside the application
 window instead of matplotlib's interactive figures that live in separate
 windows.
 
 .. _interactive_demos:
 
 Interactive demos with IPython
 ==============================
 
 IPython ships with a basic system for running scripts interactively in
 sections, useful when presenting code to audiences. A few tags embedded
 in comments (so that the script remains valid Python code) divide a file
 into separate blocks, and the demo can be run one block at a time, with
 IPython printing (with syntax highlighting) the block before executing
 it, and returning to the interactive prompt after each block. The
 interactive namespace is updated after each block is run with the
 contents of the demo's namespace.
 
 This allows you to show a piece of code, run it and then execute
 interactively commands based on the variables just created. Once you
 want to continue, you simply execute the next block of the demo. The
 following listing shows the markup necessary for dividing a script into
 sections for execution as a demo:
 
 .. literalinclude:: ../../../examples/IPython Kernel/example-demo.py
     :language: python
 
 In order to run a file as a demo, you must first make a Demo object out
 of it. If the file is named myscript.py, the following code will make a
 demo::
 
     from IPython.lib.demo import Demo
 
     mydemo = Demo('myscript.py')
 
 This creates the mydemo object, whose blocks you run one at a time by
 simply calling the object with no arguments. Then call it to run each step
 of the demo::
 
     mydemo()
 
 Demo objects can be
 restarted, you can move forward or back skipping blocks, re-execute the
 last block, etc. See the :mod:`IPython.lib.demo` module and the
 :class:`~IPython.lib.demo.Demo` class for details.
 
 Limitations: These demos are limited to
 fairly simple uses. In particular, you cannot break up sections within
 indented code (loops, if statements, function definitions, etc.)
 Supporting something like this would basically require tracking the
 internal execution state of the Python interpreter, so only top-level
 divisions are allowed. If you want to be able to open an IPython
 instance at an arbitrary point in a program, you can use IPython's
 :ref:`embedding facilities <Embedding>`.
 
 .. include:: ../links.txt

docs/source/interactive/tutorial.rst

@@ -1,205 +1,216 b''
 .. _tutorial:
 
 ======================
 Introducing IPython
 ======================
 
 You don't need to know anything beyond Python to start using IPython – just type
 commands as you would at the standard Python prompt. But IPython can do much
 more than the standard prompt. Some key features are described here. For more
 information, check the :ref:`tips page <tips>`, or look at examples in the
 `IPython cookbook <https://github.com/ipython/ipython/wiki/Cookbook%3A-Index>`_.
 
 If you've never used Python before, you might want to look at `the official
 tutorial <http://docs.python.org/tutorial/>`_ or an alternative, `Dive into
 Python <http://diveintopython.net/toc/index.html>`_.
 
 The four most helpful commands 
 ===============================
 
 The four most helpful commands, as well as their brief description, is shown
 to you in a banner, every time you start IPython:
 
 ==========    =========================================================
 command       description
 ==========    =========================================================
 ?             Introduction and overview of IPython's features.
 %quickref     Quick reference.
 help          Python's own help system.
 object?       Details about 'object', use 'object??' for extra details.
 ==========    =========================================================
 
 Tab completion
 ==============
 
 Tab completion, especially for attributes, is a convenient way to explore the
 structure of any object you're dealing with. Simply type ``object_name.<TAB>``
-to view the object's attributes (see :ref:`the readline section <readline>` for
-more). Besides Python objects and keywords, tab completion also works on file
-and directory names.
+to view the object's attributes. Besides Python objects and keywords, tab
+completion also works on file and directory names.
 
 Exploring your objects
 ======================
 
 Typing ``object_name?`` will print all sorts of details about any object,
 including docstrings, function definition lines (for call arguments) and
 constructor details for classes. To get specific information on an object, you
 can use the magic commands ``%pdoc``, ``%pdef``, ``%psource`` and ``%pfile``
 
 .. _magics_explained:
 
 Magic functions
 ===============
 
 IPython has a set of predefined 'magic functions' that you can call with a
 command line style syntax.  There are two kinds of magics, line-oriented and
-cell-oriented.  **Line magics** are prefixed with the ``%`` character and work much
-like OS command-line calls: they get as an argument the rest of the line, where
-arguments are passed without parentheses or quotes.  **Cell magics** are
-prefixed with a double ``%%``, and they are functions that get as an argument
-not only the rest of the line, but also the lines below it in a separate
-argument.
+cell-oriented.  **Line magics** are prefixed with the ``%`` character and work
+much like OS command-line calls: they get as an argument the rest of the line,
+where arguments are passed without parentheses or quotes. **Lines magics** can
+return results and can be used in the right hand side of an assignment.  **Cell
+magics** are prefixed with a double ``%%``, and they are functions that get as
+an argument not only the rest of the line, but also the lines below it in a
+separate argument.
 
-The following examples show how to call the builtin :magic:`timeit` magic, both in
-line and cell mode::
+Magics are useful as convenient functions where Python syntax is not the most
+natural one, or when one want to embed invalid python syntax in their work flow. 
+
+The following examples show how to call the builtin :magic:`timeit` magic, both
+in line and cell mode::
 
       In [1]: %timeit range(1000)
       100000 loops, best of 3: 7.76 us per loop
 
       In [2]: %%timeit x = range(10000)
 	 ...: max(x)
 	 ...: 
       1000 loops, best of 3: 223 us per loop
 
 The builtin magics include:
 
-- Functions that work with code: :magic:`run`, :magic:`edit`, :magic:`save`, :magic:`macro`,
-  :magic:`recall`, etc.
-- Functions which affect the shell: :magic:`colors`, :magic:`xmode`, :magic:`autoindent`,
-  :magic:`automagic`, etc.
-- Other functions such as :magic:`reset`, :magic:`timeit`, :cellmagic:`writefile`, :magic:`load`, or
-  :magic:`paste`.
+- Functions that work with code: :magic:`run`, :magic:`edit`, :magic:`save`,
+  :magic:`macro`, :magic:`recall`, etc.
+
+- Functions which affect the shell: :magic:`colors`, :magic:`xmode`,
+  :magic:`autoindent`, :magic:`automagic`, etc.
+
+- Other functions such as :magic:`reset`, :magic:`timeit`,
+  :cellmagic:`writefile`, :magic:`load`, or :magic:`paste`.
 
-You can always call them using the ``%`` prefix, and if you're calling a line
-magic on a line by itself, you can omit even that::
+You can always call magics using the ``%`` prefix, and if you're calling a line
+magic on a line by itself, as long as the identifier is not defined in your
+namespace, you can omit even that::
 
     run thescript.py
 
-You can toggle this behavior by running the :magic:`automagic` magic.  Cell magics
-must always have the ``%%`` prefix.
+You can toggle this behavior by running the :magic:`automagic` magic.  Cell
+magics must always have the ``%%`` prefix.
 
 A more detailed explanation of the magic system can be obtained by calling
 ``%magic``, and for more details on any magic function, call ``%somemagic?`` to
 read its docstring. To see all the available magic functions, call
 ``%lsmagic``.
 
 .. seealso::
 
-    :doc:`magics`
+    The :ref:`magic` section of the documentation goes more in depth into how
+    the magics works and how to define your own, and :doc:`magics` for a list of
+    built-in magics.
 
     `Cell magics`_ example notebook
 
 Running and Editing
 -------------------
 
-The :magic:`run` magic command allows you to run any python script and load all of
-its data directly into the interactive namespace. Since the file is re-read
+The :magic:`run` magic command allows you to run any python script and load all
+of its data directly into the interactive namespace. Since the file is re-read
 from disk each time, changes you make to it are reflected immediately (unlike
-imported modules, which have to be specifically reloaded). IPython also
-includes :ref:`dreload <dreload>`, a recursive reload function.
+imported modules, which have to be specifically reloaded). IPython also includes
+:ref:`dreload <dreload>`, a recursive reload function.
 
 ``%run`` has special flags for timing the execution of your scripts (-t), or
 for running them under the control of either Python's pdb debugger (-d) or
 profiler (-p).
 
 The :magic:`edit` command gives a reasonable approximation of multiline editing,
 by invoking your favorite editor on the spot. IPython will execute the
-code you type in there as if it were typed interactively.
+code you type in there as if it were typed interactively. Note that for
+:magic:`edit` to work, the call to startup your editor has to be a blocking
+call. In a GUI environment, your editor likely will have such an option.
 
 Debugging
 ---------
 
 After an exception occurs, you can call :magic:`debug` to jump into the Python
 debugger (pdb) and examine the problem. Alternatively, if you call :magic:`pdb`,
 IPython will automatically start the debugger on any uncaught exception. You can
-print variables, see code, execute statements and even walk up and down the
-call stack to track down the true source of the problem. This can be an efficient
-way to develop and debug code, in many cases eliminating the need for print
+print variables, see code, execute statements and even walk up and down the call
+stack to track down the true source of the problem. This can be an efficient way
+to develop and debug code, in many cases eliminating the need for print
 statements or external debugging tools.
 
 You can also step through a program from the beginning by calling
 ``%run -d theprogram.py``.
 
 History
 =======
 
 IPython stores both the commands you enter, and the results it produces. You
 can easily go through previous commands with the up- and down-arrow keys, or
 access your history in more sophisticated ways.
 
 Input and output history are kept in variables called ``In`` and ``Out``, keyed
 by the prompt numbers, e.g. ``In[4]``. The last three objects in output history
 are also kept in variables named ``_``, ``__`` and ``___``.
 
 You can use the ``%history`` magic function to examine past input and output.
 Input history from previous sessions is saved in a database, and IPython can be
 configured to save output history.
 
 Several other magic functions can use your input history, including ``%edit``, 
 ``%rerun``, ``%recall``, ``%macro``, ``%save`` and ``%pastebin``. You can use a
 standard format to refer to lines::
 
     %pastebin 3 18-20 ~1/1-5
     
 This will take line 3 and lines 18 to 20 from the current session, and lines
 1-5 from the previous session.
 
 System shell commands
 =====================
 
-To run any command at the system shell, simply prefix it with !, e.g.::
+To run any command at the system shell, simply prefix it with ``!``, e.g.::
 
     !ping www.bbc.co.uk
     
 You can capture the output into a Python list, e.g.: ``files = !ls``. To pass
 the values of Python variables or expressions to system commands, prefix them
 with $: ``!grep -rF $pattern ipython/*``. See :ref:`our shell section
 <system_shell_access>` for more details.
 
 Define your own system aliases
 ------------------------------
 
-It's convenient to have aliases to the system commands you use most often.
-This allows you to work seamlessly from inside IPython with the same commands
-you are used to in your system shell. IPython comes with some pre-defined
-aliases and a complete system for changing directories, both via a stack (see
-:magic:`pushd`, :magic:`popd` and :magic:`dhist`) and via direct :magic:`cd`. The latter keeps a history of
-visited directories and allows you to go to any previously visited one.
+It's convenient to have aliases to the system commands you use most often. This
+allows you to work seamlessly from inside IPython with the same commands you are
+used to in your system shell. IPython comes with some pre-defined aliases and a
+complete system for changing directories, both via a stack (see :magic:`pushd`,
+:magic:`popd` and :magic:`dhist`) and via direct :magic:`cd`. The latter keeps a
+history of visited directories and allows you to go to any previously visited
+one.
 
 
 Configuration
 =============
 
 Much of IPython can be tweaked through :doc:`configuration </config/intro>`.
 To get started, use the command ``ipython profile create`` to produce the
 default config files. These will be placed in
 :file:`~/.ipython/profile_default`, and contain comments explaining
 what the various options do.
 
 Profiles allow you to use IPython for different tasks, keeping separate config
 files and history for each one. More details in :ref:`the profiles section
 <profiles>`.
 
 .. _startup_files:
 
 Startup Files
 -------------
 
 If you want some code to be run at the beginning of every IPython session, the
 easiest way is to add Python (.py) or IPython (.ipy) scripts to your
 :file:`profile_default/startup/` directory. Files here will be executed as soon
 as the IPython shell is constructed, before any other code or scripts you have
 specified. The files will be run in order of their names, so you can control the
 ordering with prefixes, like ``10-myimports.py``.
 
 .. include:: ../links.txt