notebook docs touchup

closes  #3902

incorporating doc changes from David Sanders, minor revisions my own

-@ivanov

docs/source/interactive/nbconvert.rst

@@ -1,212 +1,212
 .. _nbconvert:
 
 Converting notebooks to other formats
 =====================================
 
 Newly added in the 1.0 release of IPython is the ``nbconvert`` tool, which 
 allows you to convert an ``.ipynb`` notebook document file into various static 
 formats. 
 
 Currently, ``nbconvert`` is provided as a command line tool, run as a script 
 using IPython. A direct export capability from within the 
 IPython Notebook web app is planned. 
 
 The command-line syntax to run the ``nbconvert`` script is::
 
   $ ipython nbconvert --to FORMAT notebook.ipynb
 
 This will convert the IPython document file ``notebook.ipynb`` into the output 
 format given by the ``FORMAT`` string.
 
 The default output format is html, for which the ``--to`` argument may be 
 omitted::
   
   $ ipython nbconvert notebook.ipynb
 
 IPython provides a few templates for some output formats, and these can be
 specified via an additional ``--template`` argument.
 
 The currently supported export formats are:
 
 * ``--to html``
 
   - ``--template full`` (default)
   
     A full static HTML render of the notebook.
     This looks very similar to the interactive view.
 
   - ``--template basic``
   
     Simplified HTML, useful for embedding in webpages, blogs, etc.
     This excludes HTML headers.
 
 * ``--to latex``
 
   Latex export.  This generates ``NOTEBOOK_NAME.tex`` file,
   ready for export.  You can automatically run latex on it to generate a PDF
   by adding ``--post PDF``.
   
   - ``--template article`` (default)
   
     Latex article, derived from Sphinx's howto template.
 
   - ``--template book``
   
     Latex book, derived from Sphinx's manual template.
 
   - ``--template basic``
   
     Very basic latex output - mainly meant as a starting point for custom templates.
 
 * ``--to slides``
 
   This generates a Reveal.js HTML slideshow.
   It must be served by an HTTP server.  The easiest way to get this is to add
   ``--post serve`` on the command-line.
 
 * ``--to markdown``
 
   Simple markdown output.  Markdown cells are unaffected,
-  and code cells are placed in triple-backtick (``\`\`\```) blocks.
+  and code cells are placed in triple-backtick (```````) blocks.
 
 * ``--to rst``
 
   Basic reStructuredText output. Useful as a starting point for embedding notebooks
   in Sphinx docs.
 
 * ``--to python``
 
   Convert a notebook to an executable Python script.
   This is the simplest way to get a Python script out of a notebook.
   If there were any magics in the notebook, this may only be executable from
   an IPython session.
   
 .. note::
 
   nbconvert uses pandoc_ to convert between various markup languages,
   so pandoc is a dependency of most nbconvert transforms,
   excluding Markdown and Python.
 
 .. _pandoc: http://johnmacfarlane.net/pandoc/
 
 The output file created by ``nbconvert`` will have the same base name as
 the notebook and will be placed in the current working directory. Any
 supporting files (graphics, etc) will be placed in a new directory with the
 same base name as the notebook, suffixed with ``_files``::
 
   $ ipython nbconvert notebook.ipynb
   $ ls
   notebook.ipynb   notebook.html    notebook_files/
 
 For simple single-file output, such as html, markdown, etc.,
 the output may be sent to standard output with::
     
   $ ipython nbconvert --to markdown notebook.ipynb --stdout
     
 Multiple notebooks can be specified from the command line::
     
   $ ipython nbconvert notebook*.ipynb
   $ ipython nbconvert notebook1.ipynb notebook2.ipynb
     
 or via a list in a configuration file, say ``mycfg.py``, containing the text::
 
   c = get_config()
   c.NbConvertApp.notebooks = ["notebook1.ipynb", "notebook2.ipynb"]
 
 and using the command::
 
   $ ipython nbconvert --config mycfg.py
 
 
 .. _notebook_format:
 
 Notebook JSON file format
 -------------------------
 
 Notebook documents are JSON files with an ``.ipynb`` extension, formatted
 as legibly as possible with minimal extra indentation and cell content broken
 across lines to make them reasonably friendly to use in version-control
 workflows.  You should be very careful if you ever manually edit this JSON
 data, as it is extremely easy to corrupt its internal structure and make the
 file impossible to load.  In general, you should consider the notebook as a
 file meant only to be edited by the IPython Notebook app itself, not for 
 hand-editing.
 
 .. note::
 
      Binary data such as figures are also saved directly in the JSON file.  
      This provides convenient single-file portability, but means that the 
      files can be large; a ``diff`` of binary data is also not very 
      meaningful.  Since the binary blobs are encoded in a single line, they 
      affect only one line of the ``diff`` output, but they are typically very 
      long lines.  You can use the ``Cell | All Output | Clear`` menu option to 
      remove all output from a notebook prior to committing it to version 
      control, if this is a concern.
 
 The notebook server can also generate a pure Python version of your notebook, 
 using the ``File | Download as`` menu option. The resulting ``.py`` file will 
 contain all the code cells from your notebook verbatim, and all Markdown cells 
 prepended with a comment marker.  The separation between code and Markdown
 cells is indicated with special comments and there is a header indicating the
 format version.  All output is removed when exporting to Python.
 
 As an example, consider a simple notebook called ``simple.ipynb`` which 
 contains one Markdown cell, with the content ``The simplest notebook.``, one 
 code input cell with the content ``print "Hello, IPython!"``, and the 
 corresponding output.
 
 The contents of the notebook document ``simple.ipynb`` is the following JSON 
 container::
 
   {
    "metadata": {
     "name": "simple"
    },
    "nbformat": 3,
    "nbformat_minor": 0,
    "worksheets": [
     {
      "cells": [
       {
        "cell_type": "markdown",
        "metadata": {},
        "source": "The simplest notebook."
       },
       {
        "cell_type": "code",
        "collapsed": false,
        "input": "print \"Hello, IPython\"",
        "language": "python",
        "metadata": {},
        "outputs": [
         {
          "output_type": "stream",
          "stream": "stdout",
          "text": "Hello, IPython\n"
         }
        ],
        "prompt_number": 1
       }
      ],
      "metadata": {}
     }
    ]
   }
 
 
 The corresponding Python script is::
 
   # -*- coding: utf-8 -*-
   # <nbformat>3.0</nbformat>
 
   # <markdowncell>
 
   # The simplest notebook.
 
   # <codecell>
 
   print "Hello, IPython"
 
 Note that indeed the output of the code cell, which is present in the JSON 
 container, has been removed in the ``.py`` script.
 

docs/source/interactive/notebook.rst

@@ -1,581 +1,590
 .. _htmlnotebook:
 
 The IPython Notebook
 ====================
 
 The IPython Notebook is part of the IPython package, which aims to provide a 
 powerful, interactive approach to scientific computation.
 The IPython Notebook extends the previous text-console-based approach, and the 
 later Qt console, in a qualitatively new diretion, providing a web-based
 application suitable for capturing the whole scientific computation process.
 
 .. seealso::
 
     :ref:`Installation requirements <installnotebook>` for the Notebook.
 
 
 .. Basic structure
 .. ---------------
 
 Introduction
 ------------
 
 The IPython Notebook combines two components:
 
 * **The IPython Notebook web application**:
 
       The *IPython Notebook web app* is a browser-based tool for interactive 
       authoring of literate computations, in which explanatory text, 
       mathematics, computations and rich media output may be combined. Input 
       and output are stored in persistent cells that may be edited in-place.
 
 * **Notebook documents**:
 
       *Notebook documents*, or *notebooks*, are plain text documents which 
       record all inputs and outputs of the computations, interspersed with 
       text, mathematics and HTML 5 representations of objects, in a literate 
       style.
 
 Since the similarity in names can lead to some confusion, in this 
 documentation we will  use capitalization of the word "notebook" to 
 distinguish the Notebook app and notebook documents, thinking of the 
 Notebook app as being a proper noun. We will also always refer to the 
 "Notebook app" when we are referring to the browser-based interface, 
 and usually to "notebook documents", instead of "notebooks", for added
 precision.
 
 We refer to the current state of the computational process taking place in the 
 Notebook app, i.e. the (numbered) sequence of input and output cells, as the 
 *notebook space*. Notebook documents provide an *exact*, *one-to-one* record 
 of all the content in the notebook space, as a plain text file in JSON format. 
 The Notebook app automatically saves, at certain intervals, the contents of 
 the notebook space to a notebook document stored on disk, with the same name 
 as the title of the notebook space, and the file extension ``.ipynb``. For 
 this reason, there is no confusion about using the same word "notebook" for 
 both the notebook space and the corresponding notebook document, since they are 
 really one and the same concept (we could say that they are "isomorphic").
 
 
 Main features of the IPython Notebook web app
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The main features of the IPython Notebook app include:
 
 * In-browser editing for code, with automatic syntax highlighting and 
   indentation and tab completion/introspection.
 
 * Literate combination of code with rich text using the Markdown_ markup 
   language.
 
 * Mathematics is easily included within the Markdown using LaTeX notation, and 
   rendered natively by MathJax_.
 
 * Displays rich data representations (e.g. HTML / LaTeX / SVG) as the result 
   of computations.
 
 * Publication-quality figures in a range of formats (SVG / PNG), rendered by 
   the matplotlib_ library, may be included inline and exported.
 
 
 .. _MathJax: http://www.mathjax.org/
 .. _matplotlib: http://matplotlib.org/
 .. _Markdown: http://daringfireball.net/projects/markdown/syntax
 
 
 Notebook documents
 ~~~~~~~~~~~~~~~~~~
 
 Notebook document files are simple JSON_ files with the 
 extension ``.ipynb``.
 Since JSON is just plain text, they can be easily version-controlled and shared with colleagues.
 The notebook stores a *complete*, *reproducible*, *one-to-one* copy of the state of the
 computational state as it is inside the Notebook app. All computations
 carried out, and the corresponding results obtained, can be combined in
 a literate way, interleaving executable code with rich text, mathematics, 
 and rich representations of objects.
 
 .. _JSON: http://en.wikipedia.org/wiki/JSON
 
 Notebooks may easily be exported to a range of static formats, including 
 HTML (for example, for blog posts), PDF and slide shows, 
 via the new nbconvert_ command.
 
 Furthermore, any  ``.ipynb`` notebook document available from a public 
 URL can be shared via the `IPython Notebook Viewer <nbviewer>`_ service.
-This service loads the notebook document from the URL and will 
-render it as a static web page. The results may thus be shared with a 
+This service loads the notebook document from the URL and renders
+it as a static web page. The results may thus be shared with a 
 colleague, or as a public blog post, without other users needing to install 
-IPython themselves.  NbViewer is simply NbConvert as a simple heroku webservice.
+IPython themselves.  NbViewer is simply nbconvert_ as a simple webservice.
 
 See the :ref:`installation documentation <install_index>` for directions on
 how to install the notebook and its dependencies.
 
+.. _nbconvert: ./nbconvert.html
+
 .. _nbviewer: http://nbviewer.ipython.org
 
 .. note::
 
    You can start more than one notebook server at the same time, if you want 
    to work on notebooks in different directories.  By default the first 
    notebook server starts on port 8888, and later notebook servers search for  
    ports near that one.  You can also manually specify the port with the 
    ``--port`` option.
    
 
 Basic workflow in the IPython Notebook web app
 ----------------------------------------------
 
 Starting up
 ~~~~~~~~~~~~
 
 You can start running the Notebook web app using the following command::
 
     $ ipython notebook
 
 (Here, and in the sequel, the initial ``$`` represents the shell prompt, 
 indicating that the command is to be run from the command line in a shell.)
 
 The landing page of the IPython Notebook application, the *dashboard*, shows 
 the notebooks currently available in the *notebook directory* (By default, the directory 
 from which the notebook was started).
 You can create new notebooks from the dashboard with the ``New Notebook``
 button, or open existing ones by clicking on their name.
 You can also drag and drop ``.ipynb`` notebooks and standard ``.py`` Python 
 source code files into the notebook list area.
 
 
 You can open an existing notebook directly, without having to go via the 
-dashboard, with:
+dashboard, with::
 
   ipython notebook my_notebook
 
-The `.ipynb` extension is assumed if no extension is given.
+The ``.ipynb`` extension is assumed if no extension is given.
 
 The `File | Open...` menu option will open the dashboard in a new browser tab, 
 to allow you to select a current notebook 
 from the notebook directory or to create a new notebook.
 
 
 
 Notebook user interface
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 When you open a new notebook document in the Notebook, you will be presented 
 with the title associated to the notebook space/document, a *menu bar*, a 
 *toolbar* and an empty *input cell*.
 
 Notebook title
 ^^^^^^^^^^^^^^
 The title of the notebook document that is currently being edited is displayed 
 at the top of the page, next to the ``IP[y]: Notebook`` logo. This title may 
 be edited directly by clicking on it. The title is reflected in the name of 
 the ``.ipynb`` notebook document file that is saved.
 
 Menu bar
 ^^^^^^^^
 The menu bar presents different options that may be used to manipulate the way 
 the Notebook functions.
 
 Toolbar
 ^^^^^^^
 The tool bar gives a quick way of accessing the most-used operations within 
 the Notebook, by clicking on an icon.
 
 
 Creating a new notebook document
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 A new notebook space/document may be created at any time, either from the 
 dashboard, or using the `File | New` menu option from within an active 
 notebook. The new notebook is created within the same directory and 
 will open in a new browser tab. It will also be reflected as a new entry in 
 the notebook list on the dashboard.
 
 
 Structure of a notebook document
 --------------------------------
 
 Input cells
 ~~~~~~~~~~~
 Input cells are at the core of the functionality of the IPython Notebook.
 They are regions in the document in which you can enter different types of 
 text and commands. To *execute* or *run* the *current cell*, i.e. the cell 
 under the cursor, you can use the :kbd:`Shift-Enter` key combination. 
 This tells the Notebook app to perform the relevant operation for each type of 
 cell (see below), and then to display the resulting output.
 
 The notebook consists of a sequence of input cells, labelled ``In[n]``, which 
 may be executed in a non-linear way, and outputs ``Out[n]``, where ``n`` is a 
 number which denotes the order in which the cells were executed over the 
 history of the computational process. The contents of all of these cells are 
 accessible as Python variables with the same names, forming a complete record 
 of the history of the computation.
 
 
 
 Input cell types
 ~~~~~~~~~~~~~~~~
 Each IPython input cell has a *cell type*, of which there is a restricted 
 number. The type of a cell may be set by using the cell type dropdown on the 
 toolbar, or via the following keyboard shortcuts:
 
 * **code**: :kbd:`Ctrl-m y`
 * **markdown**: :kbd:`Ctrl-m m`
 * **raw**: :kbd:`Ctrl-m t`
 * **heading**: :kbd:`Ctrl-m 1` - :kbd:`Ctrl-m 6`
 
 Upon initial creation, each input cell is by default a code cell.
 
 
 Code cells
 ^^^^^^^^^^
 A *code input cell* allows you to edit code inline within the cell, with full 
 syntax highlighting and autocompletion/introspection. By default, the language 
 associated to a code cell is Python, but other languages, such as ``julia`` 
 and ``R``, can be handled using magic commands (see below).
 
 When a code cell is executed with :kbd:`Shift-Enter`, the code that it 
 contains is transparently exported and run in that language (with automatic 
 compiling, etc., if necessary). The result that is returned from this 
 computation  is then displayed in the notebook space as the cell's 
 *output*. If this output is of a textual nature, it is placed into a 
 numbered *output cell*. However, many other possible forms of output are also 
 possible, including ``matplotlib`` figures and HTML tables (as used, for 
 example, in the ``pandas`` data analyis package). This is known as IPython's 
 *rich display* capability.
 
 
 Markdown cells
 ^^^^^^^^^^^^^^
 You can document the computational process in a literate way, alternating 
 descriptive text with code, using *rich text*. In IPython this is accomplished 
 by marking up text with the Markdown language. The corresponding cells are 
 called *Markdown input cells*. The Markdown language provides a simple way to 
 perform this text markup, that is, to specify which parts of the text should 
 be emphasized (italics), bold, form lists, etc. 
 
 
 When a Markdown input cell is executed, the Markdown code is converted into 
 the corresponding formatted rich text. This output then *replaces* the 
 original Markdown input cell, leaving just the visually-significant marked up 
 rich text.  Markdown allows arbitrary HTML code for formatting.
 
 Within Markdown cells, you can also include *mathematics* in a straightforward 
 way, using standard LaTeX notation: ``$...$`` for inline mathematics and 
 ``$$...$$`` for displayed mathematics. When the Markdown cell is executed, 
 the LaTeX portions are automatically rendered in the HTML output as equations 
 with high quality typography. This is made possible by MathJax_, which 
 supports a `large subset <mathjax_tex>`_ of LaTeX functionality 
 
 .. _mathjax_tex: http://docs.mathjax.org/en/latest/tex.html
 
 Standard mathematics environments defined by LaTeX and AMS-LaTeX (the 
 `amsmath` package) also work, such as 
 ``\begin{equation}...\end{equation}``, and ``\begin{align}...\end{align}``.
 New LaTeX macros may be defined using standard methods, 
 such as ``\newcommand``, by placing them anywhere *between math delimiters* in 
 a Markdown cell. These definitions are then available throughout the rest of 
 the IPython session. (Note, however, that more care must be taken when using 
 nbconvert_ to output to LaTeX).
 
 Raw input cells
 ~~~~~~~~~~~~~~~
 
 *Raw* input cells provide a place in which you can write *output* directly.
 Raw cells are not evaluated by the Notebook, and have no output.
 When passed through nbconvert, Raw cells arrive in the destination format unmodified,
 allowing you to type full latex into a raw cell, which will only be rendered
 by latex after conversion by nbconvert.
 
 Heading cells
 ~~~~~~~~~~~~~
 
 You can provide a conceptual structure for your computational document as a 
 whole using different levels of headings; there are 6 levels available, from 
 level 1 (top level) down to level 6 (paragraph). These can be used later for 
 constructing tables of contents, etc.
 
 As with Markdown cells, a heading input cell is replaced by a rich text 
 rendering of the heading when the cell is executed.
 
 
 Basic workflow
 --------------
 
 The normal workflow in a notebook is, then, quite similar to a standard 
 IPython session, with the difference that you can edit cells in-place multiple 
 times until you obtain the desired results, rather than having to 
 rerun separate scripts with the ``%run`` magic command. (Magic commands do, 
 however, also work in the notebook; see below).   
 
 Typically, you will work on a computational problem in pieces, organizing 
 related ideas into cells and moving forward once previous parts work 
 correctly. This is much more convenient for interactive exploration than 
 breaking up a computation into scripts that must be executed together, as was 
 previously necessary, especially if parts of them take a long time to run
 
-The only significant limitation that the Notebook currently has, compared to 
-the Qt console, is that it cannot run any code that expects input from the 
-kernel (such as scripts that call :func:`raw_input`).  Very importantly, this 
-means that the ``%debug`` magic does *not* currently work in the notebook!  
-
-This limitation will be overcome in the future, but in the meantime, there is 
-a simple solution for debugging: you can attach a Qt console to your existing 
-notebook kernel, and run ``%debug`` from the Qt console.
-If your notebook is running on a local computer (i.e. if you are accessing it 
-via your localhost address at ``127.0.0.1``), then you can just type 
-``%qtconsole`` in the notebook and a Qt console will open up, connected to 
-that same kernel.
-
 At certain moments, it may be necessary to interrupt a calculation which is 
 taking too long to complete. This may be done with the ``Kernel | Interrupt`` 
 menu option, or the :kbd:``Ctrl-i`` keyboard shortcut.
 Similarly, it may be necessary or desirable to restart the whole computational 
 process, with the ``Kernel | Restart`` menu option or :kbd:``Ctrl-.`` 
 shortcut. This gives an equivalent state to loading the notebook document 
 afresh.
 
+A notebook may be downloaded in either ``.ipynb`` or raw ``.py`` form from the
+menu option ``File | Download as``. Choosing the ``.py`` option downloads a
+Python ``.py`` script, in which all output has been removed and the content of
+Markdown cells  in comment areas.  See ref:`below <notebook_format>` for more
+details on the notebook format.
     
 .. warning::
 
    While in simple cases you can "roundtrip" a notebook to Python, edit the
    Python file, and then import it back without loss of main content, this is 
    in general *not guaranteed to work*.  First, there is extra metadata
    saved in the notebook that may not be saved to the ``.py`` format.  And as
    the notebook format evolves in complexity, there will be attributes of the
    notebook that will not survive a roundtrip through the Python form.  You
    should think of the Python format as a way to output a script version of a
    notebook and the import capabilities as a way to load existing code to get 
    a notebook started.  But the Python version is *not* an alternate notebook
    format.
 
 
 Keyboard shortcuts
 ~~~~~~~~~~~~~~~~~~
 All actions in the notebook can be performed with the mouse, but keyboard 
 shortcuts are also available for the most common ones. The essential shortcuts
 to remember are the following:
 
 * :kbd:`Shift-Enter`:  run cell
     Execute the current cell, show output (if any), and jump to the next cell 
     below. If :kbd:`Shift-Enter` is invoked on the last input cell, a new code 
     cell will also be created. Note that in the notebook, typing :kbd:`Enter` 
     on its own *never* forces execution, but rather just inserts a new line in 
     the current input cell. :kbd:`Shift-Enter` is equivalent to clicking the 
     ``Cell | Run`` menu item.
 
 * :kbd:`Ctrl-Enter`: run cell in-place
     Execute the current cell as if it were in "terminal mode", where any 
     output is shown, but the cursor *remains* in the current cell. The cell's
     entire contents are selected after execution, so you can just start typing
     and only the new input will be in the cell. This is convenient for doing
     quick experiments in place, or for querying things like filesystem
     content, without needing to create additional cells that you may not want
     to be saved in the notebook.
 
 * :kbd:`Alt-Enter`: run cell, insert below
     Executes the current cell, shows the output, and inserts a *new* input 
     cell between the current cell and the cell below (if one exists). This  
     is thus a shortcut for the sequence :kbd:`Shift-Enter`, :kbd:`Ctrl-m a`.
     (:kbd:`Ctrl-m a` adds a new cell above the current one.)
   
 * :kbd:`Ctrl-m`: 
   This is the prefix for *all* other shortcuts, which consist of :kbd:`Ctrl-m` 
   followed by a single letter or character. For example, if you type 
   :kbd:`Ctrl-m h` (that is, the sole letter :kbd:`h` after :kbd:`Ctrl-m`), 
   IPython will show you all the available keyboard shortcuts.
 
 
 ..
     TODO: these live in IPython/html/static/notebook/js/quickhelp.js
     They were last updated for IPython 1.0 release, so update them again for
     future releases.
 
 Here is the complete set of keyboard shortcuts available:
 
 ============  ==========================
 **Shortcut**        **Action**
 ------------  --------------------------
 Shift-Enter    run cell
 Ctrl-Enter     run cell in-place
 Alt-Enter      run cell, insert below
 Ctrl-m x       cut cell
 Ctrl-m c       copy cell
 Ctrl-m v       paste cell
 Ctrl-m d       delete cell
 Ctrl-m z       undo last cell deletion
 Ctrl-m -       split cell
 Ctrl-m a       insert cell above
 Ctrl-m b       insert cell below
 Ctrl-m o       toggle output
 Ctrl-m O       toggle output scroll
 Ctrl-m l       toggle line numbers
 Ctrl-m s       save notebook
 Ctrl-m j       move cell down
 Ctrl-m k       move cell up
 Ctrl-m y       code cell
 Ctrl-m m       markdown cell
 Ctrl-m t       raw cell
 Ctrl-m 1-6     heading 1-6 cell
 Ctrl-m p       select previous
 Ctrl-m n       select next
 Ctrl-m i       interrupt kernel
 Ctrl-m .       restart kernel
 Ctrl-m h       show keyboard shortcuts
 ============  ==========================
 
    
 
 Magic commands
 --------------
 Magic commands, or *magics*, are commands for controlling IPython itself.
 They all begin with ``%`` and are entered into code input cells; the code 
 cells are executed as usual with :kbd:`Shift-Enter`.
 
 The magic commands call special functions defined by IPython which manipulate 
 the computational state in certain ways.
 
 There are two types of magics:
 
   - **line magics**:
 
      These begin with a single ``%`` and take as arguments the rest of the 
      *same line* of the code cell. Any other lines of the code cell are 
      treated as if they were part of a standard code cell.
 
   - **cell magics**:
 
       These begin with ``%%`` and operate on the *entire* remaining contents 
       of the code cell.
 
 Line magics
 ~~~~~~~~~~~
 Some of the available line magics are the following:
 
   * ``%load filename``:
 
         Loads the contents of the file ``filename`` into a new code cell. This 
         can be a URL for a remote file.
 
   * ``%timeit code``: 
 
       An easy way to time how long the single line of code ``code`` takes to 
       run
 
   * ``%config``:
 
       Configuration of the IPython Notebook
 
   * ``%lsmagic``:
 
       Provides a list of all available magic commands
 
 Cell magics
 ~~~~~~~~~~~
 
   * ``%%latex``:
 
       Renders the entire contents of the cell in LaTeX, without needing to use 
       explicit LaTeX delimiters.
 
   * ``%%bash``:
 
       The code cell is executed by sending it to be executed by ``bash``. The 
       output of the ``bash`` commands is captured and displayed in the 
       notebook.
 
   * ``%%file filename``:
 
       Writes the contents of the cell to the file ``filename``.
       **Caution**: The file is over-written without warning!
 
   * ``%%R``:
 
       Execute the contents of the cell using the R language.
 
   * ``%%timeit``:
 
       Version of ``%timeit`` which times the entire block of code in the 
       current code cell.
 
 
 
 Several of the cell magics provide functionality to manipulate the filesystem 
 of a remote server to which you otherwise do not have access.  
 
 
 Plotting
 --------
 One major feature of the Notebook is the ability to interact with 
 plots that are the output of running code cells. IPython 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`` magic command. 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 is the ``inline`` backend.
 This is applicable only for the IPython Notebook and the IPython QtConsole.
 It can be invoked as follows::
 
   %matplotlib inline
 
 With this backend, output of plotting commands is displayed *inline* within 
 the notebook format, directly below the input cell that produced it. The 
 resulting plots will then also be stored in the notebook document. This 
 provides a key part of the functionality for reproducibility_ that the IPython 
 Notebook provides.
 
 .. _reproducibility: https://en.wikipedia.org/wiki/Reproducibility
 
 
 
 Configuring the IPython Notebook
 --------------------------------
 The IPython Notebook can be run with a variety of command line arguments. 
 To see a list of available options enter::
 
   $ ipython notebook --help 
 
 Defaults for these options can also be set by creating a file named 
 ``ipython_notebook_config.py`` in your IPython *profile folder*. The profile 
 folder is a subfolder of your IPython directory; to find out where it is 
 located, run::
 
   $ ipython locate
 
 To create a new set of default configuration files, with lots of information 
 on available options, use::
 
   $ ipython profile create
 
-.. seealso:
+.. seealso::
 
     :ref:`config_overview`, in particular :ref:`Profiles`.
 
 
-Importing `.py` files
-----------------------
-
+Importing ``.py`` files
+-----------------------
 
 ``.py`` files will be imported into the IPython Notebook as a notebook with 
 the same basename, but an ``.ipynb`` extension, located in the notebook 
 directory. The notebook created will have just one cell, which will contain 
 all the code in the ``.py`` file. You can later manually partition this into 
 individual cells using the ``Edit | Split Cell`` menu option, or the 
 :kbd:`Ctrl-m -` keyboard shortcut.
 
-.. Alternatively, prior to importing the ``.py``, you can manually add ``# <
-nbformat>2</nbformat>`` at the start of the file, and then add separators for 
-text and code cells, to get a cleaner import with the file already broken into 
-individual cells.
+Note that ``.py`` scripts obtained from a notebook document using nbconvert_ 
+maintain the structure of the notebook in comments. Reimporting such a
+script back into the Notebook will preserve this structxure.
+
+
+.. warning::
 
+   You can "roundtrip" a notebook to Python, by exporting the
+   notebook to a ``.py`` script, editing the script, and then importing it back
+   into the Notebook without loss of main content. However, 
+   in general this is *not guaranteed* to work.  First, there is extra metadata
+   saved in the notebook that may not be saved to the ``.py`` format.  Second,
+   as the notebook format evolves in complexity, there will be attributes of 
+   the notebook that will not survive a roundtrip through the Python form.  You
+   should think of the Python format as a way to output a script version of a
+   notebook and the import capabilities as a way to load existing code to get 
+   a notebook started.  But the Python version is *not* an alternate notebook
+   format.
+
+.. seealso::
+    :ref:`notebook_format`

docs/source/interactive/working_remotely.rst

@@ -1,182 +1,187
 .. _working_remotely.txt
 
 Working remotely
 ================
 
 
 The IPython Notebook web app is based on a server-client structure. 
-This server uses a two-process kernel architecture based on ZeroMQ, as well as 
-Tornado for serving HTTP requests. Other clients may connect to the same 
+This server uses a two-process kernel architecture based on ZeroMQ_, as well
+as Tornado_ for serving HTTP requests. Other clients may connect to the same 
 underlying IPython kernel; see below.
 
+.. _ZeroMQ: http://zeromq.org
+
+.. _Tornado: http://www.tornadoweb.org
+
+
 .. _notebook_security:
 
 Security
 --------
 
 You can protect your Notebook server with a simple single password by
 setting the :attr:`NotebookApp.password` configurable. You can prepare a
 hashed password using the function :func:`IPython.lib.security.passwd`:
 
 .. sourcecode:: ipython
 
     In [1]: from IPython.lib import passwd
     In [2]: passwd()
     Enter password: 
     Verify password: 
     Out[2]: 'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
     
 .. note::
 
   :func:`~IPython.lib.security.passwd` can also take the password as a string
   argument. **Do not** pass it as an argument inside an IPython session, as it
   will be saved in your input history.
 
 You can then add this to your :file:`ipython_notebook_config.py`, e.g.::
 
     # Password to use for web authentication
     c = get_config()
     c.NotebookApp.password = 
     u'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'
 
 When using a password, it is a good idea to also use SSL, so that your 
 password is not sent unencrypted by your browser. You can start the notebook 
 to communicate via a secure protocol mode using a self-signed certificate with 
 the command::
 
     $ ipython notebook --certfile=mycert.pem
 
 .. note::
 
     A self-signed certificate can be generated with ``openssl``.  For example, 
     the following command will create a certificate valid for 365 days with 
     both the key and certificate data written to the same file::
 
         $ openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout mycert.
         pem -out mycert.pem
 
 Your browser will warn you of a dangerous certificate because it is
 self-signed.  If you want to have a fully compliant certificate that will not
 raise warnings, it is possible (but rather involved) to obtain one,
-`as explained in detailed in this tutorial`__.
+as explained in detail in `this tutorial`__.
 
 .. __: http://arstechnica.com/security/news/2009/12/how-to-get-set-with-a-
 secure-sertificate-for-free.ars
 	
 Keep in mind that when you enable SSL support, you will need to access the
 notebook server over ``https://``, not over plain ``http://``.  The startup
 message from the server prints this, but it is easy to overlook and think the
 server is for some reason non-responsive.
 
 
 Connecting to an existing kernel
 ---------------------------------
 
 The notebook server always prints to the terminal the full details of 
 how to connect to each kernel, with messages such as the following::
 
     [IPKernelApp] To connect another client to this kernel, use:
     [IPKernelApp] --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
 
 This long string is the name of a JSON file that contains all the port and 
 validation information necessary to connect to the kernel.  You can then, for 
 example, manually start a Qt console connected to the *same* kernel with::
 
     $ ipython qtconsole --existing 
     kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
 
 If you have only a single kernel running, simply typing::
 
     $ ipython qtconsole --existing
 
 will automatically find it. (It will always find the most recently 
 started kernel if there is more than one.)  You can also request this 
 connection data by typing ``%connect_info``; this will print the same 
 file information as well as the content of the JSON data structure it 
 contains.
 
 
 Running a public notebook server
 --------------------------------
 
 If you want to access your notebook server remotely via a web browser,
 you can do the following.  
 
 Start by creating a certificate file and a hashed password, as explained 
 above.  Then create a custom profile for the notebook, with the following 
 command line, type::
 
   $ ipython profile create nbserver
 
 In the profile directory just created, edit the file 
 ``ipython_notebook_config.py``.  By default, the file has all fields 
 commented; the minimum set you need to uncomment and edit is the following::
 
      c = get_config()
 
      # Kernel config
      c.IPKernelApp.pylab = 'inline'  # if you want plotting support always
 
      # Notebook config
      c.NotebookApp.certfile = u'/absolute/path/to/your/certificate/mycert.pem'
      c.NotebookApp.ip = '*'
      c.NotebookApp.open_browser = False
      c.NotebookApp.password = u'sha1:bcd259ccf...[your hashed password here]'
      # It is a good idea to put it on a known, fixed port
      c.NotebookApp.port = 9999
 
 You can then start the notebook and access it later by pointing your browser 
 to ``https://your.host.com:9999`` with ``ipython notebook 
 --profile=nbserver``.
 
 Running with a different URL prefix
 -----------------------------------
 
 The notebook dashboard (the landing page with an overview
 of the notebooks in your working directory) typically lives at the URL
 ``http://localhost:8888/``. If you prefer that it lives, together with the 
 rest of the notebook, under a sub-directory,
 e.g. ``http://localhost:8888/ipython/``, you can do so with
 configuration options like the following (see above for instructions about
 modifying ``ipython_notebook_config.py``)::
 
     c.NotebookApp.base_project_url = '/ipython/'
     c.NotebookApp.base_kernel_url = '/ipython/'
     c.NotebookApp.webapp_settings = {'static_url_prefix':'/ipython/static/'}
 
 Using a different notebook store
 --------------------------------
 
 By default, the Notebook app stores the notebook documents that it saves as 
 files in the working directory of the Notebook app, also known as the 
 ``notebook_dir``. This  logic is implemented in the 
 :class:`FileNotebookManager` class. However, the server can be configured to 
 use a different notebook manager class, which can 
 store the notebooks in a different format. 
 
 Currently, we ship a :class:`AzureNotebookManager` class that stores notebooks 
 in Azure blob storage. This can be used by adding the following lines to your 
 ``ipython_notebook_config.py`` file::
 
     c.NotebookApp.notebook_manager_class = 
     'IPython.html.services.notebooks.azurenbmanager.AzureNotebookManager'
     c.AzureNotebookManager.account_name = u'paste_your_account_name_here'
     c.AzureNotebookManager.account_key = u'paste_your_account_key_here'
     c.AzureNotebookManager.container = u'notebooks'
 
 In addition to providing your Azure Blob Storage account name and key, you 
 will have to provide a container name; you can use multiple containers to 
 organize your notebooks.
 
 
 Known issues
 ------------
 
 When behind a proxy, especially if your system or browser is set to autodetect
 the proxy, the Notebook app might fail to connect to the server's websockets,
 and present you with a warning at startup. In this case, you need to configure
 your system not to use the proxy for the server's address.
 
 For example, in Firefox, go to the Preferences panel, Advanced section,
 Network tab, click 'Settings...', and add the address of the notebook server
 to the 'No proxy for' field.