My IPython-powered semi-automatic git workflow

%pwd

!mkdir devel_example

%cd devel_example/

project_name = "ipython"
project_remote = "git://github.com/ipython/ipython.git"
project_remote_name = "origin"
my_fork_remote = "git@github.com:damianavila/ipython.git"
my_fork_remote_name = "damianavila"

# Get a read-only copy of the project
!git clone $project_remote

# cd into the local project folder
%cd $project_name

# Link the local repo with my Github fork
!git remote add $my_fork_remote_name $my_fork_remote

# Check remotes
!git remote -v

master_branch = "master"
feature_branch = "doc_post_serve"

# Make sure we are in master branch
!git checkout $master_branch

# Pull the changes from origin/master
!git pull $project_remote_name

# Start a new branch to work on
!git checkout -b $feature_branch

# Check where we are
!git status

# list the files structure to find the needed files
%ls

%load docs/source/interactive/nbconvert.rst
# After executing %load, a new cell containing the source code will be added.
# Be sure to add the next line (with the proper path) to overwrite the file
# with you changes.
#
# %%writefile docs/source/interactive/nbconvert.rst

%%writefile docs/source/interactive/nbconvert.rst
.. _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 do this is adding
  ``--post serve`` on the command-line. The ``--post serve`` post-processor 
  proxies Reveal.js requests to a CDN if no local Reveal.js library is present. 
  For low connectivity environments, just place the Reveal.js library in the 
  same directory where your_talk.slides.html is located or point to another 
  directory using the ``--reveal-prefix`` alias.

* ``--to markdown``

  Simple markdown output.  Markdown cells are unaffected,
  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:

LaTeX citations
---------------

``nbconvert`` now has support for LaTeX citations. With this capability you
can:

* Manage citations using BibTeX.
* Cite those citations in Markdown cells using HTML data attributes.
* Have ``nbconvert`` generate proper LaTeX citations and run BibTeX.

For an example of how this works, please see the citations example in
the nbconvert-examples_ repository.

.. _nbconvert-examples: https://github.com/ipython/nbconvert-examples

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.

# Check status
!git status

# See the diff
!git diff

# Add the modified files to the stage
!git add .

# And do your commit
!git commit -am "Added --post-serve explanation into the nbconvert docs."

# Push updates from your local branch to your github branch
!git push $my_fork_remote_name $feature_branch