Document notebook format and quick howto for a public nb server.

Closes  #1047.

docs/source/interactive/htmlnotebook.txt

@@ -1,273 +1,375 b''
 .. _htmlnotebook:
 
 =========================
 An HTML Notebook IPython
 =========================
 
 .. seealso::
 
     :ref:`Installation requirements <installnotebook>` for the Notebook.
 
 The IPython Notebook consists of two related components:
 
 * An JSON based Notebook document format for recording and distributing
   Python code and rich text.
 * A web-based user interface for authoring and running notebook documents.
 
 The Notebook can be used by starting the Notebook server with the 
 command::
 
     $ ipython notebook
 
 Note that by default, the notebook doesn't load pylab, it's just a normal
 IPython session like any other.  If you want pylab support, you must use::
     
     $ ipython notebook --pylab
 
 which will behave similar to the terminal and Qt console versions, using your
 default matplotlib backend and providing floating interactive plot windows.  If
 you want inline figures, you must manually select the ``inline`` backend::
 
-    $ ipython notebook --pylab=inline
+    $ ipython notebook --pylab inline
 
 This server uses the same ZeroMQ-based two process kernel architecture as
 the QT Console as well Tornado for serving HTTP/S requests. Some of the main
 features of the Notebook include:
 
 * Display rich data (png/html/latex/svg) in the browser as a result of
   computations.
 * Compose text cells using HTML and Markdown.
 * Import and export notebook documents in range of formats (.ipynb, .py).
 * In browser syntax highlighting, tab completion and autoindentation.
 * Inline matplotlib plots that can be stored in Notebook documents and opened
   later.
 
 See :ref:`our installation documentation <install_index>` for directions on
 how to install the notebook and its dependencies.
 
 .. 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 in port 8888, later notebooks search for random ports near
    that one.  You can also manually specify the port with the ``--port``
    option.
    
 
 Basic Usage
 ===========
 
 The landing page of the notebook server application, which we call the IPython
 Notebook *dashboard*, shows the notebooks currently available in the directory
 in which the application was started, and allows you to create new notebooks.
 
 A notebook is a combination of two things:
 
 1. An interactive session connected to an IPython kernel, controlled by a web
-   application that can send input to the console and display many types of output
-   (text, graphics, mathematics and more).  This is the same kernel used by the
-   :ref:`Qt console <qtconsole>`, but in this case the web console sends input in
-   persistent cells that you can edit in-place instead of the vertically scrolling
-   terminal style used by the Qt console.
+   application that can send input to the console and display many types of
+   output (text, graphics, mathematics and more).  This is the same kernel used
+   by the :ref:`Qt console <qtconsole>`, but in this case the web console sends
+   input in persistent cells that you can edit in-place instead of the
+   vertically scrolling terminal style used by the Qt console.
 
 2. A document that can save the inputs and outputs of the session as well as
-   additional text that accompanies the code but is not meant for execution.  In
-   this way, notebook files serve as a complete computational record of a session
-   including explanatory text and mathematics, code and resulting figures.  These
-   documents are internally JSON files and are saved with the ``.ipynb``
-   extension.
+   additional text that accompanies the code but is not meant for execution.
+   In this way, notebook files serve as a complete computational record of a
+   session including explanatory text and mathematics, code and resulting
+   figures.  These documents are internally JSON files and are saved with the
+   ``.ipynb`` extension.
 
 If you have ever used the Mathematica or Sage notebooks (the latter is also
 web-based__) you should feel right at home.  If you have not, you should be
 able to learn how to use it in just a few minutes.
 
 .. __: http://sagenb.org
 
 
 Creating and editing notebooks
 ------------------------------
 
 You can create new notebooks from the dashboard with the ``New Notebook``
 button or open existing ones by clicking on their name.  Once in a notebook,
 your browser tab will reflect the name of that notebook (prefixed with "IPy:").
 The URL for that notebook is not meant to be human-readable and is *not*
 persistent across invocations of the notebook server.
 
 You can also drag and drop into the area listing files any python file: it
 will be imported into a notebook with the same name (but ``.ipynb`` extension)
 located in the directory where the notebook server was started.  This notebook
 will consist of a single cell with all the code in the file, which you can
 later manually partition into individual cells for gradual execution, add text
 and graphics, etc.
 
+
 Workflow and limitations
 ------------------------
 
 The normal workflow in a notebook is quite similar to a normal IPython session,
 with the difference that you can edit a cell in-place multiple times until you
 obtain the desired results rather than having to rerun separate scripts with
 the ``%run`` magic (though magics also work in the notebook).   Typically
 you'll work on a problem in pieces, organizing related pieces into cells and
 moving forward as previous parts work correctly.  This is much more convenient
 for interactive exploration than breaking up a computation into scripts that
 must be executed together, especially if parts of them take a long time to run
 (In the traditional terminal-based IPython, you can use tricks with namespaces
 and ``%run -i`` to achieve this capability, but we think the notebook is a more
 natural solution for  that kind of problem).
 
 The only significant limitation the notebook currently has, compared to the qt
 console, is that it can not 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* work in the notebook!  We intend to
 correct this limitation, but in the meantime, there is a way to debug problems
 in the notebook: 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), you can just type ``%qtconsole`` in the notebook and a Qt console
 will open up connected to that same kernel.
 
 In general, the notebook server prints the full details of how to connect to
 each kernel at the terminal, with lines like::
 
     [IPKernelApp] To connect another client to this kernel, use:
     [IPKernelApp] --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
 
 This is the name of a JSON file that contains all the port and validation
 information necessary to connect to the kernel.  You can manually start a
 qt console with::
 
     ipython qtconsole --existing kernel-3bb93edd-6b5a-455c-99c8-3b658f45dde5.json
 
 and if you only have 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.
 
     
 Text input
 ----------
 
 In addition to code cells and the output they produce (such as figures), you
 can also type text not meant for execution.  To type text, change the type of a
 cell from ``Code`` to ``Markdown`` by using the button or the :kbd:`Ctrl-m m`
 keybinding (see below).  You can then type any text in Markdown_ syntax, as
 well as mathematical expressions if you use ``$...$`` for inline math or
 ``$$...$$`` for displayed math.
 
-Exporting a notebook
---------------------
+
+Exporting a notebook and importing existing scripts
+---------------------------------------------------
 
 If you want to provide others with a static HTML or PDF view of your notebook,
 use the ``Print`` button.  This opens a static view of the document, which you
 can print to PDF using your operating system's facilities, or save to a file
 with your web browser's 'Save' option (note that typically, this will create
 both an html file *and* a directory called `notebook_name_files` next to it
 that contains all the necessary style information, so if you intend to share
 this, you must send the directory along with the main html file).
 
 The `Download` button lets you save a notebook file to the Download area
 configured by your web browser (particularly useful if you are running the
 notebook server on a remote host and need a file locally).  The notebook is
 saved by default with the ``.ipynb`` extension and the files contain JSON data
 that is not meant for human editing or consumption.  But you can always export
 the input part of a notebook to a plain python script by choosing Python format
 in the `Download` drop list.  This removes all output and saves the text cells
-in comment areas.
+in comment areas.  See ref:`below <notebook_format>` for more details on the
+notebook format.
+
+The notebook can also *import* ``.py`` files as notebooks, by dragging and
+dropping the file into the notebook dashboard file list area.  By default, the
+entire contents of the file will be loaded into a single code cell.  But if
+prior to import, you manually add the ``# <nbformat>2</nbformat>`` marker at
+the start and then add separators for text/code cells, you can get a cleaner
+import with the file broken into individual cells.
 
 .. warning::
 
    While in simple cases you can roundtrip a notebook to Python, edit the
-   python file and import it back without loss, this is in general *not
-   guaranteed to work at all*.  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.
+   python file and import it back without loss of main content, this is in
+   general *not guaranteed to work at all*.  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 use
 ------------
 
 All actions in the notebook can be achieved with the mouse, but we have also
 added keyboard shortcuts for the most common ones, so that productive use of
 the notebook can be achieved with minimal mouse intervention.  The main
 key bindings you need to remember are:
 
 * :kbd:`Shift-Enter`: execute the current cell (similar to the Qt console),
   show output (if any) and create a new cell below.  Note that in the notebook,
   simply using :kbd:`Enter` *never* forces execution, it simply inserts a new
   line in the current cell.  Therefore, in the notebook you must always use
   :kbd:`Shift-Enter` to get execution (or use the mouse and click on the ``Run
   Selected`` button).
 
 * :kbd:`Ctrl-Enter`: execute the current cell in "terminal mode", where any
   output is shown but the cursor stays in the current cell, whose input
   area is flushed empty.  This is convenient to do quick in-place experiments
   or query things like filesystem content without creating additional cells you
   may not want saved in your notebook.
 
 * :kbd:`Ctrl-m`: this is the prefix for all other keybindings, which consist
   of an additional single letter.  Type :kbd:`Ctrl-m h` (that is, the sole
   letter :kbd:`h` after :kbd:`Ctrl-m`) and IPython will show you the remaining
   available keybindings.
 
+
+.. _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.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 in the clear. You can start the notebook to communicate via a secure
-protocol mode using a self-signed certificate by typing::
+is not sent unencripted by your browser. You can start the notebook to
+communicate via a secure protocol mode using a self-signed certificate by
+typing::
 
     $ ipython notebook --certfile=mycert.pem
 
 .. note::
 
-    A self-signed certificate can be generated with openssl. For example::
+    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 for free,
+`as explained in detailed 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'll need to access the
+notebook server over ``https://``, not over plain ``http://``.  The startup
+message from the server prints this, but it's easy to overlook and think the
+server is for some reason non-responsive.
+
+
+Quick Howto: running a public notebook server
+=============================================
+
+If you want to access your notebook server remotely with just a web browser,
+here is a quick set of instructions.  Start by creating a certificate file and
+a hashed password as explained above.  Then, create a custom profile for the
+notebook.  At the command line, type::
+
+  ipython profile create nbserver
+
+In the profile directory, 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 here::
+
+     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's 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``.
+
+.. _notebook_format:
+
+The notebook format
+===================
+
+The notebooks themselves 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 edit manually 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 IPython itself, not for hand-editing.
+
+.. note::
+
+     Binary data such as figures are directly saved in the JSON file.  This
+     provides convenient single-file portability but means the files can be
+     large and diffs of binary data aren't very meaningful.  Since the binary
+     blobs are encoded in a single line they only affect one line of the diff
+     output, but they are typically very long lines.  You can use the
+     'ClearAll' button 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,
+by clicking on the 'Download' button and selecting ``py`` as the format.  This
+file will contain all the code cells from your notebook verbatim, and all text
+cells prepended with a comment marker.  The separation between code and text
+cells is indicated with special comments and there is a header indicating the
+format version.  All output is stripped out when exporting to python.
+
+Here is an example of a simple notebook with one text cell and one code input
+cell, when exported to python format::
+
+    # <nbformat>2</nbformat>
+
+    # <markdowncell>
+
+    # A text cell
+
+    # <codecell>
+
+    print "hello IPython"
+
+
 Known Issues
 ============
 
 When behind a proxy, especially if your system or browser is set to autodetect
 the proxy, the html notebook 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.
 
 In Firefox, for example, 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.
 
-Notebook document format
-========================
-
-
+    
 .. _Markdown: http://daringfireball.net/projects/markdown/basics