Rearranged htmlnotebook.txt

docs/source/interactive/htmlnotebook.txt

@@ -1,482 +1,470 b''
 .. _htmlnotebook:
 
-=========================
-An HTML Notebook IPython
-=========================
+====================
+The IPython Notebook
+====================
 
 .. 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.
+* A web application for interactive authoring of literate computations, combining explanatory text, mathematics, computations and rich media output. Input and output are stored  in persistent cells that may be edited in-place.
+
+* Notebook documents for recording and distributing
+  the results.
+
+
+Features of the IPython Notebook web app
+----------------------------------------
+
+Some of the main
+features of the IPython Notebook app include:
+
+* Display rich data representations (e.g. HTML / LaTeX / SVG) in the browser as a result of computations.
+* Compose text cells using Markdown and HTML.
+* Include mathematical equations, rendered directly in the browser by MathJax.
+* Import standard Python scripts
+* In-browser editing, syntax highlighting, tab completion and autoindentation.
+* Inline figures rendered by the ``matplotlib`` library with publication quality, in a range of formats (SVG / PDF / PNG).
+
+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 will be
+able to learn how to use it in just a few minutes.
+
+.. __: http://sagenb.org
+
 
-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::
+Notebook documents
+------------------
 
-    $ ipython notebook --pylab inline
+Notebook documents, or *notebooks*, are files which record all computations carried out and the results obtained in a literate way, including inputs, outputs, toegether with descriptive text and mathematics.
 
-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:
+They are plain text files, which are thus easy to share with colleagues and place under version control. But, by using the
+JSON format, they can record all aspects of the computation, including embedding rich media output.
+The standard file extension for notebook documents is ``.ipynb``.
+
+Notebooks may easily be exported to a range of static formats, including HTML (for example, for blog posts), PDF and slide shows.
+Furthermore, any publicly
+available notebook may be shared via the `IPython Notebook Viewer
+<http://nbviewer.ipython.org>`_ service, which will provide it as a static web
+page. The results may thus be shared without having to install anything.
 
-* 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
+   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 Usage
-===========
+Starting the IPython Notebook web app
+=====================================
 
-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.
+The Notebook web app can be started with the command::
 
-A notebook is a combination of two things:
+    $ ipython notebook
 
-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.
+The landing page of the notebook server application, the *dashboard*, shows the notebooks currently available in the working directory (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.
 
-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.
 
-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.
+You can also drag and drop into the area listing files any ``.py`` 
+file:  it will be imported into a notebook with the same name (but 
+``.ipynb``  extension), located in the working directory.  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, and add text
+and graphics, etc. 
+Alternatively,
+prior to import, you can manually add ``# <nbformat>2</nbformat>`` 
+markers at the start and then add separators for text/code cells, to get a cleaner import with the file already broken into individual cells.
 
-.. __: http://sagenb.org
 
+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 underlying IPython kernel.
 
-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.
+Basic workflow
+------------------------
 
 
-Workflow and limitations
-------------------------
+Once in a notebook, your browser tab will reflect the name of that notebook (prefixed with "IPy").
+The URL for that notebook is currently not meant to be human-readable and is not persistent across invocations of the notebook server; however, this will change soon.
+
+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 resultsj, 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
+
+The only significant limitation that 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* currently work in the notebook!  This limitation will 
+be overcome in the future, 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.
+
+
+Connecting to an existing kernel
+---------------------------------
 
-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::
+The notebook server always prints to the terminal the full details of 
+how to connect to each kernel, 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::
+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.
+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 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.  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 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.
 
    
 Importing or executing a notebook as a normal Python file
 ---------------------------------------------------------
 
 The native format of the notebook, a file with a ``.ipynb`` extension, is a
 JSON container of all the input and output of the notebook, and therefore not
 valid Python by itself.  This means that by default, you can not import a
 notebook or execute it as a normal python script.  But if you want use
 notebooks as regular Python files, you can start the notebook server with::
 
   ipython notebook --script
 
 or you can set this option permanently in your configuration file with::
 
     c.NotebookManager.save_script=True
 
 This will instruct the notebook server to save the ``.py`` export of each
 notebook adjacent to the ``.ipynb`` at every save.  These files can be
 ``%run``, imported from regular IPython sessions or other notebooks, or
 executed at the command-line as normal Python files.  Since we export the raw
 code you have typed, for these files to be importable from other code you will
 have to avoid using syntax such as ``%magics`` and other IPython-specific
 extensions to the language.
 
 In regular practice, the standard way to differentiate importable code from the
 'executable' part of a script is to put at the bottom::
 
   if __name__ == '__main__':
     # rest of the code...
 
 Since all cells in the notebook are run as top-level code, you'll need to
 similarly protect *all* cells that you do not want executed when other scripts
 try to import your notebook.  A convenient shortand for this is to define early
 on::
 
   script = __name__ == '__main__'
 
 and then on any cell that you need to protect, use::
 
   if script:
     # rest of the cell...
 
 Configuration
 -------------
 
 The IPython notebook server 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 (`ipython locate` will show you where that
 is). To create default configuration files (with lots of info on available 
 options) use:
 
   $ ipython profile create
 
 .. seealso:
 
     :ref:`config_overview`, in particular :ref:`Profiles`.
 
 
 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 jump to the next cell below. If :kbd:`Shift-Enter` 
   was invoked on the last input line, a new code cell will also be created. 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:`Alt-Enter`: this combination is similar to the previous one, with the 
   exception that, if the next cell below is not empty, a new code cell will be 
   added to the notebook, even if the cell execution happens not in the last cell. 
   In this regard, :kbd:`Alt-Enter`: is simply a shortcut for the :kbd:`Shift-Enter`, 
   :kbd:`Ctrl-m a` sequence. 
   
 * :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 unencrypted 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, 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 how to's
 ==============
 
 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`` with ``ipython notebook --profile=nbserver``.
 
 Running with a different URL prefix
 -----------------------------------
 
 The notebook dashboard (i.e. the default landing page with an overview
 of all your notebooks) typically lives at a URL path of
 "http://localhost:8888/". If you want to have it, and the rest of the
 notebook, live under a sub-directory,
 e.g. "http://localhost:8888/ipython/", you can do so with
 configuration options like these (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 server stores notebooks as files in the working 
 directory of the notebook server, 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.
 
 .. _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.
 
     
 .. _Markdown: http://daringfireball.net/projects/markdown/basics