clean up docs

docs/command.rst

@@ -1,31 +1,38 @@
-Command
-===============
+Command (classic mode)
+===============================================================================
 
-Simple Azure supports command line tools, so a user can create virtual machines on the shell.
+Simple Azure supports command line tools, so a user can create virtual machines
+on the shell.
 
 Creating Clusters
-------------------
-The usage is based on StarCluster. We aim to provide an identical interface and command name to use clusters like StarCluster.
+-------------------------------------------------------------------------------
+
+The usage is based on StarCluster. We aim to provide an identical interface and
+command name to use clusters like StarCluster.
 
 simpleazure-cluster
-^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 A user can create one or more clusters of virtual machines on Windows Azure:
 
 ::
 
    $ simpleazure-cluster start mycluster
 
-Note. ``mycluster`` is a profile name and the config file has been stored under the default directory ``$HOME/.azure/cluster`` as a yaml file.
+Note. ``mycluster`` is a profile name and the config file has been stored under
+the default directory ``$HOME/.azure/cluster`` as a yaml file.
 
-The number of clusters can be changed in the config file (mycluster.yaml) like this:
+The number of clusters can be changed in the config file (mycluster.yaml) like
+this:
 
 ::
 
     ...
     num=5
 
 sshmaster
-''''''''''''
+'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 This command allows to login to a master node via SSH.
 
 ::

docs/configuration.rst

@@ -1,30 +1,42 @@
-Configuration
-==============
-Simple Azure uses the default directory for the azure-cli tool, ``$HOME/.azure``.
-It contains the ``config.json`` which includes an endpoint and a subscription of Windows Azure.
+Configuration (classic mode)
+===============================================================================
+
+Simple Azure uses the default directory for the azure-cli tool,
+``$HOME/.azure``.  It contains the ``config.json`` which includes an endpoint
+and a subscription of Windows Azure.
 
 SSH Keys
-------------
-``.ssh`` directory contains certificates and thumbprints (fingerprints) of key pairs on the default directory ``$HOME/.zure``.
+-------------------------------------------------------------------------------
+
+``.ssh`` directory contains certificates and thumbprints (fingerprints) of key
+pairs on the default directory ``$HOME/.zure``.
 
 pfx certificate
-^^^^^^^^^^^^^^^^
-Personal Information Exchange (pfx) certificate is required to the Cloud (hosted) service.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Personal Information Exchange (pfx) certificate is required to the Cloud
+(hosted) service.
 
-``openssl`` supports to convert your public and private keys to a pfx certificate.
+``openssl`` supports to convert your public and private keys to a pfx
+certificate.
 
 private key files
-^^^^^^^^^^^^^^^^^^^^^^
-For example, ``myPrivateKey.key`` which is a rsa 2048 private key is used to get access to virtual machines using SSH.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+For example, ``myPrivateKey.key`` which is a rsa 2048 private key is used to
+get access to virtual machines using SSH.
 
 Cluster configuration
----------------------
-Simple Azure supports cluster computing and personal profiles enable individual settings when you launch clusters.
-The default directory for cluster conf file is ``cluster`` under the ``$HOME/.azure`` default directory.
+-------------------------------------------------------------------------------
+
+Simple Azure supports cluster computing and personal profiles enable individual
+settings when you launch clusters.  The default directory for cluster conf file
+is ``cluster`` under the ``$HOME/.azure`` default directory.
 
 Cluster profile
-^^^^^^^^^^^^^^^^^^
-For example, ``mycluster`` has information in a yaml format in the cluster directory.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For example, ``mycluster`` has information in a yaml format in the cluster
+directory.
+
 ::
 
   master: myvm-81fd6840ae

docs/deliverables.rst

@@ -1,5 +1,5 @@
-Deliverables
-============
+Deliverables (TBD)
+===============================================================================
 
 * `Documentation <https://simple-azure.readthedocs.org/en/latest/>`_
 * `Source code <https://github.com/lee212/simpleazure/>`_

docs/quickstart.rst

@@ -1,10 +1,10 @@
-Quickstart
-============
+Quickstart (classic mode)
+===============================================================================
 
 This page provides a good introduction to Simple Azure.
 
 Deploying Azure Virtual Machine
---------------------------------
+-------------------------------------------------------------------------------
 
 .. code-block:: python
 
@@ -22,7 +22,8 @@ You can change an operating system image by the ``set_image()`` function. For ex
 This allows you to create a vm with the selected image. Note that ``set_image()`` must be used before calling the ``create_vm()`` function.
 
 Deploying several machines
----------------------------
+-------------------------------------------------------------------------------
+
 ``create_cluster()`` function allows you to create multiple machines at once. ``num=`` parameter can be used to specify the number of nodes.
 
 .. code-block:: python
@@ -40,7 +41,8 @@ Deploying several machines
    {'request_id': 'b1a3446ebafe47a295df4c9d1b7d743c'}
    
 Deploying a Virtual Machine from the community images (VM DEPOT)
------------------------------------------------------------------
+-------------------------------------------------------------------------------
+
 Personalized and preconfigured virtual machines images can be imported from the community repository (http://vmdepot.msopentech.com).
 This example explains as how to deploy a virtual machine with the community image, Azure Data Science Core.
 
@@ -52,7 +54,8 @@ This example explains as how to deploy a virtual machine with the community imag
    azure.create_vm()
    
 Simple Azure on Command Line Interface (CLI)
------------------------------------------------
+-------------------------------------------------------------------------------
+
 Simple Azure supports commands on a linux shell. For example, you can create clusters of virtual machines on Windows Azure like `StarCluster <http://star.mit.edu/cluster/index.html>`_ like as follows:
 (StarCluster is a cluster-computing toolkit for Amazon Cloud)
 

docs/tutorial.rst

@@ -1,42 +1,55 @@
-Tutorial
-==========
-The tutorial in this page assists you in learning how to use Simple Azure on Python. 
-In this tutorial, we creates Windows Azure Virtual Machines for Azure Data Science Core and BioLinux with IPython.
-It shows usage in pre-configured environments but it explains main features that you need to know. 
-For more detail of function APIs, module descriptions might be helpful. 
-There are several tools and libraries that we have used such as StarCluster, IPython, azure-sdk-for-python, Bioblend, etc.
+Tutorial (classic mode)
+===============================================================================
 
-You can also have an interactive python tutorial via IPython Notebook to learn Simple Azure.
+The tutorial in this page assists you in learning how to use Simple Azure on
+Python.  In this tutorial, we creates Windows Azure Virtual Machines for Azure
+Data Science Core and BioLinux with IPython.  It shows usage in pre-configured
+environments but it explains main features that you need to know.  For more
+detail of function APIs, module descriptions might be helpful.  There are
+several tools and libraries that we have used such as StarCluster, IPython,
+azure-sdk-for-python, Bioblend, etc.
+
+You can also have an interactive python tutorial via IPython Notebook to learn
+Simple Azure.
 
 Tutorial by IPython Notebook
-----------------------------
-`IPython Notebook Viewer <http://nbviewer.org>`_ supports sharing and viewing ipython notebook files. Simple Azure's tutorial can be viewed through the ipynb viewer.
+-------------------------------------------------------------------------------
+
+`IPython Notebook Viewer <http://nbviewer.org>`_ supports sharing and viewing
+ipython notebook files. Simple Azure's tutorial can be viewed through the ipynb
+viewer.
 
 Simple Azure
-^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 * `Simplified Windows Azure SDK for Python (Simple Azure) <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Simplified%2520Windows%2520Azure%2520SDK%2520for%2520Python.ipynb>`_
 * `Deploying a community image, Azure Data Science Core <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Deploy%2520ADSC%2520by%2520Simple%2520Azure.ipynb>`_
 * `Enabling IPython Cluster with Simple Azure <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Enabling%2520IPython%2520cluster%2520with%2520Simple%2520Azure.ipynb>`_
 
-azure-sdk-for-python
-^^^^^^^^^^^^^^^^^^^^^
-azure-sdk-for-python is the official python library for azure
+azure-sdk-for-python (legacy)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+azure-sdk-for-python is the official python library for azure:
 
 * `Deploying Windows Azure Virtual Machines with Python SDK (azure-sdk-for-python) <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Deploying%2520Windows%2520Azure%2520Virtual%2520Machines%2520with%2520Python%2520SDK.ipynb>`_
 * `Deploying Windows and Linux VMs through azure-sdk-for-python <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Deploying%2520Windows%2520and%2520Linux%2520VMs.ipynb>`_
 * `Deploying multiple VMs through azure-sdk-for-python <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Deploying%2520multiple%2520VMs.ipynb>`_
 
 Galaxy workflow toolkit
-^^^^^^^^^^^^^^^^^^^^^^^^
-`Galaxy project <galaxyproject.org>`_ provides a web-based platform and a python library for scientific research.
-Here, the tutorials below introduce use cases of Galaxy on IPython Notebook.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+`Galaxy project <galaxyproject.org>`_ provides a web-based platform and a
+python library for scientific research.  Here, the tutorials below introduce
+use cases of Galaxy on IPython Notebook.
 
 * `BioBlend (Galaxy Python library) with IPython <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520BioBlend%2520%28Galaxy%2520Python%2520library%29%2520with%2520IPython.ipynb>`_
 * `Finding coding exon which has the highest number of single nucleotide polymorphisms on chromosome 22 <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/%28Galaxy%29%2520Example%25201.%2520finding%2520coding%2520exon%2520which%2520has%2520the%2520highest%2520number%2520of%2520single%2520nucleotide%2520polymorphisms%2520on%2520chromosome%252022.ipynb>`_
 
 IPython
-^^^^^^^^^
-This tutorial shows how to have IPython installed on Windows Azure with a normal linux distribution.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This tutorial shows how to have IPython installed on Windows Azure with a
+normal linux distribution.
 
 * `Installing IPython on Windows Azure Virtual Machines and configuring clustering <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Installing%2520IPython%2520on%2520Windows%2520Azure%2520Virtual%2520Machines%2520and%2520configuring%2520clustering.ipynb>`_
 * `Enabling IPython Cluster with Simple Azure <http://nbviewer.ipython.org/urls/raw.github.com/lee212/simpleazure/master/ipynb/Tutorial%2520-%2520Enabling%2520IPython%2520cluster%2520with%2520Simple%2520Azure.ipynb>`_