Merge pull request #10 from jessica-mitchell/doc-doc

Further additions to docs

doc/community.rst

@@ -1,5 +1,25 @@
+NEST Community
+===============
+
+
+Mailing List
+-------------
+
+The NEST User Mailing list is intended to be a forum for questions on the usage 
+of NEST, the exchange of code and general discussions about NEST. The philosophy 
+is that all users profit by sharing their experience. All NEST core developers 
+are subscribed to this list and will participate in the discussions as far as 
+time allows.
+
+Subscription
+http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user
+
+Archive (only subscribed users)
+http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user
+
+
 Contributing to NEST
-=====================
+---------------------
 
 NEST draws its strength from the many people that use and improve it. We
 are happy to consider your contributions (e.g. own models, bug or
@@ -8,12 +28,12 @@ documentation fixes) for addition to the official version of NEST.
 Please see the `NEST developer
 space <http://nest.github.io/nest-simulator>`_ for information about
 the development workflow of NEST and for how to create a fork of our Git
-repository and pull requests against it.
+repository and make pull requests against it.
 
 .. sidebar:: See Also
 
-    :doc:`Getting Help page <getting-help>`
-    :doc:`Publications <publication>
+    :doc:`Getting Help page <getting_help>`
+    `Publications <http://www.nest-simulator.org/publications/>`_
 
 Reporting bugs
 --------------
@@ -38,6 +58,10 @@ applicable:
 
 5. A detailed transcript of how you got the error.
 
-6. A minimal script to reproduce the error.* Found a bug? 
+6. A minimal script to reproduce the error.
 
+Become a NEST member
+--------------------
 
+If you would like to be actively involved in the NEST Initiative and support its
+goals, please see our `member page <http://www.nest-initiative.org/membership>`.

doc/contents.rst

@@ -10,13 +10,13 @@ Table of Contents
    :caption: User Documentation
 
    download
-   installation
-   getting-started
+   installation/index
+   getting_started
    tutorials/index
-   guides/index
    examples/index
-   getting-help
-   reference_material/quickref
+   guides/index
+   getting_help
+   ref_material/index
 
 .. toctree::
    :maxdepth: 2
@@ -26,7 +26,6 @@ Table of Contents
    Publications <http://www.nest-simulator.org/publications/>
    Developer Space <https://nest.github.io/nest-simulator/>
    NEST-Initiative <http://www.nest-initiative.org/>
-   Contact Us <http://www.nest-simulator.org/community/>
 
 .. toctree::
    :maxdepth: 2

doc/download.rst

@@ -1,4 +1,4 @@
-Download & Releases
+Download NEST
 ===================
 
 NEST is available under the :doc:`GNU General Public License 2 or later <license>`. This means that you can
@@ -7,12 +7,8 @@ NEST is available under the :doc:`GNU General Public License 2 or later <license
 -  modify and improve NEST according to your needs,
 -  distribute NEST to others under the same license.
 
-.. sidebar:: See Also
-
-   :doc:`Installation Instructions <installation/index>`
-
-Download current version of NEST here:
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Download the current version of NEST here:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 `Current Release NEST 2.14.0 <https://github.com/nest/nest-simulator/archive/v2.14.0.tar.gz>`_
 
@@ -23,11 +19,11 @@ Get the latest developer version
 
 `Current developer version <https://github.com/nest/nest-simulator>`_
 
-Get the NEST Live Media for Virtual Machines
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Download the NEST Live Media for Virtual Machines
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Live media is available in the OVA format, and is suitable, for example, for importing into VirtualBox. 
-If you run Windows, this is the option for you or if you just want to run NEST without installing it on your computer.
+If you run **Windows**, this is the option for you or if you just want to run NEST *without installing* it on your computer.
 
 `NEST Live Media 2.14.0 <http://www.nest-simulator.org/downloads/gplreleases/nest-live.ova>`_ (OVA, 2.5G)
 
@@ -39,17 +35,16 @@ See the :doc:`install instructions for Live Media here <installation/livemedia>`
 Previous Releases
 ~~~~~~~~~~~~~~~~~~~
 We continuously aim to improve NEST and implement features and fix bugs with every new version;
-Thus, we strongly encourage our users to use the most recent version of NEST. However,
-if you do need an older version you can find `all NEST releases here  <https://github.com/nest/nest-simulator/releases/tag/v2.12.0>`_
-
-And here you can find `Older Versions of Live Media`_ 
+thus, we strongly encourage our users to use the most recent version of NEST. However,
+if you do need an older version you can find `all NEST releases here <https://github.com/nest/nest-simulator/releases/tag/v2.12.0>`_ 
+and you can find `Older Versions of Live Media`_ below. 
 
 Citing NEST
 -----------
 
-Please cite NEST if you use it in your work and :doc:`let us know <contact>` about your publications that used NEST, so we
-will add them to our `publication list <http://www.nest-simulator.org/publications/>`__; this will help make them
-visible to potential readers.
+Please cite NEST if you use it in your work. You can :doc:`let us know <community>` about your publications that used NEST, and we
+will add them to our `publication list <http://www.nest-simulator.org/publications/>`_; this will help make them
+visible to potential readers. `Download our logo here <https://github.com/nest/nest-simulator/tree/master/extras/logos>`_
 
 
 If you use NEST 2.14.0, please cite it as **Peyser, Alexander et al.

doc/getting-help.rst → doc/getting_help.rst

@@ -10,22 +10,7 @@ Have a specific question or problem with NEST?
 
 * Check out the :doc:`FAQs <faqs/index>` for common issues.
 
-If your question is not on there, ask our `Mailing List <http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user>`_.
-
-The NEST User Mailing list is intended to be a forum for questions on
-the usage of NEST, the exchange of code and general discussions about
-NEST. The philosophy is that all users profit by sharing their
-experience. All NEST core developers are subscribed to this list and
-will participate in the discussions as far as time allows.
-
-| Subscription
-| http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user
-
-
-
-| Archive (only subscribed users)
-| http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user
-
+If your question is not on there, ask our :doc:`Mailing List <community>`.
 
 Getting help on the command line interface
 -------------------------------------------
@@ -35,31 +20,33 @@ Getting help on the command line interface
 
 * To access the High-level Python API reference material you can use the commands::
 
-     #list all functions and attributes
+     # list all functions and attributes
      dir(nest)
+
      # Get docstring for function in python
      help('nest.FunctionName')
-     #or in ipython 
+
+     # or in ipython 
      nest.FunctionName?
 
-* To access a specific C++ or SLI reference page for an object, command or parameter you can use the command 
+* To access a specific C++ or SLI reference page for an object, command or parameter you can use the command::
 
-    ``nest.help('name')``
+    nest.help('name')
 
 Model Information
 ~~~~~~~~~~~~~~~~~~~
 
-* To get a complete list of the models available in NEST type
+* To get a complete list of the models available in NEST type::
 
-     ``nest.Models()``
+    nest.Models()
 
-    * To get a list of only neuron models use 
+   * To get a list of only neuron models use::
 
-    ``nest.Models(mtype='nodes', sel=None)``
+    nest.Models(mtype='nodes', sel=None)
 
-    * To get a list of only synapse models use 
+   * To get a list of only synapse models use:: 
 
-    ``nest.Models(mtype='synapses', sel=None)``
+    nest.Models(mtype='synapses', sel=None)
 
 * To get details on model parameters and usage use::
 

doc/getting-started.rst → doc/getting_started.rst

@@ -1,17 +1,15 @@
-Getting started
-===============
+Getting Started
+================
 
 If you are new to NEST, we highly recommend you read the following text to get 
 a better understanding of how NEST works. Then check out our :doc:`PyNEST tutorial <tutorials/index>`,
 which will explain how to build your first neural network simulation in NEST.
 
-:doc:`Download` and :doc:`Install <installation>` NEST. 
-
 
 .. sidebar:: See Also
 
     * :doc:`List of Models in NEST <models/index>`
-    * :doc:`Create your own model <create-model>`
+    * :doc:`Create your own model <models/create_model>`
     * :doc:`Examples of Network Models <examples/index>`
 
 NEST - a neural network simulator
@@ -39,7 +37,7 @@ experiment with the difference that it takes place inside the computer's memory
 rather than in the physical world.
 
 As the experimenter, you need a clear idea of *what* you want to learn from the experiment.
-In the context of a network `simulation <Simulation>`_, this means that you have to know
+In the context of a network `Simulation`_, this means that you have to know
 *which input* you want to give to your network and *which output* you expect.
 
 The neural system is defined by a potentially large number of neurons and their
@@ -81,24 +79,19 @@ Fundamentally, you can build a basic network with the following functions::
     # Create the device to stimulate or record simulation
     device = nest.Create("device_name")
 
-    # Modify properties the neuron and device
+    # Modify properties of the neuron and device
     nest.SetStatus(neuron, {"key" : value})
     nest.SetStatus(device, {"key" : value})
 
-    # Tell NEST how they are connected to each other, (synapse properties can be
+    # Tell NEST how they are connected to each other (synapse properties can be
     # added here) 
     nest.Connect(device, neuron, syn_spec={"key": [value1, value2]})
 
     # Simulate network providing a specific timeframe.
     nest.Simulate(time_in_ms)
 
 NEST is extensible and new models for neurons, synapses, and devices can be
-added. If you would like to create your own model, check out the `NESTML Github
-page <https://github.com/nest/nestml>`_. NESTML uses a Python based modeling language to make
-it easier to create models in NEST. The project is still under development so
-not all types of models have been implemented. You can find details about model 
-creation using our C++ source code here.
-
+added. See how you can :doc:`create your own model <models/create_model>`.
 
 Connections
 ~~~~~~~~~~~~
@@ -123,7 +116,7 @@ able to deliver this information. Likewise, if you want to send specific input
 to the network, you need a device which delivers this input.
 
 Devices have a built-in timer which controls the period they are active. Outside
-this interval, a device will remain siltent. The timer can be configured using
+this interval, a device will remain silent. The timer can be configured using
 the command ``SetStatus``.
 
 Simulation
@@ -134,7 +127,7 @@ of size ``dt``, set using the property ``resolution`` of the root node. In each
 slice, all nodes in the system are updated and pending events are delivered.
 
 The simulation is run by calling the command ``Simulate(t)``, where ``t`` is the
-simulation time in milliseconds. See below for list of physi`cal units in NEST.
+simulation time in milliseconds. See below for list of physical units in NEST.
 
 Physical units in NEST
 -----------------------