make doco internally consistent

CONTRIBUTING.rst

@@ -32,20 +32,22 @@ is open to whoever wants to implement it.
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
-Look through the GitHub issues for features. Anything tagged with "feature"
-is open to whoever wants to implement it.
+Look through the GitHub issues for new features. Anything tagged with
+"enhancement" is open to whoever wants to implement it.
 
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
 PyRate could always use more documentation, whether as part of the
 official PyRate docs, in docstrings, or even on the web in blog posts,
-articles, and such.
+articles etc.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/GeoscienceAustralia/PyRate/issues.
+The best way to send feedback is to file an Issue_.
+
+.. _Issue: https://github.com/GeoscienceAustralia/PyRate/issues
 
 If you are proposing a feature:
 
@@ -84,7 +86,7 @@ Now you can make your changes locally.
 
 6. Submit a pull request through the GitHub website.
 
-.. _Fork: https://github.com/Nekroze/PyRate/fork
+.. _Fork: https://help.github.com/articles/fork-a-repo/
 
 Pull Request Guidelines
 -----------------------

README.rst

@@ -16,9 +16,9 @@ Documentation: http://geoscienceaustralia.github.io/PyRate
 
 Issue tracking: https://github.com/GeoscienceAustralia/PyRate/issues
 
-=============
-Initial Setup
-=============
+============
+Installation
+============
 
 Before you start, you will need to have a number of packages installed on your Linux system. These can either be installed directly onto the system, or you can use a virtual environment.
 
@@ -77,9 +77,29 @@ The Python requirements should automatically be built and installed.
 For using PyRate in an Anaconda environment `use this
 guide <https://github.com/GeoscienceAustralia/PyRate/blob/master/conda.md>`_.
 
-===========
-Config File
-===========
+=====
+Tests
+=====
+
+A suite of tests have been developed for use in testing PyRate functionality
+and for further code development. The tests use
+`pytest <http://doc.pytest.org/en/latest/>`_ and can be found in the *tests/*
+directory. A small test dataset is included in the *tests/test_data/*
+directory.
+
+To run the tests, use the following command inside the top level *PyRate/*
+directory:
+
+.. code-block:: console
+
+    pip install pytest
+    cd PyRate
+    export PYRATEPATH=/path/to/PyRate
+    pytest tests/
+
+==================
+Configuration File
+==================
 
 Example configuration files for running PyRate with GAMMA or ROI\_PAC format
 interferograms are contained in the *configs/* directory.
@@ -88,7 +108,7 @@ interferograms are contained in the *configs/* directory.
 PyRate Workflow
 ===============
 
-After following the steps under Initial Setup, an executable program
+After following the steps under Installation, an executable program
 ``pyrate`` is created.
 
 Use ``help`` for the different command line options:
@@ -109,7 +129,7 @@ Use ``help`` for the different command line options:
       prepifg
 
 The ``pyrate`` program has three command line options corresponding to 
-different parts of the PyRate workflow.
+different parts of the PyRate workflow:
 
 1. ``prepifg``
 2. ``linrate``
@@ -223,7 +243,7 @@ Non-optional pre-processing steps include:
 - Identification of a suitable reference pixel
 - Removal of reference phase from interferograms
 - Calculation of interferogram covariance
-- Assembly of the varianec-covariance matrix
+- Assembly of the variance-covariance matrix
 
 ***********************************************
 3. postprocess: Putting the tiles back together
@@ -249,26 +269,6 @@ previous ``linrate`` step:
 
     pyrate postprocess path/to/config_file -c 3 -r 4
 
-=====
-Tests
-=====
-
-A suite of tests have been developed for use in testing PyRate functionality
-and for further code development. The tests use
-`pytest <http://doc.pytest.org/en/latest/>`_ and can be found in the *tests/*
-directory. A small test dataset is included in the *tests/test_data/*
-directory.
-
-To run the tests, use the following command inside the top level *PyRate/*
-directory:
-
-.. code-block:: console
-
-    pip install pytest
-    cd PyRate
-    export PYRATEPATH=/path/to/PyRate
-    pytest tests/
-
 ===========
 MPI Support
 ===========

docs/index.rst

@@ -24,13 +24,13 @@ Contents:
    :maxdepth: 2
 
    installation
-   hpc
    usage
+   hpc
    contributing
    authors
    history
+   scripts   
    modules
-   scripts
 
 
 Feedback

docs/installation.md

@@ -1,40 +1,73 @@
 # Installation
 
-## Quickstart
+Before you start, you will need to have a number of packages installed on your
+Linux system. These can either be installed directly onto the system, or you
+can use a virtual environment.
 
-Before you start, make sure your system has the following packages installed:
+
+## Direct Install
+
+Make sure your system has the following packages installed. If not, run the
+command:
 
     sudo apt-get install gdal-bin libgdal-dev libpng12-dev libblas-dev liblapack-dev libatlas-dev libatlas-base-dev gfortran libproj-dev openmpi-bin libopenmpi-dev netcdf-bin libnetcdf11 libnetcdf-dev
 
 
-We strongly recommend using a [`virtualenv`](https://gist.github.com/basaks/b33ea9106c7d1d72ac3a79fdcea430eb).
+## Virtual Environment
+
+You can use one of the two virtual environment options below:
+
+Note: if you are using a HPC environment, refer to [these instructions instead](hpc.html).
+
+
+### Virtualenv
+
+1. Install [`virtualenv`](https://gist.github.com/basaks/b33ea9106c7d1d72ac3a79fdcea430eb).
+
+2. You may need to install a slightly older `python-daemon` to install PyRate:
 
-One might need to install a slightly older `python-daemon` to install `PyRate`:
 
     pip install python-daemon==2.1.1
 
-To install, simply run ``setup.py``:
+3. Install PyRate by using one of the following options.
+
+-- Run ``setup.py``:
+
 
     python setup.py install
 
-or install with ``pip``:
+-- Install the latest version of PyRate with ``pip`` from github:
+
 
     pip install git+https://github.com/GeoscienceAustralia/PyRate
 
-The python requirements should automatically be built and installed.
+-- PyRate is also on ``pypi``, the Python package manager. To install, run:
+
+
+    pip install Py-Rate
+
+The Python requirements should automatically be built and installed.
+
 
+### Anaconda
 
-## Anaconda setup for `PyRate`
+For using PyRate in an Anaconda environment [use this
+guide](https://github.com/GeoscienceAustralia/PyRate/blob/master/conda.md).
 
-For anaconda installation and `virtualenv` instruction, [see this guide](https://github.com/GeoscienceAustralia/PyRate/blob/master/conda.md).
 
 ## Tests
 
-Tests use [pytest](http://doc.pytest.org/en/latest/) and can be found in *tests*.
+A suite of tests have been developed for use in testing PyRate functionality
+and for further code development. The tests use
+[pytest](http://doc.pytest.org/en/latest/) and can be found in the *tests/*
+directory. A small test dataset is included in the *tests/test_data/*
+directory.
 
-To run the tests, use the following command inside the `PyRate` directory:
+To run the tests, use the following command inside the top level *PyRate/*
+directory:
 
-	pip install pytest
-	cd PyRate
-	export PYRATEPATH=/path/to/PyRate
-	pytest tests/
+    pip install pytest
+    cd PyRate
+    export PYRATEPATH=/path/to/PyRate
+    pytest tests/
+