HYPERNETS · shunt16 · Nov 7, 2020 · Nov 7, 2020
diff --git a/docs/sphinx/atbd.rst b/docs/sphinx/atbd.rst
@@ -0,0 +1,11 @@
+.. atbd - algorithm theoretical basis
+   Author: seh2
+   Email: sam.hunt@npl.co.uk
+   Created: 23/3/20
+
+.. _atbd:
+
+Algorithm Theoretical Basis
+===========================
+
+.. include:: content/atbd/atbd.rst
diff --git a/docs/sphinx/conf.py b/docs/sphinx/conf.py
@@ -76,6 +76,8 @@ def setup(app):
 
 # The master toctree document.
 master_doc = 'index'
+atbd = 'atbd'
+userguide = 'userguide'
 
 # General information about the project.
 project = u'hypernets_processor'
@@ -295,7 +297,9 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'hypernets_processor.tex', u'Hypernets Processor Documentation',
+    (userguide, 'hypernets_processor_userguide.tex', u'Hypernets Processor User Guide',
+     u'Hypernets Project Team', 'manual'),
+    (atbd, 'hypernets_processor_atbd.tex', u'Hypernets Processor Algorithm Theoretical Basis Document',
      u'Hypernets Project Team', 'manual'),
 ]
 
@@ -352,7 +356,7 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'hypernets_processor', u'hypernets_processor Documentation',
+    (master_doc, 'hypernets_processor', u'Hypernets Processor User Guide',
      author, 'hypernets_processor', 'One line description of project.',
      'Miscellaneous'),
 ]

diff --git a/docs/sphinx/content/atbd/atbd.rst b/docs/sphinx/content/atbd/atbd.rst
@@ -1,11 +1,12 @@
 .. atbd - algorithm theoretical basis
    Author: seh2
    Email: sam.hunt@npl.co.uk
-   Created: 23/3/20
+   Created: 6/11/20
 
 .. _atbd:
 
+
 Algorithm Theoretical Basis
-===========================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For more information see the project document.
+TBC
diff --git a/docs/sphinx/content/developers/developers.rst b/docs/sphinx/content/developers/developers.rst
diff --git a/...developers/developers_getting_started.rst → ...nx/content/developers/getting_started.rst b/...developers/developers_getting_started.rst → ...nx/content/developers/getting_started.rst
diff --git a/docs/sphinx/content/users/user_adhoc.rst → docs/sphinx/content/users/adhoc.rst b/docs/sphinx/content/users/user_adhoc.rst → docs/sphinx/content/users/adhoc.rst
@@ -5,8 +5,8 @@
 
 .. _user_adhoc:
 
-User Guide - Ad-hoc Sequence Processing
-=======================================
+Ad-hoc Sequence Processing
+==========================
 
 This section provides a user guide for running the **hypernets_processor** module to process specified field acquisitions, or sequences, on an ad-hoc basis outside of any automated processing.
 
@@ -43,7 +43,7 @@ where:
 
 * `input_directory` - directory of raw sequence product, or directory containing a number of raw sequence products, to process.
 * `output_directory` - directory to write output data to.
-* `network` - network name, land or water. The default configuration for this network is applied for the processing.
+* `network` - network name, `land` or `water`. The default configuration for this network is applied for the processing.
 
 To see more options, try::
 

diff --git a/docs/sphinx/content/users/user_automated.rst → docs/sphinx/content/users/automated.rst b/docs/sphinx/content/users/user_automated.rst → docs/sphinx/content/users/automated.rst
@@ -5,8 +5,8 @@
 
 .. _user_automated:
 
-User Guide - Automated Processing
-=================================
+Automated Processing
+====================
 
 This section provides a user guide for running the **hypernets_processor** module as an automated processor of incoming field data. In this scenario, a set of field hypstar systems are regularly syncing raw data to a server.  Running on this server, the **hypernets_processor** processes the data and adds it to an archive that can be accessed through a user portal.
 

diff --git a/docs/sphinx/index.rst b/docs/sphinx/index.rst
@@ -8,36 +8,32 @@ hypernets_processor: Hypernets field and land network data processor
 
 The **hypernets_processor** module is a Python software package to process the `Hypernets <http://hypernets.eu/from_cms/summary>`_ land and water network in-situ hyperspectral data to surface reflectance products for distribution to users.
 
+There are two main use cases for the **hypernets_processor** module. The primary function of the software is the automated preparation of data retrieved from network sites for distribution to users. Additionally, the software may also be used for ad-hoc processing of particular field acquisitions, for example for testing instrument operation in the field.
+
 This documentation aimed at both users and developers of the software, find the relevant sections below.
 
-For Users:
-~~~~~~~~~~
+.. toctree::
+   :maxdepth: 1
+   :caption: User Guide
+
+   content/users/adhoc
+   content/users/automated
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
+   :caption: ATBD
 
-   content/users/users
    content/atbd/atbd
 
-For Developers:
-~~~~~~~~~~~~~~~
-
 .. toctree::
-   :maxdepth: 2
-
-   content/developers/developers
+   :maxdepth: 1
+   :caption: Developer Guide
 
-API Documentation
-~~~~~~~~~~~~~~~~~
+   content/developers/getting_started
+   content/developers/software_design
 
 .. toctree::
    :maxdepth: 2
+   :caption: API Documentation
 
-   content/API/hypernets_processor
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   content/API/hypernets_processor
diff --git a/docs/sphinx/content/users/users.rst → docs/sphinx/userguide.rst b/docs/sphinx/content/users/users.rst → docs/sphinx/userguide.rst
@@ -14,5 +14,5 @@ There are two main use cases for the **hypernets_processor** module. The primary
 .. toctree::
    :maxdepth: 1
 
-   user_adhoc
-   user_automated
+   content/users/adhoc
+   content/users/automated