.. CRTomo user manual documentation master file, created by
   sphinx-quickstart on Mon Feb 20 10:17:50 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to CRTomo user manual's documentation!
==============================================

:mod:`crtomo`

Contents:

.. toctree::
   :maxdepth: 2

   misc/installation.rst
   crtomo/crtomo.rst
   tutorials.rst
   developers.rst
   crtomo_tools/crtomo_tools.rst
   crtomo_test/crtomo_test.rst

.. todo::

    import inversion tutorials

.. todo::

    jg: incorporate python requirements etc somewhere else

Introduction
------------

The CRTomo-ecosystem is maintained in four repositories:

* *crtomo*: the CRMod/CRTomo/CutMcK programs, written in the Fortran
  programming language
* *crtomo_tools*: user space tools that help with the various tasked associated
  with using CRMod/CRTomo, such as grid creation, analysis of
  modeling/inversion results, and plotting of various results. Mostly written
  in the Python programming language.
* *crtomo_doc*: this documentation. The documentation should provide links to
  external literature, but should be self-contained in the way that novice
  users should be able to install, configure, and use CRMod/CRTomo only by
  reading this documentation.
* *crtomo_test*: Test and use cases for CRTomo. This is part automatic test
  suite, part manual storage location for 'interesting' use cases.

We aim at full usability on both Linux and Windows operating systems.

.. todo::

    jg: add short general description of CRTomo

History of CRTomo
-----------------

.. todo::

    jg: add history; development history or general?

Example blockdiagram
--------------------

.. blockdiag::
    :scale: 110%

    blockdiag workflow{
        "data/frequencies" -> "batch file (.sh/.bat)";
        "batch file (.sh/.bat)" -> "execution";
        "execution" -> "output directory";
        "output directory" -> "post processing";
    }

.. todo::

    jg: move somewhere else? -> seems lost here

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`