.. TESFDMtools documentation master file, created by
   sphinx-quickstart on Mon May  1 10:08:53 2017.
   You can adapt this file completely to your liking, but it should at least
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Welcome to TESFDMtools's documentation!
=======================================

Using TESFDMtools software for the first time
---------------------------------------------

Before you install or use the software for the first time, please make sure that the packages mentioned in :doc:`debpackages` are installed.

If you are running TESFDMtools on an SRON machine, please see "Initialize TESFDMtools software" below for instructions how to run the software.


Initialize TESFDMtools software
-------------------------------

To make all executables and modules of TESFDMtools available in your terminal type:

For bash shells:
  "source /opt/local/TN/env/tesfdmtools.sh"

For csh shells:
  "source /opt/local/TN/env/tesfdmtools.csh"

These files set the PATH variable for executables and the PYTHONPATH variable for python modules. In principle, the source command
can be added to the .bashrc or .cshrc file in your home directory to set these variables automatically. However, be aware that
this environment could conflict with other software packages. 


TESFDMtools pipeline processing scripts and tools
-------------------------------------------------

Your path should include "/opt/local/TN/tesfdmtools/bin" to use these scripts.
(This path will be automatically set when sourcing the above .csh or .sh files)

Contents:

.. toctree::
   :maxdepth: 2

   scripts/scripts
   scripts/runscripts


TESFDMtools Python3 module library
----------------------------------

The PYTHONPATH environment variable must be set to  "/opt/local/TN/tesfdmtools/lib/python3.5/site-packages" to make the
`tesfdmtools` module library available.

Contents:

.. toctree::
   :maxdepth: 2

   hdf/hdf
   methods/methods
   utils/widgets/widgets
   utils/utils

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

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