From 76582859cb7df9678fa82d72e4d3d599a1bbd0ea Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 10 Aug 2015 15:29:59 +0200
Subject: [PATCH] Added documentation

---
 core/doc/CMakeLists.txt  |  1 +
 core/doc/index.rst       |  4 +++-
 core/doc/pm3argparse.rst | 33 +++++++++++++++++++++++++++++++++
 doc/conf.py.in           |  3 +++
 4 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 core/doc/pm3argparse.rst

diff --git a/core/doc/CMakeLists.txt b/core/doc/CMakeLists.txt
index fbf3f9ec..30f7cad1 100644
--- a/core/doc/CMakeLists.txt
+++ b/core/doc/CMakeLists.txt
@@ -1,6 +1,7 @@
 set(CORE_RST
 index.rst
 argcheck.rst
+pm3argparse.rst
 helper.rst
 setcompoundschemlib.rst
 )
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 1e2eccaf..8adefa26 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -9,7 +9,9 @@ modeling per se but cover standard programming issues.
 
 .. toctree:: 
   :maxdepth: 2
-  
+
+  pm3argparse
+
   argcheck
 
   helper
diff --git a/core/doc/pm3argparse.rst b/core/doc/pm3argparse.rst
new file mode 100644
index 00000000..cc823ef3
--- /dev/null
+++ b/core/doc/pm3argparse.rst
@@ -0,0 +1,33 @@
+:mod:`~promod3.core.pm3argparse` - Parsing Command Lines
+================================================================================
+
+.. currentmodule:: promod3.core.pm3argparse
+
+Introduction
+--------------------------------------------------------------------------------
+
+A lot of the actions in |project| have a bunch of command line parameters/
+arguments in common. For example we need an input alignment quite often and
+usually for an alignment we need information on what is the target sequence,
+what identifies a template sequence and eventually a hint on the format. That
+means we need the same functionality on the command line in several actions.
+There :class:`pm3argparse.PM3ArgumentParser` serves as a simplification. It
+provides a set of standard arguments you just need to activate for your action
+plus it comes with some verification functionality for input.
+
+.. synopsis/ example
+
+Argument Parser
+--------------------------------------------------------------------------------
+
+.. autoclass:: PM3ArgumentParser
+  :members:
+
+  .. automethod:: __init__
+
+.. |descattr| replace:: :attr:`description`
+.. |argpinit| replace:: :meth:`ArgumentParser.__init__`
+.. |progattr| replace:: :attr:`prog`
+
+..  LocalWords:  currentmodule argparse ArgumentParser autoclass automethod
+..  LocalWords:  init descattr attr argpinit meth progattr prog
diff --git a/doc/conf.py.in b/doc/conf.py.in
index f3bbada7..a122ac3f 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -286,6 +286,9 @@ rst_epilog = """
 .. _ost_s: http://www.OpenStructure.org
 .. _nameattr: @PYTHON_DOC_URL@/library/__main__.html
 .. _mainattr: @PYTHON_DOC_URL@/library/__main__.html
+.. _descattr: @PYTHON_DOC_URL@/library/argparse.html#description
+.. _progattr: @PYTHON_DOC_URL@/library/argparse.html#prog
+.. _argpinit: @PYTHON_DOC_URL@/library/argparse.html#argparse.ArgumentParser
 .. |pep8| replace:: PEP 8
 .. _pep8: https://www.python.org/dev/peps/pep-0008/
 """ % project
-- 
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