From 9a30f193f94d325301471cd302330cb57fc85cd6 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 17 Dec 2014 17:54:38 +0100
Subject: [PATCH] Updated documentation
---
doc/html/_modules/index.html | 2 +-
doc/html/_modules/promod3/core/argcheck.html | 2 +-
doc/html/_modules/promod3/core/helper.html | 2 +-
doc/html/_modules/promod3/rawmodel.html | 2 +-
doc/html/_sources/cmake/index.txt | 2 ++
doc/html/_sources/contributing.txt | 16 +++++++++-------
doc/html/cmake/index.html | 4 ++--
doc/html/contributing.html | 14 +++++++-------
doc/html/core/argcheck.html | 2 +-
doc/html/core/helper.html | 2 +-
doc/html/core/index.html | 2 +-
doc/html/developers.html | 2 +-
doc/html/genindex.html | 2 +-
doc/html/index.html | 2 +-
doc/html/objects.inv | 5 ++++-
doc/html/py-modindex.html | 2 +-
doc/html/rawmodel/index.html | 2 +-
doc/html/search.html | 2 +-
doc/html/searchindex.js | 2 +-
19 files changed, 38 insertions(+), 31 deletions(-)
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index ec0ee24d..e8a7903e 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -86,7 +86,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index a93ba9d3..1cf987a2 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -193,7 +193,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index ed1ae044..de9b8e2c 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/rawmodel.html b/doc/html/_modules/promod3/rawmodel.html
index 97ba70ba..30aa1ae1 100644
--- a/doc/html/_modules/promod3/rawmodel.html
+++ b/doc/html/_modules/promod3/rawmodel.html
@@ -90,7 +90,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_sources/cmake/index.txt b/doc/html/_sources/cmake/index.txt
index 8fb98c96..ca224d7d 100644
--- a/doc/html/_sources/cmake/index.txt
+++ b/doc/html/_sources/cmake/index.txt
@@ -1,3 +1,5 @@
+.. _pm3-cmake-doc:
+
|project|'s Share Of |cmake|
===============================================================================
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index be7f6cf0..fb68988f 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -169,10 +169,10 @@ tell it which files have to be considered packaging, compiling, etc.. Also
documentation. |cmake| is a rather complex topic (unfortunately all usable
build systems seem to be) so we skip a detailed view, here, and just advice you
to go by example. There is a tiny bit of documentation on our additions to
-|cmake| in the top-level :file:`cmake_support` directory. If you really need to
-make changes to the build system, other than adding new files and modules, you
-have to dive into |cmake| documentation all by yourself and on your own
-responsibility. You have been warned.
+|cmake| :ref:`here <pm3-cmake-doc>`. If you really need to make changes to the
+build system, other than adding new files and modules, you have to dive into
+|cmake| documentation all by yourself and on your own responsibility. You have
+been warned.
--------------------------------------------------------------------------------
The :file:`stage` Directory
@@ -191,7 +191,7 @@ tutorial on unit testing here. Again, have a look at how other modules treat
this topic and then there is quite a lot of educated material to be found on
the Internet. Nevertheless, here is a short list of most important advices:
-* Tests go into dedicated scripts in the :file:`tests` directory
+* Tests go into dedicated scripts/ source files in the :file:`tests` directory
* No external data dependencies, if tests need data, they find it in
:file:`tests/data`
* If 'exotic' |python| modules are used, consider making the test aware of the
@@ -431,7 +431,7 @@ top level :file:`CMakeLists.txt`:
COMPONENTS io mol seq seq_alg mol_alg conop)
find_package(QMEAN 1.0 REQUIRED)
- #The KIC loop closing algorithm requires a solver for a generalized eigen
+ #The KIC loop closing algorithm requires a solver for a generalised eigen
#problem. Eigen3 would provide such a solver, but only allows to extract
#the resulting eigenvalues and not the eigenvectors.
#As soon as there is an Eigen3 release with the required functionality,
@@ -643,4 +643,6 @@ contributions to web pages using |project|.
.. LocalWords: changelog Optimized DOPTIMIZE gitignore cd conf subtree attr
.. LocalWords: unittest TestCase nameattr testcode staticmethod builtin cp
.. LocalWords: SomethingTests testFileExistsFalse testutils RunTests DQMEAN
-.. LocalWords: pre
+.. LocalWords: pre API inline CMake hh ProMod Bienchen OST OPENSTRUCTURE
+.. LocalWords: mol alg conop QMEAN KIC eigen eigenvectors Lapack rawmodel
+.. LocalWords: OpenStructure ost
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index b37ddcc5..4d924791 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -55,7 +55,7 @@
<div class="body">
<div class="section" id="project-s-share-of-cmake">
-<h1>ProMod3‘s Share Of CMake<a class="headerlink" href="#project-s-share-of-cmake" title="Permalink to this headline">¶</a></h1>
+<span id="pm3-cmake-doc"></span><h1>ProMod3‘s Share Of CMake<a class="headerlink" href="#project-s-share-of-cmake" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>This section describes the set of ProMod3‘s own set of CMake functions (or
@@ -194,7 +194,7 @@ build directory.</dd>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 94cb4f14..550edc96 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -200,10 +200,10 @@ Python modules are declared there as well as which files belong to the
documentation. CMake is a rather complex topic (unfortunately all usable
build systems seem to be) so we skip a detailed view, here, and just advice you
to go by example. There is a tiny bit of documentation on our additions to
-CMake in the top-level <tt class="file docutils literal"><span class="pre">cmake_support</span></tt> directory. If you really need to
-make changes to the build system, other than adding new files and modules, you
-have to dive into CMake documentation all by yourself and on your own
-responsibility. You have been warned.</p>
+CMake <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><em>here</em></a>. If you really need to make changes to the
+build system, other than adding new files and modules, you have to dive into
+CMake documentation all by yourself and on your own responsibility. You have
+been warned.</p>
</div>
<div class="section" id="the-stage-directory">
<h2>The <tt class="file docutils literal"><span class="pre">stage</span></tt> Directory<a class="headerlink" href="#the-stage-directory" title="Permalink to this headline">¶</a></h2>
@@ -220,7 +220,7 @@ tutorial on unit testing here. Again, have a look at how other modules treat
this topic and then there is quite a lot of educated material to be found on
the Internet. Nevertheless, here is a short list of most important advices:</p>
<ul class="simple">
-<li>Tests go into dedicated scripts in the <tt class="file docutils literal"><span class="pre">tests</span></tt> directory</li>
+<li>Tests go into dedicated scripts/ source files in the <tt class="file docutils literal"><span class="pre">tests</span></tt> directory</li>
<li>No external data dependencies, if tests need data, they find it in
<tt class="file docutils literal"><span class="pre">tests/data</span></tt></li>
<li>If ‘exotic’ Python modules are used, consider making the test aware of the
@@ -550,7 +550,7 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
<span class="s">COMPONENTS</span> <span class="s">io</span> <span class="s">mol</span> <span class="s">seq</span> <span class="s">seq_alg</span> <span class="s">mol_alg</span> <span class="s">conop</span><span class="p">)</span>
<span class="nb">find_package</span><span class="p">(</span><span class="s">QMEAN</span> <span class="s">1.0</span> <span class="s">REQUIRED</span><span class="p">)</span>
-<span class="c">#The KIC loop closing algorithm requires a solver for a generalized eigen</span>
+<span class="c">#The KIC loop closing algorithm requires a solver for a generalised eigen</span>
<span class="c">#problem. Eigen3 would provide such a solver, but only allows to extract</span>
<span class="c">#the resulting eigenvalues and not the eigenvectors.</span>
<span class="c">#As soon as there is an Eigen3 release with the required functionality,</span>
@@ -802,7 +802,7 @@ contributions to web pages using ProMod3.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 4178be9a..c10e0669 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:01, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 5690b18b..13a1ce9a 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -160,7 +160,7 @@ traditionally reserved to successful commands.</li>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:01, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index b322dd3d..75d97737 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -129,7 +129,7 @@ modeling per se but cover standard programming issues.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:01, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 7c507c83..ce43872e 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -145,7 +145,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 6f5b46d3..d6ae56c8 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -229,7 +229,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/index.html b/doc/html/index.html
index b7e39fb3..3a5a7926 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -133,7 +133,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 7fdd6319..979d022a 100644
--- a/doc/html/objects.inv
+++ b/doc/html/objects.inv
@@ -3,4 +3,7 @@
# Version: 0.1
# The remainder of this file is compressed using zlib.
xڝ��N�0��y
-Kp�!�HE�!*�\{q��'��jx{b٩���)����5N(+`$E��4�2|Ԧ h�FߐΉ���TI��Y-�l
�<��Vl����$T�ìh��o�*DH�a'h˘4��n���UIQ�<LК�|O��4�A��xv���27�?dS=e^� ��>+
���l�{��czo2�Ź��ѧ��8�s7#-:��V4=�<��y����Q�Mq~�2c(+�Fz9C��~�u�O�!��n��*`���WP��k��O�x&�
\ No newline at end of file
+K q���-7@A�Q��\{�X�Odo���IpR�J(Г�ٙ��5N(+�%E��4IW�>�f�
+��#����K���!���ե1j�m
k&!�M�r��
+�/3�������먲�@��@>���\ w�0+�ڻ��gc"�%�0&��i2�(w]g}�M��酩9�iƳcwv���(����)�W��Mi(Z��}ݾ� ��*���3��=��(-6�X�H��%�M�O� ���h.� ΟYF e�B������5���'Y �[��s0ܸ�T��5 �
+��>c
\ No newline at end of file
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 7823911e..55097bcb 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index 7441ae35..f49dd1d4 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -214,7 +214,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:01, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 2cf86f8a..b589a56c 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Dec 16 17:54, 2014.
+ Last updated on Dec 17 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index e2cee77e..735ff48f 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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