diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index a0608c2c640cd6939b2234cff2209735817db72f..5b24bb3c5d13289075f1aae105755f787c82cdb2 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,7 +85,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 3d7cfa89c5013e41946992c688b8d2f5ffbde62b..6b6f952c996a86b27904f39e45f915e5c2c20918 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -47,6 +47,10 @@
<div class="body">
<h1>Source code for promod3.core.argcheck</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+<span class="sd">Basic helpers for arguments.</span>
+<span class="sd">"""</span>
+
<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
<div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
@@ -105,7 +109,7 @@
<span class="sd"> :returns: (base name of ``file`` (:class:`str`), extension of file without a</span>
<span class="sd"> ".gz" (:class:`str`), flag to indicate an additional ".gz"</span>
<span class="sd"> (:class:`bool`)) **if** ``gz`` is set, (base name of ``file``</span>
-<span class="sd"> (:class:`str`), extension of file if not).</span>
+<span class="sd"> (:class:`str`), extension of file) **if not**.</span>
<span class="sd"> '''</span>
<span class="n">filename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">False</span>
@@ -113,10 +117,16 @@
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">filename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">gz</span><span class="p">:</span>
- <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">))</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="o">+</span><span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
<span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">''</span><span class="p">:</span>
- <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">))</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="o">+</span><span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
<span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">for</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">extensions</span><span class="p">:</span>
@@ -125,7 +135,11 @@
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">fileext</span><span class="p">,</span> <span class="n">is_gz</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">fileext</span>
- <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">))</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="o">+</span><span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
</div>
<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span>
@@ -174,7 +188,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index 248a7207b59e1ccf6cfd58729921fa86fe71c8c9..df9d374eef9b2ff7036fa06e5fc6955fe4dadfe3 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -7,7 +7,7 @@ Dependencies
1.4, and |qmean|_. To create the build system, |cmake|_ is required in version
2.8.7 or higher. |python|_ works well from version 2.7. For |ost_s| and the
|C++| bit of |project|, |boost|_ is required in version 1.47.0 (the same as
-used for |ost_s|). To build documentation, |sphinx|_ 1.2b1 is used.
+used for |ost_s|). Also |eigen3|_, at least version 3.2.1, is needed. To build documentation, |sphinx|_ 1.2b1 is used.
* |ost_s|_ 1.4
* |qmean|_
@@ -15,6 +15,7 @@ used for |ost_s|). To build documentation, |sphinx|_ 1.2b1 is used.
* |python|_ 2.7
* |boost|_ 1.47.0
* |sphinx|_ 1.2b1
+* |eigen3|_ 3.2.1
--------------------------------------------------------------------------------
Using |cmake|
@@ -32,7 +33,10 @@ For us, at least pointers to the |ost_s| and |qmean| installation directories
are needed, handed over to |cmake| by ``-D`` into the variables ``OST_ROOT``
and ``QMEAN_ROOT``. Other important variables would be ``BOOST_ROOT``, set to
the same path as for |ost_s| and probably ``PYTHON_ROOT`` if you want to use a
-certain |python|. Don't forget to put a ``-D`` in front of options.
+certain |python|. Also |eigen3| can be pulled in like this, e.g. if you have to
+download it by yourself because its not installed on your system. Just point
+``EIGEN3_INCLUDE_DIR`` to the path which provides the :file:`Eigen` header
+directory. Don't forget to put a ``-D`` in front of options.
Here is a list of more options used within |project|:
@@ -84,11 +88,13 @@ special targets:
* ``help`` :index:`make help` Prints a list of targets available
.. |qmean| replace:: QMEAN
+.. |eigen3| replace:: Eigen 3
.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi?
.. _ost_l: http://www.OpenStructure.org
.. _cmake: http://www.cmake.org/
.. _python: https://www.python.org/
.. _boost: http://www.boost.org/
+.. _eigen3: http://eigen.tuxfamily.org/
.. LocalWords: cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
-.. LocalWords: doctest linkcheck qmean DQMEAN
+.. LocalWords: doctest linkcheck qmean DQMEAN eigen
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index dff3640e9ad87a0749104b2a3126b0a9c51c5f0e..16777995889be1ef15ace977e1f43b2b3da3f940 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -252,6 +252,17 @@ from it. As an example, your feature will go by the name of 'sidechains'.
This time, |git| should tell you about going for **a new** branch.
+Before starting to create anything for real, now is the perfect moment to
+install our very own |git| hook to check some coding rules on commit.
+
+.. code-block:: console
+
+ $ cp extras/pre-commit .git/hooks/
+ $
+
+With that in place, changes which break our coding standards will abort any
+commit.
+
Now create the directory structure where your project will live. Here is the
list of directories which are likely to be used in every project.
@@ -559,6 +570,37 @@ you.
Now tests should be available by ``make check``, ``make codetest`` and
``make test_something.py_run``.
+--------------------------------------------------------------------------------
+Third Party Contributions (License Issues)
+--------------------------------------------------------------------------------
+For some tasks you may want to make use of third party contributions in your
+module, for example
+
+* calling/ using the output of third party binaries
+* external libraries
+* smallish bits of source code included into the |project| directory tree
+* |python| modules not distributed as part of the |python|
+ :py_docs:`standard library <library/>`,
+
+where modules from the |python| standard library are covered by the |python|
+`license <https://www.python.org/download/releases/2.7.5/license>`_. And
+licenses is what you have to watch out for with this subject. While the |python|
+license is save to be used, in the past several projects went restrictive
+because of exclusive terms of use. Those issues often came from 'academic
+licenses', allowing use if free of charge but for commercial entities. To
+prevent this is one reason for the existence of |project|. This means, before
+utilising external code, third party libraries, basically anything not created
+within this project (including pictures, test data, etc.), check licensing.
+What cannot be used at all are items without any license. Those things are not
+'free' but more in a legally uncertain state. Also forbidden are licenses which
+exclude commercial entities.
+
+There are a lot of rather permissive licenses out there, very often asking for
+acknowledgements. We definitively support this. Either go by example phrases
+suggested in the license itself or find some nice paragraph yourself and place
+it in the documentation. We should also not forget to promote those
+contributions to web pages using |project|.
+
.. |fedora| replace:: Fedora
.. |nameattr| replace:: :attr:`__name__`
@@ -569,5 +611,6 @@ Now tests should be available by ``make check``, ``make codetest`` and
.. LocalWords: mkdir linenos subdirectory abrv emphasize CXX GNUCXX gcc fno
.. LocalWords: ARGS endif OPTIMIZE LIBEXEC Wno DIRS dirs subdirs config dbg
.. LocalWords: changelog Optimized DOPTIMIZE gitignore cd conf subtree attr
-.. LocalWords: unittest TestCase nameattr testcode staticmethod builtin
-.. LocalWords: SomethingTests testFileExistsFalse testutils RunTests
+.. LocalWords: unittest TestCase nameattr testcode staticmethod builtin cp
+.. LocalWords: SomethingTests testFileExistsFalse testutils RunTests DQMEAN
+.. LocalWords: pre
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index f3e8ab05ff4a55f448aaafec108e1ddb5dbc92fb..4c6e894a2934d7d11c1fdf876ec5af1d534265e3 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -62,7 +62,7 @@
1.4, and <a class="reference external" href="http://swissmodel.expasy.org/qmean/cgi/index.cgi?">QMEAN</a>. To create the build system, <a class="reference external" href="http://www.cmake.org/">CMake</a> is required in version
2.8.7 or higher. <a class="reference external" href="https://www.python.org/">Python</a> works well from version 2.7. For OST and the
C++ bit of ProMod3, <a class="reference external" href="http://www.boost.org/">Boost</a> is required in version 1.47.0 (the same as
-used for OST). To build documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is used.</p>
+used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/">Eigen 3</a>, at least version 3.2.1, is needed. To build documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is used.</p>
<ul class="simple">
<li><a class="reference external" href="http://www.OpenStructure.org">OST</a> 1.4</li>
<li><a class="reference external" href="http://swissmodel.expasy.org/qmean/cgi/index.cgi?">QMEAN</a></li>
@@ -70,6 +70,7 @@ used for OST). To build documentation, <a class="reference external" href="http:
<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7</li>
<li><a class="reference external" href="http://www.boost.org/">Boost</a> 1.47.0</li>
<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1</li>
+<li><a class="reference external" href="http://eigen.tuxfamily.org/">Eigen 3</a> 3.2.1</li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -85,7 +86,10 @@ right from a shell with the directory containing the top-level
are needed, handed over to CMake by <tt class="docutils literal"><span class="pre">-D</span></tt> into the variables <tt class="docutils literal"><span class="pre">OST_ROOT</span></tt>
and <tt class="docutils literal"><span class="pre">QMEAN_ROOT</span></tt>. Other important variables would be <tt class="docutils literal"><span class="pre">BOOST_ROOT</span></tt>, set to
the same path as for OST and probably <tt class="docutils literal"><span class="pre">PYTHON_ROOT</span></tt> if you want to use a
-certain Python. Don’t forget to put a <tt class="docutils literal"><span class="pre">-D</span></tt> in front of options.</p>
+certain Python. Also Eigen 3 can be pulled in like this, e.g. if you have to
+download it by yourself because its not installed on your system. Just point
+<tt class="docutils literal"><span class="pre">EIGEN3_INCLUDE_DIR</span></tt> to the path which provides the <tt class="file docutils literal"><span class="pre">Eigen</span></tt> header
+directory. Don’t forget to put a <tt class="docutils literal"><span class="pre">-D</span></tt> in front of options.</p>
<p>Here is a list of more options used within ProMod3:</p>
<ul class="simple">
<li><tt class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></tt> Don’t build documentation, don’t search for Sphinx</li>
@@ -197,7 +201,7 @@ builder</li>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 09:50, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 897b211d3de4fc56f253f188d425fce2e0d95192..b130401c078e6a83787778ff52d62b20098cb933 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -127,7 +127,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jun 19 11:04, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 5fd2f52ba779ba2eb2b3754615a91e275e78c2ee..1564617236456abd2e4b705547b7b25d0004cc77 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -270,6 +270,14 @@ from it. As an example, your feature will go by the name of ‘sidechains
</pre></div>
</div>
<p>This time, Git should tell you about going for <strong>a new</strong> branch.</p>
+<p>Before starting to create anything for real, now is the perfect moment to
+install our very own Git hook to check some coding rules on commit.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre-commit .git/hooks/
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>With that in place, changes which break our coding standards will abort any
+commit.</p>
<p>Now create the directory structure where your project will live. Here is the
list of directories which are likely to be used in every project.</p>
<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir -p sidechains/doc
@@ -636,6 +644,35 @@ you.</p>
<p>Now tests should be available by <tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt>, <tt class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></tt> and
<tt class="docutils literal"><span class="pre">make</span> <span class="pre">test_something.py_run</span></tt>.</p>
</div>
+<div class="section" id="third-party-contributions-license-issues">
+<h2>Third Party Contributions (License Issues)<a class="headerlink" href="#third-party-contributions-license-issues" title="Permalink to this headline">ΒΆ</a></h2>
+<p>For some tasks you may want to make use of third party contributions in your
+module, for example</p>
+<ul class="simple">
+<li>calling/ using the output of third party binaries</li>
+<li>external libraries</li>
+<li>smallish bits of source code included into the ProMod3 directory tree</li>
+<li>Python modules not distributed as part of the Python
+<a class="reference external" href="https://docs.python.org/2.7/library/">standard library</a>,</li>
+</ul>
+<p>where modules from the Python standard library are covered by the Python
+<a class="reference external" href="https://www.python.org/download/releases/2.7.5/license">license</a>. And
+licenses is what you have to watch out for with this subject. While the Python
+license is save to be used, in the past several projects went restrictive
+because of exclusive terms of use. Those issues often came from ‘academic
+licenses’, allowing use if free of charge but for commercial entities. To
+prevent this is one reason for the existence of ProMod3. This means, before
+utilising external code, third party libraries, basically anything not created
+within this project (including pictures, test data, etc.), check licensing.
+What cannot be used at all are items without any license. Those things are not
+‘free’ but more in a legally uncertain state. Also forbidden are licenses which
+exclude commercial entities.</p>
+<p>There are a lot of rather permissive licenses out there, very often asking for
+acknowledgements. We definitively support this. Either go by example phrases
+suggested in the license itself or find some nice paragraph yourself and place
+it in the documentation. We should also not forget to promote those
+contributions to web pages using ProMod3.</p>
+</div>
</div>
@@ -654,6 +691,7 @@ you.</p>
<li><a class="reference internal" href="#unit-tests">Unit Tests</a></li>
<li><a class="reference internal" href="#writing-documentation">Writing Documentation</a></li>
<li><a class="reference internal" href="#how-to-start-your-own-module">How To Start Your Own Module</a></li>
+<li><a class="reference internal" href="#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
</ul>
</li>
</ul>
@@ -707,7 +745,7 @@ you.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 6741990a6cfe54153bb54753ac62a08ab5133b71..2f9b0bd2d9b69e34ed0ee1212a7b8e1fd02b3c05 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -142,7 +142,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <tt class="docutils literal"><span class="pre">file</span></tt> (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), extension of file without a
”.gz” (<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), flag to indicate an additional ”.gz”
(<tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt>)) <strong>if</strong> <tt class="docutils literal"><span class="pre">gz</span></tt> is set, (base name of <tt class="docutils literal"><span class="pre">file</span></tt>
-(<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), extension of file if not).</p>
+(<tt class="xref py py-class docutils literal"><span class="pre">str</span></tt>), extension of file) <strong>if not</strong>.</p>
</td>
</tr>
</tbody>
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 09:50, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 992edc9e82b9c71fa06eaf623efeb97519aefdc3..61373e9a0a2ee7f2d119ae22e2446402dc710892 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,7 +123,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 09:50, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index f50bf07cc4a387f45be06dfcf076ff093ad94a1c..4198ed7194c60bff02f162ad9d59db9f411013b6 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -79,6 +79,7 @@
<li class="toctree-l2"><a class="reference internal" href="contributing.html#unit-tests">Unit Tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#writing-documentation">Writing Documentation</a></li>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#how-to-start-your-own-module">How To Start Your Own Module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="contributing.html#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
</ul>
</li>
</ul>
@@ -139,7 +140,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 228223819fc382dfd4dd98ad29bd6cbc6eec9c5e..338067fcc562c174b490fd36d57440e9b43f64a5 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -334,7 +334,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/index.html b/doc/html/index.html
index f6469e9d8676b93dc1b0945c083822929bd55dc6..9f457b6468d31f1edaa042527323be92ee1a68b4 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/index.html b/doc/html/meld/index.html
index ee4af64ac7bbe3a199af6eb92190138c8bec0cc2..11f75c69a756dc5d4317143c7db987254fd3abcf 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -127,7 +127,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jun 19 11:04, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/loop.html b/doc/html/meld/loop.html
index 9c486901bd05513404169dd1c46fe210ee4c0746..4c96dedd051543932f4bbe16cebb17748f4204a3 100644
--- a/doc/html/meld/loop.html
+++ b/doc/html/meld/loop.html
@@ -338,7 +338,7 @@ extension of the gap.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jun 19 11:04, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/rawmodel.html b/doc/html/meld/rawmodel.html
index 2ada8943e78f374c805283ff302d719f60edf4c6..6ce3448981d235303154f7350e1125d6f1ea0196 100644
--- a/doc/html/meld/rawmodel.html
+++ b/doc/html/meld/rawmodel.html
@@ -221,7 +221,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jun 19 11:04, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 12044229f7d8f4641a521777fef1c1f27935d098..fa69201d044980768da879cf410081d7f709e4d1 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index b39703852981793d5c099921721236011bc5dc01..543390b6446f33313b8a9c7bbda3d32dbc1f5a1f 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/search.html b/doc/html/search.html
index ef7e789a64f59b9d6de0a370a0c1f24360dc2443..beab970fcf713ba870ed4b8cae113a2f37f267e9 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jul 07 10:40, 2014.
+ Last updated on Aug 07 14:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index c1acd1872f521fbeb3ae719aacb58ce889084408..b52058020aa72497284d3e6fc3154b1172f2b72a 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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ve:8,hit:8,unus:8,variou:5,get:[8,5],watch:8,cannot:8,loadpdb:6,increas:1,toolbox:8,requir:[8,5,1],setup_compiler_flag:8,add_changelog_to_doc:8,enabl:0,coord:1,"default":[8,5],common:[8,0],contain:[8,0,5,6,9],python_root:5,where:8,remov:5,view:8,set:[8,0,1,5,6],seq:8,allatom_scor:1,frame:8,abort:8,ost_include_dir:8,see:8,temporarili:8,result:6,arg:8,testcas:8,reserv:0,sport:8,subject:8,awar:8,statu:8,detect:0,extend:8,someth:8,version_great:8,enumer:8,label:8,state:[8,5],score:1,subdir:8,simplest:8,"import":[8,0,5,6],awai:8,paramet:[0,1,6],approach:8,attribut:8,accord:8,parent:6,sole:8,cmake_cxx_compiler_vers:8,test_your_modul:8,recent:8,solv:8,come:[8,0],addit:[8,0],fail:[8,1],extens:[0,1],howev:1,disable_doctest:[8,5],promod3_version_patch:8,tutori:8,grain:8,fno:8,modif:6,whole:[8,6],pdb:[0,6],comment:8,sidechains_rst:8,"1ake":6,point:[8,5,1],cxx:8,overview:8,unittest:8,argumentpars:0,pop:8,walk:8,residu:[1,6],header:[8,5],featur:8,littl:8,test_submodule1:8,assum:8,torsion:1,quit:8,template_structur:6,creat:[8,5],coupl:8,rebuild:[8,5],three:8,been:8,sinc:[8,0],compon:8,trigger:8,besid:5,treat:[8,6],basic:[8,5,6],txt:[8,5],ost_root:[8,5],popul:[8,5],seq_alg:8,tini:8,quickli:8,life:[8,1],convert:6,ani:8,coordin:[],togeth:8,els:8,fileexist:0,educ:8,those:[8,5],"case":8,cmake_c_compiler_vers:8,uncertain:8,look:[8,0],raw:9,testfileexistsfals:8,straight:8,properti:8,commerci:8,formatt:8,invok:[8,5],boost_root:5,abov:8,error:0,dost_root:[8,5],loop:9,pack:1,methionin:6,bin:8,smng:3,helper:1,readi:5,sidechain:[8,1,6],henc:8,non:8,itself:8,clutter:8,conf:[8,5],protein:[9,6],calpha_onli:6,"__init__":8,reviv:8,develop:[],fedora:8,etc:8,suggest:8,belong:8,savepdb:6,files_to_be_remov:8,"while":[8,0],member:[8,6],fragment:1,complex:8,advis:8,admir:8,document:3,conflict:8,higher:5,http:8,optim:8,bienchen:8,make_directori:8,hand:5,driven:8,moment:8,rais:[1,6],disable_linkcheck:[8,5],user:[],extern:8,respons:8,tradition:0,expand:8,codetest:8,task:8,conop:8,pymod:8,find_packag:8,macro:8,markup:8,well:[8,5,1,6],without:[8,0,6],command:[],branchnam:8,thi:[0,1,5,6,7,8,9],endif:8,gzip:0,model:7,academ:8,spend:8,piec:8,usual:[8,5],add_doc_sourc:8,clash_scor:1,just:[8,5],entri:8,elabor:8,reduced_scor:1,obtain:6,rest:[0,1,2,3,4,5,6,7,8,9,10],touch:8,web:[8,5],loopcandid:1,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,5],except:8,param:1,add:[8,1],densiti:1,input:0,subsequ:6,match:[8,6],opt:0,around:8,format:8,handl:6,specimen:0,term:8,source2:8,source1:8,mol:8,bit:[8,5],you:[8,0,5],mod:8,eigen3_include_dir:5,loss:8,like:[8,5,6],success:[0,1],incred:6,manual:[8,5],html:[8,5,3],test_:8,test_awesome_featur:8,"boolean":0,either:[8,6],output:[8,0],hook:8,page:[8,4,5],www:8,right:[8,5],often:[8,0],acknowledg:8,some:[8,0],begin:8,resolv:8,intern:8,proper:8,librari:8,qmean:[8,5],thu:0,smallish:[8,5],lead:0,avoid:8,definit:8,subclass:8,exit:0,select:6,recognis:8,devot:7,condit:8,amino:6,core:0,plu:8,cmake_source_dir:8,backbon:[1,6],step:8,promot:8,repositori:[8,3],"__name__":8,add_subdirectori:8,intervent:8,mmcif:0,stage:[],trustworthi:8,src:8,about:[8,6],rare:8,materi:8,manag:8,coars:8,commit:8,mol_alg:8,disabl:8,qmean_root:[8,5],real:8,"float":1,automat:[8,0],due:[1,6],promod3_version_str:8,empti:8,cmake_cxx_flag:8,strip:6,announc:8,merg:8,git:3,log:8,wai:[8,5],pictur:8,qmean_include_dir:8,support:[8,0],renumb:6,custom:8,avail:[8,5],strict:8,sortbycorrel:1,much:[8,6],interfac:8,author:8,lot:[8,0],suit:8,forward:8,stai:8,parse_arg:0,unfortun:8,"function":0,headach:8,enough:8,tupl:0,buildrawmodel:6,somethingtest:8,back:8,link:[8,5],atom:[1,6],don:[8,5],line:[],inlin:8,"true":[8,0,1,6],setup_stag:8,pull:[8,5],tripl:0,immedi:8,consist:8,possibl:[8,6],whether:0,type:[0,1,6],insertinto:1,displai:0,below:8,otherwis:8,problem:8,similar:5,testutil:8,gather:[8,7],evalu:8,"int":0,certain:5,utilis:[8,0],fellow:8,incomplet:6,exist:[8,0,1],file:[],dqmean_root:[8,5],deuterium:6,check:[8,0,5],fill:8,echo:8,again:[8,5],calpha:6,when:[8,6],detail:[8,6],other:[8,5,6],bool:[0,1],seem:8,test:[],cmake_compiler_is_gnucxx:8,phosphoserin:6,nice:8,correl:1,bb_list:1,toentiti:1,additional_make_clean_fil:8,determin:0,rawmodelingresult:6,sequenc:[9,1,6],cmake_build_typ:8,cmake_minimum_requir:8,briefli:8,consid:8,gap:[1,6],homolog:7,doptim:8,fatal_error:8,legal:8,reduc:1,peptid:[1,6],algorithm:6,project_binary_dir:8,directori:[],descript:8,pseudo:6,rule:8,ignor:6,time:[8,6],push:8},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:attribute","4":"py:class"},objnames:{"0":["py","module","Python 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diff --git a/doc/html/users.html b/doc/html/users.html
index 1da95c9d164c976ae56567a70f2d22ac0507ab7a..1a37587fdd946ddb792483677bd3853567f0414d 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -110,7 +110,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Jun 19 11:04, 2014.
+ Last updated on Aug 07 11:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/extras/pre-commit b/extras/pre-commit
index a8b949b7cde019f6fc31acf7632433a6cfb36e02..28a5fd75d1d66103f6543b1f7529a66363149354 100755
--- a/extras/pre-commit
+++ b/extras/pre-commit
@@ -7,7 +7,11 @@ MIN_GIT_VERSION = "1.7.5.1"
## Files to be excluded from whitespace check have to be declared as regexp
## referring to the full path. So '.*\.pdf' skips ANY PDF file, while
## 'doc/html/.*\.html' only skips HTML files in the doc directory.
-WHITESPACECHECK_EXCLUDES = ['.*\.pdf', '.*\.pdb', '^doc/html/.*\.html']
+WHITESPACECHECK_EXCLUDES = ['.*\.pdf', '.*\.pdb']
+## Files to be excluded from any check. This is most likely only for 'produced'
+## files like documentation as HTML files.
+EXCLUDE_COMPLETELY = ['^doc/html/.*\.html', '^doc/html/.*\.js',
+ '^doc/html/.*\.inv', '^doc/html/.*\.txt']
PYCODECHECK_EXCLUDES = ['extras/pre-commit']
## For now, we just call 'git' from PATH. If there is need, we may change it
@@ -77,6 +81,8 @@ def CheckWithespaces():
# we have trailing whitespaces, compile exclude list into regexps and
# prepare output
re_excludes = list()
+ for ex in EXCLUDE_COMPLETELY:
+ re_excludes.append(re.compile(ex))
for ex in WHITESPACECHECK_EXCLUDES:
re_excludes.append(re.compile(ex))
output = list()
@@ -116,6 +122,7 @@ def GetModFiles():
py_files = list()
rst_files = list()
ukn_files = list()
+ re_excludes = list()
# get path to repo root
try:
cdup = subprocess.check_output(['git','rev-parse','--show-cdup'],
@@ -128,9 +135,19 @@ def GetModFiles():
gso = subprocess.check_output(['git', 'status', '--porcelain'], shell=False)
except Exception, e:
FailMsg("Failed to run 'git status --porcelain': '%s'" % str(e), 9)
+ # prepare exclude list
+ for ex in EXCLUDE_COMPLETELY:
+ re_excludes.append(re.compile(ex))
# sort into file type-lists
for line in gso.splitlines():
f = os.path.join(cdup, line.split()[-1])
+ skip = False
+ for ex_re in re_excludes:
+ if re.match(ex_re, f):
+ skip = True
+ break
+ if skip:
+ continue
ft = GetFileType(f)
if ft == 'python':
py_files.append(f)