diff --git a/doc/html/.doctrees/buildsystem.doctree b/doc/html/.doctrees/buildsystem.doctree
index 5f9e2c5f075b2f98ea8153f7f77e0dc10fb896f1..2fb7ff2b8e5d02d46cceac30a5d15ef878f572be 100644
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diff --git a/doc/html/.doctrees/changelog.doctree b/doc/html/.doctrees/changelog.doctree
index d14fd28689a1e1aa6b7f31fe9206d132f07e49be..d0599ee2fd2f720fc3f49b08fc37e8b9bcc3290a 100644
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diff --git a/doc/html/.doctrees/contributing.doctree b/doc/html/.doctrees/contributing.doctree
index b7270fcd1c9444295a5bd86354bd7c8d7d20157c..cd3a762ae78de5d13235855bb513b6c66f4b48b1 100644
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diff --git a/doc/html/.doctrees/core/argcheck.doctree b/doc/html/.doctrees/core/argcheck.doctree
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diff --git a/doc/html/.doctrees/core/index.doctree b/doc/html/.doctrees/core/index.doctree
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diff --git a/doc/html/.doctrees/developers.doctree b/doc/html/.doctrees/developers.doctree
index 30600b32fca18052563d582fbd40dd582b72ae55..84da9b65a424669ba1f919955cb5a532d2bad0e2 100644
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diff --git a/doc/html/.doctrees/environment.pickle b/doc/html/.doctrees/environment.pickle
index 2099d9ed44a91ecaf0445217435d9f12823d3eeb..48afb07ce387b44ebc278cf9e55502182ccc4d32 100644
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diff --git a/doc/html/.doctrees/index.doctree b/doc/html/.doctrees/index.doctree
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diff --git a/doc/html/.doctrees/meld/index.doctree b/doc/html/.doctrees/meld/index.doctree
index 4421e0f8b9d6bebb167930640db7132592140f48..aee602ffc10f87bf7e1dbebdf9ea59b38ea86234 100644
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diff --git a/doc/html/.doctrees/meld/loop.doctree b/doc/html/.doctrees/meld/loop.doctree
index 540bcc07b0e6b82f8fcc683364cffbe12287986f..9ada519758867fc9d74baa48009eea65bf15f74b 100644
Binary files a/doc/html/.doctrees/meld/loop.doctree and b/doc/html/.doctrees/meld/loop.doctree differ
diff --git a/doc/html/.doctrees/meld/rawmodel.doctree b/doc/html/.doctrees/meld/rawmodel.doctree
index 78503f04f2aba7fcffafc912c4227cd0be08e307..51747294b6e754df7f3a094d947577c373ea1576 100644
Binary files a/doc/html/.doctrees/meld/rawmodel.doctree and b/doc/html/.doctrees/meld/rawmodel.doctree differ
diff --git a/doc/html/.doctrees/users.doctree b/doc/html/.doctrees/users.doctree
index 72fa011da097a545a83fd5ba6046696fba77dda7..ac4d870c25b776223eafcbe016fe9a8312cd05a8 100644
Binary files a/doc/html/.doctrees/users.doctree and b/doc/html/.doctrees/users.doctree differ
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 30923bd52cb8a7c485414dfc7c06005493f56d59..e9d171da247be33dbecd890d76f39bac6e5a66c0 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,7 +85,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 c91c0ab7ccc167f704ea65318ffba146d8339b70..c1a3e1a187759bec0707d795f6f6737ad338ab0a 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -69,7 +69,7 @@
 <span class="sd">            missing.</span>
 <span class="sd">  &#39;&#39;&#39;</span>
   <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="s">&#39;</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">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">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</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">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>
 <div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</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> <span class="n">extensions</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
@@ -113,10 +113,10 @@
     <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="k">print</span> <span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">&#39;</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">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">&#39;</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">&#39;</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">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">&#39;&#39;</span><span class="p">:</span>
-    <span class="k">print</span> <span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">&#39;</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">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">&#39;</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">&#39;</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">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 +125,7 @@
         <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="k">print</span> <span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">&#39;</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">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">&#39;</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">&#39;</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">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>
@@ -133,7 +133,8 @@
   <span class="s">&#39;FileExtension&#39;</span><span class="p">,</span>
 <span class="p">)</span>
 
-<span class="c">#  LocalWords:  gz pdb gzip bool</span>
+<span class="c">#  LocalWords:  gz pdb gzip bool os sys FileExists FileExtension filename</span>
+<span class="c">#  LocalWords:  fileext</span>
 </pre></div>
 
           </div>
@@ -173,7 +174,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 c4124270a1741bec5e4448b7ca28d39b0f812fe3..fbb9656f7142cfcb43fa62643f03ca3e3cb866e2 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -36,9 +36,9 @@ put a ``-D`` in front of options.
 Here is a list of more options used within |project|:
 
 * ``DISABLE_DOCUMENTATION`` Don't build documentation, don't search for |sphinx|
-* ``DISABLE_DOCTEST`` Don't run example code from documentation on 'make check'
-  (implicit by ``DISABLE_DOCUMENTATION``)
-* ``DISABLE_LINKCHECK`` Don't test links from documentation on 'make check
+* ``DISABLE_DOCTEST`` Don't run example code from documentation on
+  ``make check`` (implicit by ``DISABLE_DOCUMENTATION``)
+* ``DISABLE_LINKCHECK`` Don't test links from documentation on ``make check``
   (implicit by ``DISABLE_DOCUMENTATION``)
 
 Instead of calling |cmake| by yourself, there is the :file:`conf-scripts`
@@ -68,7 +68,6 @@ special targets:
 
 
 .. _ost_l: http://www.OpenStructure.org
-.. _ost_s: http://www.OpenStructure.org
 .. _cmake: http://www.cmake.org/
 .. _python: https://www.python.org/
 .. _boost: http://www.boost.org/
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 869300d8702b2334086fa46095eebe7cfa8eac00..e83104db1a5c72517b334c929b4f8bcde1623fce 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -269,7 +269,6 @@ version control, create a couple of files which are always needed.
 .. code-block:: console
 
    $ touch sidechains/pymod/__init__.py
-   $ echo "FOO" >> sidechains/doc/index.rst
    $ echo ":mod:\`~promod3.sidechains\` - ProMod3 side chain optimiser" >> sidechains/doc/index.rst
    $ echo "================================================================================" >> sidechains/doc/index.rst
    $
@@ -330,7 +329,7 @@ a couple of examples around in this repository. Here is the most basic
 :file:`CMakeLists.txt`:
 
 .. code-block:: cmake
-   :linenos:
+  :linenos:
 
    set(SIDECHAINS_PYMOD
    __init__.py
@@ -348,8 +347,8 @@ The final step towards |cmake| is to register your module's directory in the
 top level :file:`CMakeLists.txt`:
 
 .. code-block:: cmake
-   :linenos:
-   :emphasize-lines: 80
+  :linenos:
+  :emphasize-lines: 80
 
    #-------------------------------------------------------------------------------
    # Author: Bienchen
@@ -481,14 +480,90 @@ a new configuration script. The following example assumes |fedora| 19.
 From this point, :command:`make` should work and you could start adding your
 files to the repository using ``git add``.
 
+Up to now, we did not cover the :file:`tests` branch of a new module. But its
+good practice to develop new functionality along tests and that right from the
+beginning. At some point, new code needs testing anyway to see if it does what
+it should, so just do this by writing unit tests. Test sources are stored in
+files with a prefix :file:`test_` and usually come per submodule instead of
+sporting a single monolithic :file:`test_sidechains.py`.
+
+|python| code is evaluated using its own
+:py_docs:`unit testing framework <library/unittest.html>` with a little help
+from |ost_s|_. The basic scheme is to import your module, subclass
+:class:`unittest.TestCase` and make the whole file runnable as script using the
+most common |nameattr|_ attribute. A file :file:`tests/test_something.py` could
+look like this, carrying a single test case:
+
+.. testcode:: promod3unittest
+  :hide:
+
+  import unittest
+
+  class something():
+      @staticmethod
+      def Else():
+          return 1
+
+  class SomethingTests(unittest.TestCase):
+      def testFileExistsFalse(self):
+          self.assertEquals(something.Else(), 1)
+
+  if __name__ == "__builtin__":
+      suite = unittest.TestLoader().loadTestsFromTestCase(SomethingTests)
+      unittest.TextTestRunner().run(suite)
+
+.. code-block:: python
+  :linenos:
+
+   import unittest
+   from promod3.sidechains import something
+
+   class SomethingTests(unittest.TestCase):
+       def testFileExistsFalse(self):
+           self.assertEquals(something.Else(), 1)
+
+   if __name__ == "__main__":
+       from ost import testutils
+       testutils.RunTests()
+
+To hook up your tests with ``make codetest`` (and to create a
+``test_something.py_run`` target), everything has to be introduced to |cmake|.
+First, tell |cmake| to search :file:`tests` for a :file:`CMakeLists.txt` file
+by extending the list of sub-directories in :file:`sidechains/CMakeLists.txt`:
+
+.. code-block:: cmake
+  :linenos:
+
+   add_subdirectory(pymod)
+   add_subdirectory(doc)
+   add_subdirectory(tests)
+
+Then fill :file:`sidechains/tests/CMakeLists.txt` with your new test script and
+``make`` will recognise the changes next time it is run and fix the rest for
+you.
+
+.. code-block:: cmake
+  :linenos:
+
+   set(SIDECHAINS_UNIT_TESTS
+   test_something.py
+   )
+
+   promod3_unittest(MODULE sidechains SOURCES "${SIDECHAINS_UNIT_TESTS}")
+
+Now tests should be available by ``make check``, ``make codetest`` and
+``make test_something.py_run``.
+
 
 .. _restructuredtext: http://docutils.sourceforge.net/rst.html
 .. |fedora| replace:: Fedora
-
+.. |nameattr| replace:: :attr:`__name__`
 
 ..  LocalWords:  cmake hotfix doctest linkcheck rebase BRANCHNAME rebasing py
 ..  LocalWords:  CMakeLists txt rst pymod init submodule src restructuredtext
 ..  LocalWords:  makefiles formatters Changelog codetest promod sidechains io
 ..  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
+..  LocalWords:  changelog Optimized DOPTIMIZE gitignore cd conf subtree attr
+..  LocalWords:  unittest TestCase nameattr testcode staticmethod builtin
+..  LocalWords:  SomethingTests testFileExistsFalse testutils RunTests
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index e38c28162d03ba1653564dd8d407b4ebcd14f3b6..82a4b4ce7fdbca0dae91ff5a35f896229bde851f 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -88,9 +88,9 @@ put a <tt class="docutils literal"><span class="pre">-D</span></tt> in front of
 <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&#8217;t build documentation, don&#8217;t search for Sphinx</li>
-<li><tt class="docutils literal"><span class="pre">DISABLE_DOCTEST</span></tt> Don&#8217;t run example code from documentation on &#8216;make check&#8217;
-(implicit by <tt class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></tt>)</li>
-<li><tt class="docutils literal"><span class="pre">DISABLE_LINKCHECK</span></tt> Don&#8217;t test links from documentation on &#8216;make check
+<li><tt class="docutils literal"><span class="pre">DISABLE_DOCTEST</span></tt> Don&#8217;t run example code from documentation on
+<tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt> (implicit by <tt class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></tt>)</li>
+<li><tt class="docutils literal"><span class="pre">DISABLE_LINKCHECK</span></tt> Don&#8217;t test links from documentation on <tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt>
 (implicit by <tt class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></tt>)</li>
 </ul>
 <p>Instead of calling CMake by yourself, there is the <tt class="file docutils literal"><span class="pre">conf-scripts</span></tt>
@@ -186,7 +186,7 @@ configuration also Sphinx with the <tt class="docutils literal"><span class="pre
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 abd8194403d23abe1f5fdfdcda2bbb58d6f34ed4..8c290bd61b248d092825d92bee7c88ea3db5a9e3 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -127,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 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 559d94b89daddd9ff7b6392e561dcbe06615621f..a523228be31d67cd588947f2bb4f365112156ef8 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -282,7 +282,6 @@ list of directories which are likely to be used in every project.</p>
 is, Git does not admire empty directories. Before you bring your module under
 version control, create a couple of files which are always needed.</p>
 <div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechains/pymod/__init__.py
-<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">&quot;FOO&quot;</span> &gt;&gt; sidechains/doc/index.rst
 <span class="gp">$</span> <span class="nb">echo</span> <span class="s2">&quot;:mod:\`~promod3.sidechains\` - ProMod3 side chain optimiser&quot;</span> &gt;&gt; sidechains/doc/index.rst
 <span class="gp">$</span> <span class="nb">echo</span> <span class="s2">&quot;================================================================================&quot;</span> &gt;&gt; sidechains/doc/index.rst
 <span class="gp">$</span>
@@ -341,11 +340,11 @@ a couple of examples around in this repository. Here is the most basic
 2
 3
 4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_PYMOD</span>
-<span class="s">__init__.py</span>
-<span class="p">)</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_PYMOD</span>
+ <span class="s">__init__.py</span>
+ <span class="p">)</span>
 
-<span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">PY</span> <span class="o">${</span><span class="nv">SIDECHAINS_PYMOD</span><span class="o">}</span><span class="p">)</span>
+ <span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">PY</span> <span class="o">${</span><span class="nv">SIDECHAINS_PYMOD</span><span class="o">}</span><span class="p">)</span>
 </pre></div>
 </td></tr></table></div>
 <p>Source files should be again listed in a dedicated variable. Later, you
@@ -446,98 +445,98 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
 89
 90
 91
-92</pre></div></td><td class="code"><div class="highlight"><pre><span class="c">#-------------------------------------------------------------------------------</span>
-<span class="c"># Author: Bienchen</span>
-<span class="c">#-------------------------------------------------------------------------------</span>
-<span class="c"># Options to CMake:</span>
-<span class="c">#    DISABLE_DOCUMENTATION: Don&#39;t build documentation, don&#39;t search for Sphinx</span>
-<span class="c">#    DISABLE_DOCTEST: Don&#39;t run example code from documentation on &#39;make check&#39;</span>
-<span class="c">#    DISABLE_LINKCHECK: Don&#39;t test links from documentation on &#39;make check&#39;</span>
-<span class="c"># (if documentation is disabled, there is no doctest, linkcheck at all)</span>
-<span class="nb">cmake_minimum_required</span><span class="p">(</span><span class="s">VERSION</span> <span class="s">2.6.4</span> <span class="s">FATAL_ERROR</span><span class="p">)</span>
-<span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_MODULE_PATH</span> <span class="o">${</span><span class="nv">CMAKE_MODULE_PATH</span><span class="o">}</span> <span class="o">${</span><span class="nv">CMAKE_SOURCE_DIR</span><span class="o">}</span><span class="s">/cmake_support</span><span class="p">)</span>
+92</pre></div></td><td class="code"><div class="highlight"><pre> <span class="c">#-------------------------------------------------------------------------------</span>
+ <span class="c"># Author: Bienchen</span>
+ <span class="c">#-------------------------------------------------------------------------------</span>
+ <span class="c"># Options to CMake:</span>
+ <span class="c">#    DISABLE_DOCUMENTATION: Don&#39;t build documentation, don&#39;t search for Sphinx</span>
+ <span class="c">#    DISABLE_DOCTEST: Don&#39;t run example code from documentation on &#39;make check&#39;</span>
+ <span class="c">#    DISABLE_LINKCHECK: Don&#39;t test links from documentation on &#39;make check&#39;</span>
+ <span class="c"># (if documentation is disabled, there is no doctest, linkcheck at all)</span>
+ <span class="nb">cmake_minimum_required</span><span class="p">(</span><span class="s">VERSION</span> <span class="s">2.6.4</span> <span class="s">FATAL_ERROR</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_MODULE_PATH</span> <span class="o">${</span><span class="nv">CMAKE_MODULE_PATH</span><span class="o">}</span> <span class="o">${</span><span class="nv">CMAKE_SOURCE_DIR</span><span class="o">}</span><span class="s">/cmake_support</span><span class="p">)</span>
 
-<span class="nb">project</span><span class="p">(</span><span class="s">PROMOD3</span> <span class="s">CXX</span> <span class="s">C</span><span class="p">)</span>
+ <span class="nb">project</span><span class="p">(</span><span class="s">PROMOD3</span> <span class="s">CXX</span> <span class="s">C</span><span class="p">)</span>
 
-<span class="nb">include</span><span class="p">(</span><span class="s">PROMOD3</span><span class="p">)</span>
+ <span class="nb">include</span><span class="p">(</span><span class="s">PROMOD3</span><span class="p">)</span>
 
-<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MAJOR</span> <span class="s">0</span><span class="p">)</span>
-<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MINOR</span> <span class="s">1</span><span class="p">)</span>
-<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_PATCH</span> <span class="s">0</span><span class="p">)</span>
-<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_STRING</span> <span class="o">${</span><span class="nv">PROMOD3_VERSION_MAJOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_MINOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_PATCH</span><span class="o">}</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MAJOR</span> <span class="s">0</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MINOR</span> <span class="s">1</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_PATCH</span> <span class="s">0</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_STRING</span> <span class="o">${</span><span class="nv">PROMOD3_VERSION_MAJOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_MINOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_PATCH</span><span class="o">}</span><span class="p">)</span>
 
-<span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
-  <span class="nb">exec_program</span><span class="p">(</span><span class="s">gcc</span> <span class="s">ARGS</span> <span class="s">--version</span> <span class="s">OUTPUT_VARIABLE</span> <span class="s">CMAKE_C_COMPILER_VERSION</span><span class="p">)</span>
-  <span class="nb">if</span><span class="p">(</span><span class="s">CMAKE_C_COMPILER_VERSION</span> <span class="s">MATCHES</span> <span class="s2">&quot;.*4\\.[5-9].*&quot;</span><span class="p">)</span>
-    <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">true</span><span class="p">)</span>
-  <span class="nb">else</span><span class="p">()</span>
-    <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">false</span><span class="p">)</span>
-  <span class="nb">endif</span><span class="p">()</span>
-<span class="nb">endif</span><span class="p">()</span>
+ <span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+   <span class="nb">exec_program</span><span class="p">(</span><span class="s">gcc</span> <span class="s">ARGS</span> <span class="s">--version</span> <span class="s">OUTPUT_VARIABLE</span> <span class="s">CMAKE_C_COMPILER_VERSION</span><span class="p">)</span>
+   <span class="nb">if</span><span class="p">(</span><span class="s">CMAKE_C_COMPILER_VERSION</span> <span class="s">MATCHES</span> <span class="s2">&quot;.*4\\.[5-9].*&quot;</span><span class="p">)</span>
+     <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">true</span><span class="p">)</span>
+   <span class="nb">else</span><span class="p">()</span>
+     <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">false</span><span class="p">)</span>
+   <span class="nb">endif</span><span class="p">()</span>
+ <span class="nb">endif</span><span class="p">()</span>
 
-<span class="nb">if</span> <span class="p">(</span><span class="s">OPTIMIZE</span><span class="p">)</span>
-  <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Release</span><span class="p">)</span>
-  <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">ON</span><span class="p">)</span>
-<span class="nb">else</span><span class="p">()</span>
-   <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Debug</span><span class="p">)</span>
-   <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">OFF</span><span class="p">)</span>
-<span class="nb">endif</span><span class="p">()</span>
+ <span class="nb">if</span> <span class="p">(</span><span class="s">OPTIMIZE</span><span class="p">)</span>
+   <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Release</span><span class="p">)</span>
+   <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">ON</span><span class="p">)</span>
+ <span class="nb">else</span><span class="p">()</span>
+    <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Debug</span><span class="p">)</span>
+    <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">OFF</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
 
-<span class="nb">setup_stage</span><span class="p">()</span>
-<span class="nb">file</span><span class="p">(</span><span class="s">MAKE_DIRECTORY</span> <span class="o">${</span><span class="nv">STAGE_DIR</span><span class="o">}</span>
-     <span class="o">${</span><span class="nv">EXECUTABLE_OUTPUT_PATH</span><span class="o">}</span>
-     <span class="o">${</span><span class="nv">HEADER_STAGE_PATH</span><span class="o">}</span>
-     <span class="o">${</span><span class="nv">LIB_STAGE_PATH</span><span class="o">}</span>
-     <span class="o">${</span><span class="nv">LIBEXEC_STAGE_PATH</span><span class="o">}</span><span class="p">)</span>
+ <span class="nb">setup_stage</span><span class="p">()</span>
+ <span class="nb">file</span><span class="p">(</span><span class="s">MAKE_DIRECTORY</span> <span class="o">${</span><span class="nv">STAGE_DIR</span><span class="o">}</span>
+      <span class="o">${</span><span class="nv">EXECUTABLE_OUTPUT_PATH</span><span class="o">}</span>
+      <span class="o">${</span><span class="nv">HEADER_STAGE_PATH</span><span class="o">}</span>
+      <span class="o">${</span><span class="nv">LIB_STAGE_PATH</span><span class="o">}</span>
+      <span class="o">${</span><span class="nv">LIBEXEC_STAGE_PATH</span><span class="o">}</span><span class="p">)</span>
 
-<span class="nb">setup_compiler_flags</span><span class="p">()</span>
-<span class="nb">setup_boost</span><span class="p">()</span>
+ <span class="nb">setup_compiler_flags</span><span class="p">()</span>
+ <span class="nb">setup_boost</span><span class="p">()</span>
 
-<span class="nb">find_package</span><span class="p">(</span><span class="s">Python</span> <span class="s">2.7</span> <span class="s">REQUIRED</span><span class="p">)</span>
-<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
-  <span class="nb">find_package</span><span class="p">(</span><span class="s">Sphinx</span> <span class="o">${</span><span class="nv">PYTHON_VERSION</span><span class="o">}</span> <span class="s">REQUIRED</span><span class="p">)</span>
-  <span class="nb">set</span><span class="p">(</span><span class="s">PYTHON_DOC_URL</span> <span class="s2">&quot;https://docs.python.org/${PYTHON_VERSION}&quot;</span><span class="p">)</span>
-  <span class="c"># set this to the URL corresponding to the version of OST you are using</span>
-  <span class="nb">set</span><span class="p">(</span><span class="s">OST_DOC_URL</span> <span class="s2">&quot;http://www.openstructure.org/docs/1.3&quot;</span><span class="p">)</span>
-<span class="nb">endif</span><span class="p">()</span>
-<span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
-             <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">Python</span> <span class="s">2.7</span> <span class="s">REQUIRED</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+   <span class="nb">find_package</span><span class="p">(</span><span class="s">Sphinx</span> <span class="o">${</span><span class="nv">PYTHON_VERSION</span><span class="o">}</span> <span class="s">REQUIRED</span><span class="p">)</span>
+   <span class="nb">set</span><span class="p">(</span><span class="s">PYTHON_DOC_URL</span> <span class="s2">&quot;https://docs.python.org/${PYTHON_VERSION}&quot;</span><span class="p">)</span>
+   <span class="c"># set this to the URL corresponding to the version of OST you are using</span>
+   <span class="nb">set</span><span class="p">(</span><span class="s">OST_DOC_URL</span> <span class="s2">&quot;http://www.openstructure.org/docs/1.3&quot;</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
+ <span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
+              <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">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
-  <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
-  <span class="c"># expanded with multiple -fno-strict-aliasing flags, triggering a complete</span>
-  <span class="c"># rebuild whenever cmake is run</span>
-  <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS_RELEASE</span> <span class="s2">&quot;${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing&quot;</span><span class="p">)</span>
-  <span class="nb">if</span><span class="p">(</span><span class="s2">&quot;${CMAKE_CXX_COMPILER_VERSION}&quot;</span> <span class="s">VERSION_GREATER</span> <span class="s2">&quot;4.6&quot;</span><span class="p">)</span>
-    <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS</span> <span class="s2">&quot;${CMAKE_CXX_FLAGS} -Wno-attributes&quot;</span><span class="p">)</span>
-  <span class="nb">endif</span><span class="p">(</span><span class="s2">&quot;${CMAKE_CXX_COMPILER_VERSION}&quot;</span> <span class="s">VERSION_GREATER</span> <span class="s2">&quot;4.6&quot;</span><span class="p">)</span>
-<span class="nb">endif</span><span class="p">()</span>
+ <span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+   <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
+   <span class="c"># expanded with multiple -fno-strict-aliasing flags, triggering a complete</span>
+   <span class="c"># rebuild whenever cmake is run</span>
+   <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS_RELEASE</span> <span class="s2">&quot;${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing&quot;</span><span class="p">)</span>
+   <span class="nb">if</span><span class="p">(</span><span class="s2">&quot;${CMAKE_CXX_COMPILER_VERSION}&quot;</span> <span class="s">VERSION_GREATER</span> <span class="s2">&quot;4.6&quot;</span><span class="p">)</span>
+     <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS</span> <span class="s2">&quot;${CMAKE_CXX_FLAGS} -Wno-attributes&quot;</span><span class="p">)</span>
+   <span class="nb">endif</span><span class="p">(</span><span class="s2">&quot;${CMAKE_CXX_COMPILER_VERSION}&quot;</span> <span class="s">VERSION_GREATER</span> <span class="s2">&quot;4.6&quot;</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
 
-<span class="c"># basic environment</span>
-<span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
-                    <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
+ <span class="c"># basic environment</span>
+ <span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
+                     <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
 
-<span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
-<span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
-                             <span class="s2">&quot;${FILES_TO_BE_REMOVED}&quot;</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
+ <span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
+                              <span class="s2">&quot;${FILES_TO_BE_REMOVED}&quot;</span><span class="p">)</span>
 
-<span class="c">## sub dirs to be recognised by CMake</span>
-<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
-<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
-<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
-<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
-</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
-<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
-<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
-  <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">&quot;${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG&quot;</span><span class="p">)</span>
-  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
-<span class="nb">endif</span><span class="p">()</span>
+ <span class="c">## sub dirs to be recognised by CMake</span>
+ <span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
+<span class="hll"> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
+</span> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+   <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">&quot;${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG&quot;</span><span class="p">)</span>
+   <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
 
-<span class="c">## report setup</span>
-<span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">&quot;PROMOD3 will be built with the following options:\n&quot;</span>
-        <span class="s2">&quot;   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n&quot;</span>
-        <span class="s2">&quot;   Optimized     (-DOPTIMIZE) : ${_OPT}\n&quot;</span>
-        <span class="s2">&quot;   Python                     : ${PYTHON_BINARY}\n&quot;</span><span class="p">)</span>
+ <span class="c">## report setup</span>
+ <span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">&quot;PROMOD3 will be built with the following options:\n&quot;</span>
+         <span class="s2">&quot;   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n&quot;</span>
+         <span class="s2">&quot;   Optimized     (-DOPTIMIZE) : ${_OPT}\n&quot;</span>
+         <span class="s2">&quot;   Python                     : ${PYTHON_BINARY}\n&quot;</span><span class="p">)</span>
 </pre></div>
 </td></tr></table></div>
 <p>All that needs to be done for CMake to recognise your module is adding its
@@ -571,6 +570,61 @@ a new configuration script. The following example assumes Fedora 19.</p>
 </div>
 <p>From this point, <strong class="command">make</strong> should work and you could start adding your
 files to the repository using <tt class="docutils literal"><span class="pre">git</span> <span class="pre">add</span></tt>.</p>
+<p>Up to now, we did not cover the <tt class="file docutils literal"><span class="pre">tests</span></tt> branch of a new module. But its
+good practice to develop new functionality along tests and that right from the
+beginning. At some point, new code needs testing anyway to see if it does what
+it should, so just do this by writing unit tests. Test sources are stored in
+files with a prefix <tt class="file docutils literal"><span class="pre">test_</span></tt> and usually come per submodule instead of
+sporting a single monolithic <tt class="file docutils literal"><span class="pre">test_sidechains.py</span></tt>.</p>
+<p>Python code is evaluated using its own
+<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html">unit testing framework</a> with a little help
+from <a class="reference external" href="http://www.OpenStructure.org">OST</a>. The basic scheme is to import your module, subclass
+<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></tt></a> and make the whole file runnable as script using the
+most common <a class="reference external" href="https://docs.python.org/2.7/library/__main__.html"><tt class="xref py py-attr docutils literal"><span class="pre">__name__</span></tt></a> attribute. A file <tt class="file docutils literal"><span class="pre">tests/test_something.py</span></tt> could
+look like this, carrying a single test case:</p>
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10</pre></div></td><td class="code"><div class="highlight"><pre> <span class="kn">import</span> <span class="nn">unittest</span>
+ <span class="kn">from</span> <span class="nn">promod3.sidechains</span> <span class="kn">import</span> <span class="n">something</span>
+
+ <span class="k">class</span> <span class="nc">SomethingTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
+     <span class="k">def</span> <span class="nf">testFileExistsFalse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+         <span class="bp">self</span><span class="o">.</span><span class="n">assertEquals</span><span class="p">(</span><span class="n">something</span><span class="o">.</span><span class="n">Else</span><span class="p">(),</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">&quot;__main__&quot;</span><span class="p">:</span>
+     <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+     <span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
+</pre></div>
+</td></tr></table></div>
+<p>To hook up your tests with <tt class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></tt> (and to create a
+<tt class="docutils literal"><span class="pre">test_something.py_run</span></tt> target), everything has to be introduced to CMake.
+First, tell CMake to search <tt class="file docutils literal"><span class="pre">tests</span></tt> for a <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt> file
+by extending the list of sub-directories in <tt class="file docutils literal"><span class="pre">sidechains/CMakeLists.txt</span></tt>:</p>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+2
+3</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">tests</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+<p>Then fill <tt class="file docutils literal"><span class="pre">sidechains/tests/CMakeLists.txt</span></tt> with your new test script and
+<tt class="docutils literal"><span class="pre">make</span></tt> will recognise the changes next time it is run and fix the rest for
+you.</p>
+<div class="highlight-cmake"><pre> set(SIDECHAINS_UNIT_TESTS
+ test_something.py
+ )
+
+ promod3_unittest(MODULE sidechains SOURCES "${SIDECHAINS_UNIT_TESTS}")</pre>
+</div>
+<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>
 
@@ -643,7 +697,7 @@ files to the repository using <tt class="docutils literal"><span class="pre">git
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 1b5d174d8f2ddffebb4204680e5e81b8957a0521..c6ecdcaaa615c7992598c08c7e09404d348d0352 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">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 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 14636e68b6d3287570b9f6896a115ee65475c9bb..1fe5181b6d6cda4b826887796703fdb8a423d5e8 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,7 +123,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 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 58fcbad03d41bb38b379c61bee613e1199869c6f..201c20ec229b9544ad45897ccb1772344169f485 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -139,7 +139,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 ec5e6d559ac9eda6398e3ba29df95f5e9de619d3..2ca5e3beac3786d5ff7f9971de7546cd2ae415e5 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -308,7 +308,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 9ff48fa481b166eebb839b9572531746d5476eca..97396da1ba57c33d8e8e04bfa1a107fb3885d51c 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 99d458aac43c2b1120f9a4316f0f11ef9a4f3f09..68e4bce984ff3fabd77867ce5392a53e4248c3e4 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -127,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 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 0c2db6ed37b75b55029348284503ded02a730ff9..e94d15777f4e5322ed88aaba824058b23ee8de17 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">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 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 1838d45abb78a9fad790227c95272082e928e7c3..b721bd82c916d6e5c2820b50428c5621a13d7079 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">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index c4ea1c8467e4804ea9ba47182cb319fa090ef1b1..5fdf3629560ddc601ea68faaeaf50e8c01fb0bea 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 88fa4ab3f67685c4a2cd853f97ff8a546ef341f5..e4cd620c17989bf229f51461d85841d842796376 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 14:31, 2014.
+      Last updated on Jun 14 19:22, 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 30fd4ffdeac1b7bf9050732d2f18a16b22b291b7..fabc95463533a5787dd5b15f453f461e87b5c940 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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diff --git a/doc/html/users.html b/doc/html/users.html
index 4de84604288434d99ec0071cccb779830e684a63..3de4fbbf01838cd33b3175f280b43dae0c5a94ac 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -110,7 +110,7 @@
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         &copy; Copyright 2013, Bienchen.
-      Last updated on May 26 13:39, 2014.
+      Last updated on Jun 14 18:21, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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