Updated documentation

doc/html/_modules/index.html

@@ -85,7 +85,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 09 14:45, 2014.
+      Last updated on May 26 14:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>

doc/html/_modules/promod3/core/argcheck.html

@@ -173,7 +173,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 09 14:45, 2014.
+      Last updated on May 26 14:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>

doc/html/_sources/buildsystem.txt

@@ -5,7 +5,7 @@ Dependencies
 --------------------------------------------------------------------------------
 |project| is build on top of |ost_l|_ (|ost_s|) and needs at least version
 1.4. 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
+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. To build documentation,
 |sphinx|_ 1.2b1 is used.
 

doc/html/_sources/changelog.txt

@@ -11,4 +11,8 @@ Changes in Release 0.1
  * first idea of the documentation system
  * meld included from SMNG as first module (to be modified/ renamed)
 
+Changes in Release 0.2
+--------------------------------------------------------------------------------
+ * added html documentation to repository
+
 ..  LocalWords:  Changelog reStructuredText changelog txt

doc/html/_sources/contributing.txt

@@ -11,6 +11,9 @@ documented inline. One exception exists on the example-driven approach:
 following the :mod:`~promod3.core` module for your setup is not advisable. This
 one is a bit special and provides core functionality to everybody else.
 
+In the end of this chapter you will find a little walk-through on how to get
+started.
+
 --------------------------------------------------------------------------------
 |git| Branches
 --------------------------------------------------------------------------------
@@ -201,16 +204,17 @@ will provide you with a target ``test_awesome_feature.py_run``.
 --------------------------------------------------------------------------------
 Writing Documentation
 --------------------------------------------------------------------------------
-To create documentation, we use |sphinx|_ to go from |restructuredtext|_ files
-and API documentation in source files to HTML or man pages.
-
-For each module, at least one |restructuredtext| document exists, that gives an
-idea of concepts and pulls in interfaces from source. Copying files to the
-build directory, issuing the |sphinx| call and everything else that is needed
-to create the actual documentation is done by |cmake| and its makefiles. Hence,
-the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is crucial.
-For documentation which does not relate to a particular module, the repository
-comes with a top-level :file:`doc` directory.
+To create documentation, we use |sphinx|_ to go from |restructuredtext|_
+(|restructuredtext_abrv|) files and API documentation in source files to HTML
+or man pages.
+
+For each module, at least one |restructuredtext_abrv| document exists, that
+gives an idea of concepts and pulls in interfaces from source. Copying files to
+the build directory, issuing the |sphinx| call and everything else that is
+needed to create the actual documentation is done by |cmake| and its makefiles.
+Hence, the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is
+crucial. For documentation which does not relate to a particular module, the
+repository comes with a top-level :file:`doc` directory.
 
 While you should not spend to much time thinking about how to format
 documentation, here is a helpful list of standard formatters:
@@ -219,8 +223,272 @@ http://sphinx-doc.org/markup/inline.html
 If you write new functionality for |project|, or fix bugs, feel free to extend
 the Changelog. It will be automatically pulled into the documentation.
 
+--------------------------------------------------------------------------------
+How To Start Your Own Module
+--------------------------------------------------------------------------------
+This is just a walk-through how the topics from above work together when you
+start your own module. For the entry point, lets assume that you already cloned
+the repository into a directory and just changed into it.
+
+All new features should take off from the ``develop`` branch. That way, they
+work fine with all the other new fellows waiting for release right from the
+beginning. Therefore you need to switch branches as a first step. |git| will
+tell you for which branch you went, a story of failure otherwise.
+
+.. code-block:: console
+
+   $ git checkout develop
+   Switched to branch 'develop'
+   $
+
+Sitting on top of the right code basis, you should just spawn your own branch
+from it. As an example, your feature will go by the name of 'sidechains'.
+
+.. code-block:: console
+
+   $ git checkout -b sidechains
+   Switched to a new branch 'sidechains'
+   $
+
+This time, |git| should tell you about going for **a new** branch.
+
+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.
+
+.. code-block:: console
+
+   $ mkdir -p sidechains/doc
+   $ mkdir -p sidechains/pymod
+   $ mkdir -p sidechains/tests
+   $
+
+If you run ``git status`` at this point, you will see basically nothing. That
+is, |git| does not admire empty directories. Before you bring your module under
+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
+   $
+
+Having an empty :file:`__init__.py` is perfectly fine for |python|, it just
+announces a directory as a module. But a blank :file:`index.rst` has the chance
+to give |sphinx| quite a headache so you already fill it with a headline for
+your documentation.
+
+For integration with :command:`make`, the build system needs to now about the
+new module and its members. This goes for setting up new |cmake| files and
+extending some around the directory root.
+
+.. code-block:: console
+
+   $ touch sidechains/CMakeLists.txt
+   $ touch sidechains/pymod/CMakeLists.txt
+   $ touch sidechains/doc/CMakeLists.txt
+   $
+
+Each of those files still needs a bit of content. The simplest one comes from
+the module's root, :file:`sidechains/CMakeLists.txt`:
+
+.. code-block:: cmake
+   :linenos:
+
+   add_subdirectory(pymod)
+   add_subdirectory(doc)
+
+Those two directives just tell |cmake| to go and look in directories
+:file:`pymod` and :file:`doc` below the current path for more |cmake|
+configurations. The next level in :file:`CMakeLists.txt` magic comes for the
+:file:`doc` directory:
+
+.. code-block:: cmake
+   :linenos:
+
+   set(SIDECHAINS_RST
+   index.rst
+   )
+
+   add_doc_source(NAME sidechains RST ${SIDECHAINS_RST})
+
+``add_doc_source`` is our custom |cmake| macro to register
+|restructuredtext_abrv| files for the documentation. On running
+:command:`make`, those files are placed in a :file:`doc/source` directory tree
+within the build directory. Each new submodule in your project should be
+covered by its own documentation entity, extending the list in ``RST``.
+Maintaining readability, its good practice to store this list in a separate
+variable, called ``SIDECHAINS_RST`` here.
+
+For the actual code, you should keep in mind that a |python| module may be
+rather complex. There is for sure |python| code, there could be a bit of |C++|
+and conditional compilation. In rare cases you also want to modify the
+directory structure of the package. All this has to be declared in the
+:file:`pymod` subtree. We cannot enumerate all specialities but there should be
+a couple of examples around in this repository. Here is the most basic
+:file:`CMakeLists.txt`:
+
+.. code-block:: cmake
+   :linenos:
+
+   set(SIDECHAINS_PYMOD
+   __init__.py
+   )
+
+   pymod(NAME sidechains PY ${SIDECHAINS_PYMOD})
+
+Source files should be again listed in a dedicated variable. Later, you
+probably add some |C++| code and settings diverging from the defaults via the
+``pymod`` macro. This is where things clutter up quite quickly. As set up here,
+your project would be added as a module ``sidechains`` in the |project|
+|python| package tree.
+
+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
+
+   #-------------------------------------------------------------------------------
+   # Author: Bienchen
+   #-------------------------------------------------------------------------------
+   # Options to CMake:
+   #    DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
+   #    DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
+   #    DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
+   # (if documentation is disabled, there is no doctest, linkcheck at all)
+   cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+   set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
+   
+   project(PROMOD3 CXX C)
+
+   include(PROMOD3)
+
+   set(PROMOD3_VERSION_MAJOR 0)
+   set(PROMOD3_VERSION_MINOR 1)
+   set(PROMOD3_VERSION_PATCH 0)
+   set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
+
+   if (CMAKE_COMPILER_IS_GNUCXX)  
+     exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
+     if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
+       set(PROMOD_GCC_45 true)
+     else()
+       set(PROMOD_GCC_45 false)  
+     endif()
+   endif()
+
+   if (OPTIMIZE)
+     set(CMAKE_BUILD_TYPE Release)
+     set(_OPT ON)
+   else()
+      set(CMAKE_BUILD_TYPE Debug)
+      set(_OPT OFF)
+   endif()
+
+   setup_stage()
+   file(MAKE_DIRECTORY ${STAGE_DIR}
+        ${EXECUTABLE_OUTPUT_PATH}
+        ${HEADER_STAGE_PATH}
+        ${LIB_STAGE_PATH}
+        ${LIBEXEC_STAGE_PATH})
+
+   setup_compiler_flags()
+   setup_boost()
+
+   find_package(Python 2.7 REQUIRED)
+   if(NOT DISABLE_DOCUMENTATION)
+     find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
+     set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
+     # set this to the URL corresponding to the version of OST you are using
+     set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
+   endif()
+   find_package(OPENSTRUCTURE 1.4 REQUIRED 
+                COMPONENTS io mol seq seq_alg mol_alg conop)
+
+   if (CMAKE_COMPILER_IS_GNUCXX)
+     # do not write back into cache, otherwise the compile command line gets
+     # expanded with multiple -fno-strict-aliasing flags, triggering a complete
+     # rebuild whenever cmake is run
+     set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
+     if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
+     endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+   endif()
+
+   # basic environment
+   include_directories(${Boost_INCLUDE_DIRS}
+                       ${OST_INCLUDE_DIR})
+
+   set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
+   set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
+                                "${FILES_TO_BE_REMOVED}")
+
+   ## sub dirs to be recognised by CMake
+   ## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
+   add_subdirectory(config)
+   add_subdirectory(core)
+   add_subdirectory(sidechains)
+   add_subdirectory(scripts)
+   add_subdirectory(actions)
+   if(NOT DISABLE_DOCUMENTATION)
+     add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
+     add_subdirectory(doc)
+   endif()
+
+   ## report setup
+   message(STATUS "PROMOD3 will be built with the following options:\n"
+           "   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
+           "   Optimized     (-DOPTIMIZE) : ${_OPT}\n"
+           "   Python                     : ${PYTHON_BINARY}\n")
+
+All that needs to be done for |cmake| to recognise your module is adding its
+directory as shown in line 80.
+
+This was the final step to set up the build system. Running |cmake| at this
+point would create the build environment in place. But building software in
+your code repository has several drawbacks. First of all, it puts all kind of
+new files in the directory tree and ``git status`` would show them all. Then
+its very likely, that manual intervention is needed after ``make clean``. Plus,
+this would be very static. Imagine at one point you want to switch on all
+debugging flags for your |C++| code. So you either clean the whole repository
+and rebuild or you go by two separated repositories copying code changes from A
+to B. The solution to this is instead of 'in place' you go 'out of source'. You
+still can stay in your repository while being out of the source tree by using
+sub-directories. |project| comes with a dedicated prefix 'build*' in
+:file:`.gitignore`. Have a directory :file:`build` and :file:`build-dbg` and it
+will not show up in ``git status``.
+
+.. code-block:: console
+
+   $ mkdir build
+   $ cd build
+   $
+
+To actually create all the makefiles and generated files, you may use one of
+the configuration scripts from the :file:`conf-scripts` directory. Usually
+those scripts only need to be pointed to an |ost_s| staging tree. Even if you
+are on a system not covered by available scripts, their code may help you at
+the |cmake| command. Once you managed to conquer a new system, feel free to add
+a new configuration script. The following example assumes |fedora| 19.
+
+.. code-block:: console
+
+   $ ../conf-scripts/fedora-19-conf ../../ost.git/stage
+
+From this point, :command:`make` should work and you could start adding your
+files to the repository using ``git add``.
+
+
 .. _restructuredtext: http://docutils.sourceforge.net/rst.html
+.. |fedora| replace:: Fedora
+
 
 ..  LocalWords:  cmake hotfix doctest linkcheck rebase BRANCHNAME rebasing py
 ..  LocalWords:  CMakeLists txt rst pymod init submodule src restructuredtext
-..  LocalWords:  makefiles formatters Changelog codetest promod
+..  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

doc/html/_sources/meld/index.txt

-:mod:`~sm.meld` - Coordinate modeling
+:mod:`~promod3.meld` - Coordinate modeling
 ================================================================================
 
-.. module:: sm.meld
+.. module:: promod3.meld
   :synopsis: Coordinate modeling and sampling
   
 This module contains functions and classes to model protein structures from sequence.

doc/html/buildsystem.html

@@ -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 08 10:47, 2014.
+      Last updated on May 26 14:31, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>

doc/html/changelog.html

@@ -60,6 +60,14 @@
 </ul>
 </div></blockquote>
 </div>
+<div class="section" id="changes-in-release-0-2">
+<h2>Changes in Release 0.2<a class="headerlink" href="#changes-in-release-0-2" title="Permalink to this headline">¶</a></h2>
+<blockquote>
+<div><ul class="simple">
+<li>added html documentation to repository</li>
+</ul>
+</div></blockquote>
+</div>
 </div>
 
 
@@ -72,6 +80,7 @@
   <ul>
 <li><a class="reference internal" href="#">Changelog</a><ul>
 <li><a class="reference internal" href="#changes-in-release-0-1">Changes in Release 0.1</a></li>
+<li><a class="reference internal" href="#changes-in-release-0-2">Changes in Release 0.2</a></li>
 </ul>
 </li>
 </ul>
@@ -118,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on May 08 10:47, 2014.
+      Last updated on May 26 13:39, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>