Cleanup documentation (user vs dev) and increased timeout for linkcheck

CHANGELOG

@@ -5,20 +5,7 @@
 Changelog
 ================================================================================
 
-Changes in Release 0.1
+Release 1.0
 --------------------------------------------------------------------------------
- * initial setup of the CMake build system
- * 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
- * meld renamed to rawmodel
-
-Changes in Release 0.3 (to be released)
--------------------------------------------------------------------------------
- * merged argcheck into the helper module
- * rawmodel renamed to modelling and including high-level modelling functions
-
-..  LocalWords:  Changelog reStructuredText changelog txt
+ * initial release of ProMod3
+ 
\ No newline at end of file

doc/buildsystem.rst

@@ -7,16 +7,16 @@ Building |project|
 Dependencies
 --------------------------------------------------------------------------------
 |project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-1.4. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
+1.5. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
 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|). Also |eigen3|_ and |lapack|_ are needed. To build
-documentation, |sphinx|_ 1.2b1 is used.
+documentation, |sphinx|_ 1.2b1 is required.
 
 The currently (Nov. 2015) preferred versions are:
 
-* |ost_s|_ 1.4
+* |ost_s|_ 1.5
 * |openmm|_ 6.1
 * |cmake|_ 2.8.12
 * |python|_ 2.7.5

doc/conf.py.in

@@ -56,7 +56,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'ProMod3'
-copyright = u'2015, Bienchen'# pylint: disable=redefined-builtin
+copyright = u'2016, Bienchen'# pylint: disable=redefined-builtin
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -262,10 +262,12 @@ intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None),
                        'openstructure': ('@OST_DOC_URL@', None)}
 
 # -- ProMod3 specific configuration --------------------------------------------
+
 extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s',
                          'Python documentation'),
             'ost_docs' : ('@OST_DOC_URL@/%s',
                           'OpenStructure documentation')}
+
 # The _nameattr is a bit ugly: we want to have __name__ formatted as Python
 # attribute but Sphinx does not go with calling :attr: inside extlinks. To keep
 # the Python url prefix, we define sth here. Same holds for _mainattr. But this
@@ -293,6 +295,10 @@ rst_epilog = """
 .. |pep8| replace:: PEP 8
 .. _pep8: https://www.python.org/dev/peps/pep-0008/
 """ % project
+
+# increase default timeout (5s) for linkcheck
+linkcheck_timeout = 15.0
+
 # in some versions of sphinx, doctest invokes doctest_path AFTER executing code
 doctest_global_setup = """
 import sys

doc/developers.rst

 Documentation For Developers
 ===============================================================================
-.. give an intro on what will be stored here
-.. topics: how to create a new module, how to do doc (rst_epillog),
-           little bit on doctest & linkcheck, unit tests, directory structure
+
+This section is for developers that wish to extending the functionality of
+|project|. It describes helper classes for development and how to contribute
+new features.
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
 
-   gettingstarted
-   core/setcompoundschemlib
-   core/index
-   modelling/index
-   loop/index
-   sidechain/index
-   actions/index_dev
-   buildsystem
    contributing
+   actions/index_dev
    cmake/index
-
-.. todolist::

doc/gettingstarted.rst

@@ -5,9 +5,8 @@ Get and Run |project|
 --------------------------------------------------------------------------------
 First steps to get |project| up and running:
 
-#. Get |ost_s|_.
-#. Get |project| from the ``git`` repository (see :ref:`here <git-branches>`).
-#. Compile |project| with ``cmake`` and ``make`` (see :ref:`here <building-promod>`).
+#. Obtain all dependencies and compile |project| with ``cmake`` and ``make``
+   (see :ref:`here <building-promod>`).
 #. Ensure that you have a ``stage/bin`` folder which includes a ``pm`` executable.
    For convenience, add the folder to your ``PATH`` env. variable.
 #. You can now execute |project| by running the following in your terminal:
@@ -41,7 +40,8 @@ Modelling pipeline
 Commonly, your input is a template structure and an alignment of the template to 
 the desired target sequence. The modelling steps then are:
 
-- Build a raw model from the template (see :func:`~promod3.modelling.BuildRawModel` function)
+- Build a raw model from a template by copying the part of the template which
+  is conserved
 - Perform loop modelling to close all gaps (see :mod:`~promod3.loop` module)
 - Reconstruct sidechains (see :mod:`~promod3.sidechain` module)
 - Minimize energy of final model using molecular mechanics

doc/index.rst

@@ -13,9 +13,12 @@ Contents:
 
    Users <users>
    Developers <developers>
-   changelog
 
-.. todolist::
+.. toctree::
+   :maxdepth: 1
+
+   changelog
+   
 
 Indices And Tables
 ==================

doc/users.rst

 Documentation For Users
 =======================
-.. intro, primer on concept of actions, holistic ProMod and hint towards modules
+
+This section is for users of |project|. It describes how to compile and run
+scripts using the functionality of this library.
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   gettingstarted
+   buildsystem
+   modelling/index
+   loop/index
+   sidechain/index
+   core/index
+   core/setcompoundschemlib