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Commit ebfe155b authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Cleanup documentation (user vs dev) and increased timeout for linkcheck

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...@@ -5,20 +5,7 @@ ...@@ -5,20 +5,7 @@
Changelog Changelog
================================================================================ ================================================================================
Changes in Release 0.1 Release 1.0
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
* initial setup of the CMake build system * initial release of ProMod3
* first idea of the documentation system
* meld included from SMNG as first module (to be modified/ renamed) \ No newline at end of file
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
...@@ -7,16 +7,16 @@ Building |project| ...@@ -7,16 +7,16 @@ Building |project|
Dependencies Dependencies
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version |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 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 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 |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 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: The currently (Nov. 2015) preferred versions are:
* |ost_s|_ 1.4 * |ost_s|_ 1.5
* |openmm|_ 6.1 * |openmm|_ 6.1
* |cmake|_ 2.8.12 * |cmake|_ 2.8.12
* |python|_ 2.7.5 * |python|_ 2.7.5
......
...@@ -56,7 +56,7 @@ master_doc = 'index' ...@@ -56,7 +56,7 @@ master_doc = 'index'
# General information about the project. # General information about the project.
project = u'ProMod3' 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 # The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the # |version| and |release|, also used in various other places throughout the
...@@ -262,10 +262,12 @@ intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None), ...@@ -262,10 +262,12 @@ intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None),
'openstructure': ('@OST_DOC_URL@', None)} 'openstructure': ('@OST_DOC_URL@', None)}
# -- ProMod3 specific configuration -------------------------------------------- # -- ProMod3 specific configuration --------------------------------------------
extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s', extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s',
'Python documentation'), 'Python documentation'),
'ost_docs' : ('@OST_DOC_URL@/%s', 'ost_docs' : ('@OST_DOC_URL@/%s',
'OpenStructure documentation')} 'OpenStructure documentation')}
# The _nameattr is a bit ugly: we want to have __name__ formatted as Python # 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 # 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 # the Python url prefix, we define sth here. Same holds for _mainattr. But this
...@@ -293,6 +295,10 @@ rst_epilog = """ ...@@ -293,6 +295,10 @@ rst_epilog = """
.. |pep8| replace:: PEP 8 .. |pep8| replace:: PEP 8
.. _pep8: https://www.python.org/dev/peps/pep-0008/ .. _pep8: https://www.python.org/dev/peps/pep-0008/
""" % project """ % project
# increase default timeout (5s) for linkcheck
linkcheck_timeout = 15.0
# in some versions of sphinx, doctest invokes doctest_path AFTER executing code # in some versions of sphinx, doctest invokes doctest_path AFTER executing code
doctest_global_setup = """ doctest_global_setup = """
import sys import sys
......
Documentation For Developers 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), This section is for developers that wish to extending the functionality of
little bit on doctest & linkcheck, unit tests, directory structure |project|. It describes helper classes for development and how to contribute
new features.
Contents: Contents:
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
gettingstarted
core/setcompoundschemlib
core/index
modelling/index
loop/index
sidechain/index
actions/index_dev
buildsystem
contributing contributing
actions/index_dev
cmake/index cmake/index
.. todolist::
...@@ -5,9 +5,8 @@ Get and Run |project| ...@@ -5,9 +5,8 @@ Get and Run |project|
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
First steps to get |project| up and running: First steps to get |project| up and running:
#. Get |ost_s|_. #. Obtain all dependencies and compile |project| with ``cmake`` and ``make``
#. Get |project| from the ``git`` repository (see :ref:`here <git-branches>`). (see :ref:`here <building-promod>`).
#. Compile |project| with ``cmake`` and ``make`` (see :ref:`here <building-promod>`).
#. Ensure that you have a ``stage/bin`` folder which includes a ``pm`` executable. #. Ensure that you have a ``stage/bin`` folder which includes a ``pm`` executable.
For convenience, add the folder to your ``PATH`` env. variable. For convenience, add the folder to your ``PATH`` env. variable.
#. You can now execute |project| by running the following in your terminal: #. You can now execute |project| by running the following in your terminal:
...@@ -41,7 +40,8 @@ Modelling pipeline ...@@ -41,7 +40,8 @@ Modelling pipeline
Commonly, your input is a template structure and an alignment of the template to Commonly, your input is a template structure and an alignment of the template to
the desired target sequence. The modelling steps then are: 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) - Perform loop modelling to close all gaps (see :mod:`~promod3.loop` module)
- Reconstruct sidechains (see :mod:`~promod3.sidechain` module) - Reconstruct sidechains (see :mod:`~promod3.sidechain` module)
- Minimize energy of final model using molecular mechanics - Minimize energy of final model using molecular mechanics
......
...@@ -13,9 +13,12 @@ Contents: ...@@ -13,9 +13,12 @@ Contents:
Users <users> Users <users>
Developers <developers> Developers <developers>
changelog
.. todolist:: .. toctree::
:maxdepth: 1
changelog
Indices And Tables Indices And Tables
================== ==================
......
Documentation For Users 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
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