.. Add files here that should be included in the index.rst file (as symlinks cause problems with Git versioning):
.. See http://stackoverflow.com/questions/10199233/can-sphinx-link-to-documents-that-are-not-located-in-directories-below-the-root


.. include:: ../README.rst
.. include:: ../notes/reproducibility_thoughts.rst
.. include:: ../notes/comp_bio_pipeline_approach.rst

.. include:: ../notes/notes_python_packaging.rst

.. include:: ../notes/notes_technical_documentation_tools.rst
.. include:: ../notes/rst_basics.rst
.. include:: ../notes/sphinx_rst_read_the_docs.rst
.. include:: ../notes/file_with_include.rst
.. include:: ../notes/substitution_vars.rst
.. include:: ../notes/SVG_multi_panel_plots.rst

.. include:: ../notes/continuous_integration_start.rst

.. include:: ../notes/pipeline_tools_references.rst
.. include:: ../notes/docopt_argument_parser.rst
.. include:: ../notes/docker_notes_and_dockerfile_example.rst

.. include:: ../notes/work_done_and_to_do_list.rst

.. include:: ../notes/best_practice_checklist.rst
.. .. include:: ../travis_example_R.travis.yml
.. .. include:: ../travis_example_python.travis.yml