Add grompp check for unbound atoms

[gromacs.git] / docs / conf.py

#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
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# -*- coding: utf-8 -*-
#
# GROMACS documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 13 14:28:44 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import datetime
import os
import sys

execfile('conf-vars.py')
sys.path.append(gmx_sphinx_extension_path)
if releng_path and os.path.isdir(releng_path):
    sys.path.append(releng_path)

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '1.3'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.graphviz',
    'sphinx.ext.napoleon',
    'sphinx.ext.imgmath',
    'sphinx.ext.ifconfig',
    'gmxsphinx'
]

# Add any paths that contain templates here, relative to this directory.
# templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The encoding of source files.
#source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'GROMACS'
copyright = str(datetime.datetime.now().year) + u', GROMACS development team'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = gmx_version_string
# The full version, including alpha/beta/rc tags.
release = gmx_version_string_full

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['fragments']
if not tags.has('do_man'):
    exclude_patterns += ['man']

# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False

# Configure the values for all the variables that might later configure any of the .rst files.
substitutions = ['.. |{0}| replace:: {1}'.format(*x) for x in variables if x[1]]
substitutions.extend(['.. |{0}| replace:: unknown'.format(x[0]) for x in variables if x[1] == ''])
rst_epilog = "\n".join(substitutions)
rst_epilog += """
.. |Gromacs| replace:: GROMACS
.. _gmx-manual: manual-{gmx_version_string}.pdf
.. _gmx-manual-parent-dir: ../manual-{gmx_version_string}.pdf
.. |gmx-source-package-ftp| replace:: As ftp ftp://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
.. |gmx-source-package-http| replace:: As http http://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
.. |gmx-regressiontests-package| replace:: http://gerrit.gromacs.org/download/regressiontests-{regressiontest_version}.tar.gz
.. _up-to-date installation instructions: http://www.gromacs.org/Documentation/Installation_Instructions
.. _CUDA: http://www.nvidia.com/object/cuda_home_new.html
.. _OpenCL: https://www.khronos.org/opencl/
.. _OpenMPI: http://www.open-mpi.org
.. _MPICH: http://www.mpich.org
.. _LAM-MPI: http://www.lam-mpi.org
.. _OpenMP: http://en.wikipedia.org/wiki/OpenMP
.. _CMake installation page: http://www.cmake.org/install/
.. _running CMake: http://www.cmake.org/runningcmake/
.. _CMake environment variables: http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables
.. _FFTW: http://www.fftw.org
.. _FFTW installation guide: http://www.fftw.org/doc/Installation-and-Customization.html#Installation-and-Customization
.. _MKL: https://software.intel.com/en-us/intel-mkl
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
.. _PyMOL: http://www.pymol.org
.. _continuous integration server used by GROMACS: http://jenkins.gromacs.org
.. _Jenkins: http://jenkins-ci.org
.. _webpage: http://www.gromacs.org
.. _ftp site: ftp://ftp.gromacs.org/pub/gromacs/
.. _tutorials: http://www.gromacs.org/Documentation/Tutorials
.. _download: ../download.html
""".format(gmx_version_string=gmx_version_string, regressiontest_version=regressiontest_version)

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
html_theme = 'classic'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = ['']

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
html_title = u'GROMACS ' + release + ' documentation'

# A shorter title for the navigation bar.  Default is the same as html_title.
html_short_title = u'GROMACS ' + version

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None

# The name of an image file (within the static path) to use as favicon of the
# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True

# If false, no index is generated.
#html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False

# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'Gromacsdoc'


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
'papersize': 'a4paper',

# The font size ('10pt', '11pt' or '12pt').
'pointsize': '10',

# Additional stuff for the LaTeX preamble.
#'preamble': '',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
  ('index', 'Gromacs.tex', u'GROMACS Documentation',
   u'GROMACS development team', 'manual'),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False

# If true, show page references after internal links.
#latex_show_pagerefs = False

# If true, show URL addresses after external links.
#latex_show_urls = False

# Documents to append as an appendix to all manuals.
#latex_appendices = []

# If false, no module index is generated.
#latex_domain_indices = True


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
execfile('conf-man.py')

# If true, show URL addresses after external links.
#man_show_urls = False


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
  ('index', 'GROMACS', u'GROMACS Documentation',
   u'GROMACS development team', 'GROMACS', 'One line description of project.',
   'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#texinfo_appendices = []

# If false, no module index is generated.
#texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False