2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2015, by the GROMACS development team, led by
5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 # and including many others, as listed in the AUTHORS file in the
7 # top-level source directory and at http://www.gromacs.org.
9 # GROMACS is free software; you can redistribute it and/or
10 # modify it under the terms of the GNU Lesser General Public License
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33 # the research papers on the package. Check out http://www.gromacs.org.
35 # -*- coding: utf-8 -*-
37 # Gromacs documentation build configuration file, created by
38 # sphinx-quickstart on Tue Jan 13 14:28:44 2015.
40 # This file is execfile()d with the current directory set to its
43 # Note that not all possible configuration values are present in this
46 # All configuration values have a default; values that are commented out
47 # serve to show the default.
52 execfile('conf-vars.py')
53 sys
.path
.append(gmx_sphinx_extension_path
)
55 # If extensions (or modules to document with autodoc) are in another directory,
56 # add these directories to sys.path here. If the directory is relative to the
57 # documentation root, use os.path.abspath to make it absolute, like shown here.
58 #sys.path.insert(0, os.path.abspath('.'))
60 # -- General configuration ------------------------------------------------
62 # If your documentation needs a minimal Sphinx version, state it here.
65 # Add any Sphinx extension module names here, as strings. They can be
66 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
69 'sphinx.ext.graphviz',
71 'sphinx.ext.ifconfig',
75 # Add any paths that contain templates here, relative to this directory.
76 # templates_path = ['_templates']
78 # The suffix of source filenames.
79 source_suffix
= '.rst'
81 # The encoding of source files.
82 #source_encoding = 'utf-8-sig'
84 # The master toctree document.
87 # General information about the project.
89 copyright
= u
'2015, GROMACS development team'
91 # The version info for the project you're documenting, acts as replacement for
92 # |version| and |release|, also used in various other places throughout the
95 # The short X.Y version.
96 version
= gmx_version_string
97 # The full version, including alpha/beta/rc tags.
98 release
= gmx_version_string_full
100 # The language for content autogenerated by Sphinx. Refer to documentation
101 # for a list of supported languages.
104 # There are two options for replacing |today|: either, you set today to some
105 # non-false value, then it is used:
107 # Else, today_fmt is used as the format for a strftime call.
108 #today_fmt = '%B %d, %Y'
110 # List of patterns, relative to source directory, that match files and
111 # directories to ignore when looking for source files.
112 exclude_patterns
= ['dev-manual/doxygen-links.rst']
113 if not tags
.has('do_man'):
114 exclude_patterns
+= ['man']
116 exclude_patterns
+= ['man/bytopic.rst']
118 # The reST default role (used for this markup: `text`) to use for all
122 # If true, '()' will be appended to :func: etc. cross-reference text.
123 #add_function_parentheses = True
125 # If true, the current module name will be prepended to all description
126 # unit titles (such as .. function::).
127 #add_module_names = True
129 # If true, sectionauthor and moduleauthor directives will be shown in the
130 # output. They are ignored by default.
131 #show_authors = False
133 # The name of the Pygments (syntax highlighting) style to use.
134 pygments_style
= 'sphinx'
136 # A list of ignored prefixes for module index sorting.
137 #modindex_common_prefix = []
139 # If true, keep warnings as "system message" paragraphs in the built documents.
140 #keep_warnings = False
142 # Configure the values for all the variables that might later configure any of the .rst files.
143 substitutions
= ['.. |{0}| replace:: {1}'.format(*x
) for x
in variables
if x
[1]]
144 substitutions
.extend(['.. |{0}| replace:: unknown'.format(x
[0]) for x
in variables
if x
[1] == ''])
145 rst_epilog
= "\n".join(substitutions
)
147 .. |Gromacs| replace:: GROMACS
148 .. _gmx-manual: manual-{gmx_version_string}.pdf
149 .. _gmx-manual-parent-dir: ../manual-{gmx_version_string}.pdf
150 .. |gmx-source-package| replace:: ftp://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
151 .. |gmx-regressiontests-package| replace:: http://gerrit.gromacs.org/download/regressiontests-{regressiontest_version}.tar.gz
152 .. _up-to-date installation instructions: http://www.gromacs.org/Documentation/Installation_Instructions
153 .. _CUDA: http://www.nvidia.com/object/cuda_home_new.html
154 .. _OpenMPI: http://www.open-mpi.org
155 .. _MPICH: http://www.mpich.org
156 .. _LAMMPI: http://www.lam-mpi.org
157 .. _OpenMP: http://en.wikipedia.org/wiki/OpenMP
158 .. _CMake installation page: http://www.cmake.org/install/
159 .. _running CMake: http://www.cmake.org/runningcmake/
160 .. _CMake environment variables: http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables
161 .. _FFTW: http://www.fftw.org
162 .. _FFTW installation guide: http://www.fftw.org/doc/Installation-and-Customization.html#Installation-and-Customization
163 .. _MKL: https://software.intel.com/en-us/intel-mkl
164 .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
165 .. _PyMOL: http://www.pymol.org
166 .. _continuous integration server used by Gromacs: http://jenkins.gromacs.org
167 .. _Jenkins: http://jenkins-ci.org
168 .. _webpage: http://www.gromacs.org
169 .. _ftp site: ftp://ftp.gromacs.org/pub/gromacs/
170 .. _tutorials: http://www.gromacs.org/Documentation/Tutorials
171 .. _download: ../download.html
172 """.format(gmx_version_string
=gmx_version_string
, regressiontest_version
=regressiontest_version
)
174 # -- Options for HTML output ----------------------------------------------
176 # The theme to use for HTML and HTML Help pages. See the documentation for
177 # a list of builtin themes.
178 html_theme
= 'default'
180 # Theme options are theme-specific and customize the look and feel of a theme
181 # further. For a list of options available for each theme, see the
183 #html_theme_options = {}
185 # Add any paths that contain custom themes here, relative to this directory.
186 html_theme_path
= ['']
188 # The name for this set of Sphinx documents. If None, it defaults to
189 # "<project> v<release> documentation".
190 html_title
= u
'GROMACS ' + release
+ ' documentation'
192 # A shorter title for the navigation bar. Default is the same as html_title.
193 html_short_title
= u
'GROMACS ' + version
195 # The name of an image file (relative to this directory) to place at the top
199 # The name of an image file (within the static path) to use as favicon of the
200 # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
204 # Add any paths that contain custom static files (such as style sheets) here,
205 # relative to this directory. They are copied after the builtin static files,
206 # so a file named "default.css" will overwrite the builtin "default.css".
207 html_static_path
= ['_static']
209 # Add any extra paths that contain custom files (such as robots.txt or
210 # .htaccess) here, relative to this directory. These files are copied
211 # directly to the root of the documentation.
212 #html_extra_path = []
214 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
215 # using the given strftime format.
216 #html_last_updated_fmt = '%b %d, %Y'
218 # If true, SmartyPants will be used to convert quotes and dashes to
219 # typographically correct entities.
220 #html_use_smartypants = True
222 # Custom sidebar templates, maps document names to template names.
225 # Additional templates that should be rendered to pages, maps page names to
227 #html_additional_pages = {}
229 # If false, no module index is generated.
230 #html_domain_indices = True
232 # If false, no index is generated.
233 #html_use_index = True
235 # If true, the index is split into individual pages for each letter.
236 #html_split_index = False
238 # If true, links to the reST sources are added to the pages.
239 #html_show_sourcelink = True
241 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
242 #html_show_sphinx = True
244 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
245 #html_show_copyright = True
247 # If true, an OpenSearch description file will be output, and all pages will
248 # contain a <link> tag referring to it. The value of this option must be the
249 # base URL from which the finished HTML is served.
250 #html_use_opensearch = ''
252 # This is the file name suffix for HTML files (e.g. ".xhtml").
253 #html_file_suffix = None
255 # Output file base name for HTML help builder.
256 htmlhelp_basename
= 'Gromacsdoc'
259 # -- Options for LaTeX output ---------------------------------------------
262 # The paper size ('letterpaper' or 'a4paper').
263 'papersize': 'a4paper',
265 # The font size ('10pt', '11pt' or '12pt').
268 # Additional stuff for the LaTeX preamble.
272 # Grouping the document tree into LaTeX files. List of tuples
273 # (source start file, target name, title,
274 # author, documentclass [howto, manual, or own class]).
276 ('index', 'Gromacs.tex', u
'Gromacs Documentation',
277 u
'Gromacs development team', 'manual'),
280 # The name of an image file (relative to this directory) to place at the top of
284 # For "manual" documents, if this is true, then toplevel headings are parts,
286 #latex_use_parts = False
288 # If true, show page references after internal links.
289 #latex_show_pagerefs = False
291 # If true, show URL addresses after external links.
292 #latex_show_urls = False
294 # Documents to append as an appendix to all manuals.
295 #latex_appendices = []
297 # If false, no module index is generated.
298 #latex_domain_indices = True
301 # -- Options for manual page output ---------------------------------------
303 # One entry per manual page. List of tuples
304 # (source start file, name, description, authors, manual section).
305 execfile('conf-man.py')
307 # If true, show URL addresses after external links.
308 #man_show_urls = False
311 # -- Options for Texinfo output -------------------------------------------
313 # Grouping the document tree into Texinfo files. List of tuples
314 # (source start file, target name, title, author,
315 # dir menu entry, description, category)
316 texinfo_documents
= [
317 ('index', 'Gromacs', u
'Gromacs Documentation',
318 u
'Gromacs development team', 'Gromacs', 'One line description of project.',
322 # Documents to append as an appendix to all manuals.
323 #texinfo_appendices = []
325 # If false, no module index is generated.
326 #texinfo_domain_indices = True
328 # How to display URL addresses: 'footnote', 'no', or 'inline'.
329 #texinfo_show_urls = 'footnote'
331 # If true, do not generate a @detailmenu in the "Top" node's menu.
332 #texinfo_no_detailmenu = False