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# -*- coding: utf-8 -*-
# ProDy documentation build configuration file, created by
# sphinx-quickstart on Wed Sep 15 21:31:37 2010.
# 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 sys, os, os.path, time
# 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 = '1.0'
# 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.todo',
'',]#, 'sphinxcontrib.spelling']
# 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 = 'contents'
# General information about the project.
project = u'ProDy'
copyright = u'2010-2012, Ahmet Bakan'
# 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.
def getRevisionNumber():
from subprocess import PIPE, Popen
pipe = Popen('git log --summary'.split(), stdout=PIPE, stderr=PIPE)
return str('Author:'))
version = '1.2-dev'
# The full version, including alpha/beta/rc tags.
release = version
# 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 = ['_build']
# 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 = False
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
show_authors = True
# 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 = ['prody.']
doctest_global_setup = "from prody import *"
# -- 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 = 'sphinxdoc'
# 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 = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# 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 = '_static/favicon.ico'
# 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']
# 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
html_index = 'index.html'
# Custom sidebar templates, maps document names to template names.
# 'sourcelink.html'
generic_sidebars = ['docversion.html', 'howtocite.html', 'localtoc.html',
'relations.html', 'searchbox.html']
html_sidebars = {
'index': ['slideshow.html', 'docversion.html', 'howtocite.html',
'getprody.html', 'getintouch.html', 'searchbox.html',],
'genindex': ['searchbox.html'],
'py-modindex': ['searchbox.html'],
'search': [],
'tutorial': ['docversion.html', 'howtocite.html', 'localtoc.html',
'codesnippets.html', 'searchbox.html'],
'bibliography': generic_sidebars,
'changes': generic_sidebars,
'contents': generic_sidebars,
'credits': generic_sidebars,
'features': generic_sidebars,
'getprody': ['howtocite.html', 'localtoc.html', 'relations.html',
'license': generic_sidebars,
'publications': generic_sidebars,
'examples/index': generic_sidebars,
'reference/index': generic_sidebars,
'reports/index': generic_sidebars,
'scripts/index': generic_sidebars,
'todo': generic_sidebars,
'plugins/index': ['slideshow.html'] + generic_sidebars,
'plugins/getnmwiz': ['slideshow.html'] + generic_sidebars,
'**': ['docversion.html', 'howtocite.html', 'localtoc.html',
'relations.html', 'codesnippets.html', 'searchbox.html']}
#html_sidebars = {'index': ['indexsidebar.html', 'searchbox.html']}
# Additional templates that should be rendered to pages, maps page names to
# template names.
html_additional_pages = {'index': 'index.html'}
# If true, the reST sources are included in the HTML build as _sources/<name>.
html_copy_source = False
# 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 = 'ProDydoc'
# Plot directive configuration
# ----------------------------
plot_formats = [('png', 80), ('pdf', 80)]
plot_pre_code = """import numpy as np
from prody import *
from matplotlib import pyplot as plt
plot_working_directory = os.path.join(os.getcwd(), 'doctest')
plot_template = """
{{ source_code }}
{{ only_html }}
{% for img in images %}
.. figure:: {{ build_dir }}/{{ img.basename }}.png
{%- for option in options %}
{{ option }}
{% endfor %}
{{ caption }}
{% endfor %}
{{ only_latex }}
{% for img in images %}
.. image:: {{ build_dir }}/{{ img.basename }}.pdf
{% endfor %}
plot_rcparams = {'font.size': 10,
'xtick.labelsize': 'small',
'ytick.labelsize': 'small',
'figure.figsize': [5., 4.],}
plot_apply_rcparams = True
# -- Options for LaTeX output --------------------------------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('contents', 'ProDy.tex', u'ProDy Documentation',
u'Ahmet Bakan', 'manual'),
# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = '_static/logo.png'
# 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
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
latex_elements = {
'fontpkg': '\\usepackage{palatino}',
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'prody', u'ProDy Documentation',
[u'Ahmet Bakan'], 1)
autodoc_member_order = 'groupwise'
autodoc_default_flags = []# ['members', 'undoc-members', 'show-inheritance']
autoclass_content = 'both'
todo_include_todos = True
googleanalytics_enabled = True
googleanalytics_id = 'UA-19801227-1'
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
'matplotlib': ('', None),
'python': ('', None),
'numpy': ('', None),
'scipy': ('', None)
rst_epilog = """
.. |pdf| image:: /_static/pdf.png
.. |more| image:: /_static/more.png
.. |example| image:: /_static/example.png
.. |bulb| image:: /_static/bulb.png
.. |new| image:: /_static/new.png
.. |nmwiz| replace::
.. |vmd| replace::
.. |pdb| replace::
.. |mdanalysis| replace::
.. |pyparsing| replace::
.. |matplotlib| replace::
.. |docrelease| replace:: Documentation release r{0:s}
.. |biopython| replace::
.. |pypi| replace::
.. |anm| replace::
.. |questions| replace:: To receive new release announcements, join our
ProDy-News Google Group:
.. |suggestions| replace:: Suggestions, feature requests, or
problems? Submit them to the GitHub issue tracker:
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