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# -*- coding: utf-8 -*-
import os
import sys
sys.path.append(os.path.abspath('sphinxext'))
RTD = os.environ.get('READTHEDOCS', None) == 'True'
if RTD:
tags.add('rtd')
extensions = ['sphinx.ext.todo',
'sphinx.ext.autodoc',
'sphinx.ext.doctest',
'sphinx.ext.coverage',
'sphinx.ext.extlinks',
'sphinx.ext.graphviz',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
'sphinx.ext.intersphinx',
'sphinx.ext.inheritance_diagram',
'matplotlib.sphinxext.mathmpl',
'matplotlib.sphinxext.only_directives']
# extensions that are included in docs
extensions.extend(
['IPython.sphinxext.ipython_console_highlighting',
'IPython.sphinxext.ipython_directive',
'googleanalytics',])
source_suffix = '.rst'
master_doc = 'index'
project = u'ProDy'
copyright = u'2010-2014, University of Pittsburgh'
__version__ = ''
for _ in ['../prody/__init__.py', # building docs
'ProDy/prody/__init__.py', # building complete website
'../../ProDy/prody/__init__.py']: # building tutorial PDFs
if os.path.isfile(_):
with open(_) as inp:
statement = ''.join([line for line in inp
if line[:3] in ('__v', '__r')])
exec(statement)
version, release = __version__, __release__
if release.endswith('dev'):
import shlex
from subprocess import Popen, PIPE
_ = '../.git'
if not os.path.isdir(_):
_ = 'ProDy/.git'
args = shlex.split('git --git-dir {} describe --tags --abbrev=0'.format(_))
tag = Popen(args, stdout=PIPE, stderr=PIPE)
rst_prolog = """
.. only:: html
.. note::
This documentation is for a development version of ProDy.
There may be significant differences from the latest stable
release ({}).
""".format(tag.communicate()[0].strip())
exclude_patterns = ['_build', '_workdir']
add_module_names = False
show_authors = True
pygments_style = 'sphinx'
modindex_common_prefix = ['prody.']
doctest_global_setup = "from prody import *"
# -- Options for HTML output ---------------------------------------------------
if RTD:
html_theme = 'default'
else:
templates_path = ['_theme']
html_theme = '_theme'
html_theme_path = ['.']
html_static_path = ['_static']
html_theme_options = {}
html_title = "ProDy"
html_favicon = '_static/favicon.ico'
html_last_updated_fmt = '%b %d, %Y'
html_index = 'index.html'
generic_sidebars = ['toolbox.html', 'releasenotes.html', 'howtocite.html']
html_sidebars = {'**': generic_sidebars}
html_copy_source = False
html_show_sourcelink = False
html_show_sphinx = True
html_show_copyright = True
extlinks = {
'issue': ('https://github.com/prody/ProDy/issues/%s', 'issue '),
'pdb': ('http://www.pdb.org/pdb/explore/explore.do?structureId=%s', ''),
'wiki': ('http://en.wikipedia.org/wiki/%s', ''),
'pfam': ('http://pfam-legacy.xfam.org/family/%s', ''),
'pfamprotein': ('http://pfam-legacy.xfam.org/protein/%s', ''),
'uniprot': ('http://www.uniprot.org/uniprot/%s', ''),
'pdbhet': ('http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=%s', ''),
}
# ipython directive configuration
ipython_savefig_dir = os.path.join('_static', 'figures')
# -- Options for LaTeX output --------------------------------------------------
latex_paper_size = 'letter'
latex_font_size = '10pt'
latex_documents = [
('index', 'ProDy.tex',
u'ProDy Documentation',
u'Ahmet Bakan', 'manual')
]
latex_logo = '_static/logo.png'
latex_show_pagerefs = True
latex_show_urls = 'footnote'
latex_preamble = ''
latex_appendices = []
latex_domain_indices = True
latex_elements = {
'classoptions': ',openany,oneside',
'fontpkg': '\\usepackage{palatino}',
'babel': '\\usepackage[english]{babel}'
}
autodoc_member_order = 'groupwise'
autodoc_default_flags = []
autoclass_content = 'both'
todo_include_todos = True
googleanalytics_enabled = True
googleanalytics_id = 'UA-19801227-1'
intersphinx_mapping = {
'python': ('http://docs.python.org/', None),
'numpy': ('http://docs.scipy.org/doc/numpy/', None),
'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
'matplotlib': ('http://matplotlib.sourceforge.net/', None),
'prodywebsite': ('http://prody.csb.pitt.edu/', None),
}
rst_epilog = u"""
.. _ProDy: http://prody.csb.pitt.edu
.. _Tutorials: http://prody.csb.pitt.edu/tutorials
.. _NMWiz: http://csb.pitt.edu/NMWiz
.. _VMD: http://www.ks.uiuc.edu/Research/vmd
.. _PDB: http://www.pdb.org
.. _pip: https://pypi.python.org/pypi/pip
.. _MDAnalysis: https://www.mdanalysis.org
.. _MDTraj: https://www.mdtraj.org
.. _pyparsing: http://pyparsing.wikispaces.com
.. _Matplotlib: http://matplotlib.org
.. _Biopython: http://biopython.org
.. _Chimera: https://www.cgl.ucsf.edu/chimera
.. _PyPI: http://pypi.python.org/pypi/ProDy
.. _GitHub: http://github.com/prody/ProDy
.. _IPython: http://ipython.org
.. _Python: http://www.python.org
.. _NumPy: http://www.numpy.org
.. _Scipy: http://www.scipy.org
.. _nose: http://nose.readthedocs.org
.. _Pandas: https://pandas.pydata.org/
.. |A2| replace:: Å\ :sup:`2`
"""
|
