<commit_before># -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
#
# Astropy documentation build configuration file.
#
# 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 file.
#
# All configuration values have a default. Some values are defined in
# the global Astropy configuration which is loaded here before anything else.
# See astropy.sphinx.conf for which values are set there.

# 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('..'))
# IMPORTANT: the above commented section was generated by sphinx-quickstart, but
# is *NOT* appropriate for astropy or Astropy affiliated packages. It is left
# commented out with this explanation to make it clear why this should not be
# done. If the sys.path entry above is added, when the astropy.sphinx.conf
# import occurs, it will import the *source* version of astropy instead of the
# version installed (if invoked as "make html" or directly with sphinx), or the
# version in the build directory (if "python setup.py build_sphinx" is used).
# Thus, any C-extensions that are needed to build the documentation will *not*
# be accessible, and the documentation will not build correctly.

# Load all of the global Astropy configuration
from astropy_helpers.sphinx.conf import *
from astropy.extern import six

import astropy

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

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.1'

# The intersphinx_mapping in astropy_helpers.sphinx.conf refers to astropy for
# the benefit of affiliated packages who want to refer to objects in the
# astropy core.  However, we don't want to cyclically reference astropy in its
# own build so we remove it here.
del intersphinx_mapping['astropy']

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns.append('_templates')
exclude_patterns.append('_pkgtemplate.rst')

# Add any paths that contain templates here, relative to this directory.
if 'templates_path' not in locals():  # in case parent conf.py defines it
    templates_path = []
templates_path.append('_templates')

# This is added to the end of RST files - a good place to put substitutions to
# be used globally.
rst_epilog += """
.. |minimum_numpy_version| replace:: {0.__minimum_numpy_version__}

.. Astropy
.. _Astropy: http://astropy.org
.. _`Astropy mailing list`: http://mail.scipy.org/mailman/listinfo/astropy
.. _`astropy-dev mailing list`: http://groups.google.com/group/astropy-dev
""".format(astropy)

# -- Project information ------------------------------------------------------

project = u'Astropy'
author = u'The Astropy Developers'
copyright = u'2011-2014, ' + author

# 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 = astropy.__version__.split('-', 1)[0]
# The full version, including alpha/beta/rc tags.
release = astropy.__version__

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

# A NOTE ON HTML THEMES
#
# The global astropy configuration uses a custom theme,
# 'bootstrap-astropy', which is installed along with astropy. The
# theme has options for controlling the text of the logo in the upper
# left corner. This is how you would specify the options in order to
# override the theme defaults (The following options *are* the
# defaults, so we do not actually need to set them here.)

#html_theme_options = {
#    'logotext1': 'astro',  # white,  semi-bold
#    'logotext2': 'py',     # orange, light
#    'logotext3': ':docs'   # white,  light
#    }

# A different theme can be used, or other parts of this theme can be
# modified, by overriding some of the variables set in the global
# configuration. The variables set in the global configuration are
# listed below, commented out.

# Add any paths that contain custom themes here, relative to this directory.
# To use a different custom theme, add the directory containing the theme.
#html_theme_path = []

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes. To override the custom theme, set this to the
# name of a builtin theme or the name of a custom theme in html_theme_path.
#html_theme = None

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

# 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 = ''

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

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
html_title = '{0} v{1}'.format(project, release)

# Output file base name for HTML help builder.
htmlhelp_basename = project + 'doc'

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

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [('index', project + '.tex', project + u' Documentation',
                    author, 'manual')]

latex_logo = '_static/astropy_logo.pdf'

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [('index', project.lower(), project + u' Documentation',
              [author], 1)]

# -- Options for the edit_on_github extension ----------------------------------------

extensions += ['astropy_helpers.sphinx.ext.edit_on_github']

# Don't import the module as "version" or it will override the
# "version" configuration parameter
from astropy import version as versionmod
edit_on_github_project = "astropy/astropy"
if versionmod.release:
    edit_on_github_branch = "v{0}.{1}.x".format(
        versionmod.major, versionmod.minor)
else:
    edit_on_github_branch = "master"
edit_on_github_source_root = ""
edit_on_github_doc_root = "docs"

github_issues_url = 'https://github.com/astropy/astropy/issues/'

# Enable nitpicky mode - which ensures that all references in the docs
# resolve.

nitpicky = True
nitpick_ignore = []

for line in open('nitpick-exceptions'):
    if line.strip() == "" or line.startswith("#"):
        continue
    dtype, target = line.split(None, 1)
    target = target.strip()
    nitpick_ignore.append((dtype, six.u(target)))

if six.PY2:
    nitpick_ignore.extend([('py:obj', six.u('bases'))])
<commit_msg>Hack to basically restore the functionality of running 'make' from inside the docs/ directory without having explicitly installed astropy_helpers first.  For general cases, such as building the docs on rtd, it remains preferable to simply install astropy_helpers first.<commit_after># -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
#
# Astropy documentation build configuration file.
#
# 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 file.
#
# All configuration values have a default. Some values are defined in
# the global Astropy configuration which is loaded here before anything else.
# See astropy.sphinx.conf for which values are set there.

# 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('..'))
# IMPORTANT: the above commented section was generated by sphinx-quickstart, but
# is *NOT* appropriate for astropy or Astropy affiliated packages. It is left
# commented out with this explanation to make it clear why this should not be
# done. If the sys.path entry above is added, when the astropy.sphinx.conf
# import occurs, it will import the *source* version of astropy instead of the
# version installed (if invoked as "make html" or directly with sphinx), or the
# version in the build directory (if "python setup.py build_sphinx" is used).
# Thus, any C-extensions that are needed to build the documentation will *not*
# be accessible, and the documentation will not build correctly.

try:
    import astropy_helpers
except ImportError:
    # Building from inside the docs/ directory?
    import os
    import sys
    if os.path.basename(os.getcwd()) == 'docs':
        a_h_path = os.path.abspath(os.path.join('..', 'astropy_helpers'))
        if os.path.isdir(a_h_path):
            sys.path.insert(1, a_h_path)

    # If that doesn't work trying to import from astropy_helpers below will
    # still blow up

# Load all of the global Astropy configuration
from astropy_helpers.sphinx.conf import *
from astropy.extern import six

import astropy

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

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.1'

# The intersphinx_mapping in astropy_helpers.sphinx.conf refers to astropy for
# the benefit of affiliated packages who want to refer to objects in the
# astropy core.  However, we don't want to cyclically reference astropy in its
# own build so we remove it here.
del intersphinx_mapping['astropy']

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns.append('_templates')
exclude_patterns.append('_pkgtemplate.rst')

# Add any paths that contain templates here, relative to this directory.
if 'templates_path' not in locals():  # in case parent conf.py defines it
    templates_path = []
templates_path.append('_templates')

# This is added to the end of RST files - a good place to put substitutions to
# be used globally.
rst_epilog += """
.. |minimum_numpy_version| replace:: {0.__minimum_numpy_version__}

.. Astropy
.. _Astropy: http://astropy.org
.. _`Astropy mailing list`: http://mail.scipy.org/mailman/listinfo/astropy
.. _`astropy-dev mailing list`: http://groups.google.com/group/astropy-dev
""".format(astropy)

# -- Project information ------------------------------------------------------

project = u'Astropy'
author = u'The Astropy Developers'
copyright = u'2011-2014, ' + author

# 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 = astropy.__version__.split('-', 1)[0]
# The full version, including alpha/beta/rc tags.
release = astropy.__version__

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

# A NOTE ON HTML THEMES
#
# The global astropy configuration uses a custom theme,
# 'bootstrap-astropy', which is installed along with astropy. The
# theme has options for controlling the text of the logo in the upper
# left corner. This is how you would specify the options in order to
# override the theme defaults (The following options *are* the
# defaults, so we do not actually need to set them here.)

#html_theme_options = {
#    'logotext1': 'astro',  # white,  semi-bold
#    'logotext2': 'py',     # orange, light
#    'logotext3': ':docs'   # white,  light
#    }

# A different theme can be used, or other parts of this theme can be
# modified, by overriding some of the variables set in the global
# configuration. The variables set in the global configuration are
# listed below, commented out.

# Add any paths that contain custom themes here, relative to this directory.
# To use a different custom theme, add the directory containing the theme.
#html_theme_path = []

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes. To override the custom theme, set this to the
# name of a builtin theme or the name of a custom theme in html_theme_path.
#html_theme = None

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

# 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 = ''

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

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
html_title = '{0} v{1}'.format(project, release)

# Output file base name for HTML help builder.
htmlhelp_basename = project + 'doc'

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

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [('index', project + '.tex', project + u' Documentation',
                    author, 'manual')]

latex_logo = '_static/astropy_logo.pdf'

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [('index', project.lower(), project + u' Documentation',
              [author], 1)]

# -- Options for the edit_on_github extension ----------------------------------------

extensions += ['astropy_helpers.sphinx.ext.edit_on_github']

# Don't import the module as "version" or it will override the
# "version" configuration parameter
from astropy import version as versionmod
edit_on_github_project = "astropy/astropy"
if versionmod.release:
    edit_on_github_branch = "v{0}.{1}.x".format(
        versionmod.major, versionmod.minor)
else:
    edit_on_github_branch = "master"
edit_on_github_source_root = ""
edit_on_github_doc_root = "docs"

github_issues_url = 'https://github.com/astropy/astropy/issues/'

# Enable nitpicky mode - which ensures that all references in the docs
# resolve.

nitpicky = True
nitpick_ignore = []

for line in open('nitpick-exceptions'):
    if line.strip() == "" or line.startswith("#"):
        continue
    dtype, target = line.split(None, 1)
    target = target.strip()
    nitpick_ignore.append((dtype, six.u(target)))

if six.PY2:
    nitpick_ignore.extend([('py:obj', six.u('bases'))])
<|endoftext|>


<commit_before># -*- coding: utf-8 -*-
#
# pymicro documentation build configuration file, created by
# sphinx-quickstart on Tue Oct 22 11:17:23 2013.
#
# 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
import mock

MOCK_MODULES = ['numpy', 'scipy', 'scipy.special', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.image',
                'matplotlib.cm', 'matplotlib.colors', 'scipy.ndimage', 'wx', 'wx.Panel', 'vtk', 'vtk.util',
                'vtk.util.colors', 'skimage', 'skimage.transform', '_tifffile', 'h5py']  # , 'ImPanel', 'PlotPanel']
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = mock.Mock()
# 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('..'))
sys.path.append(os.path.abspath('sphinxext'))
print(sys.path)
print('content of .')
print(os.listdir('.'))
print('content of ..')
print(os.listdir('..'))
print('content of ../..')
print(os.listdir('../..'))
try:
    import pymicro
    print('** successfully imported pymicro')
    from pymicro.crystal.lattice import Lattice
    print('** successfully imported Lattice')
except:
    print('problem during import')
    pass

try:
    import gen_rst
    print('** successfully imported gen_rst')
except:
    pass

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

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

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '1.1'
# 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.autosummary',
              'sphinx.ext.mathjax',
              'sphinxcontrib.bibtex',
              'gen_rst']
mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'

autodoc_member_order = 'bysource'
autodoc_default_flags = ['members', 'special-members', 'undoc-members', 'show-inheritance']
autosummary_generate = True

# 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'pymicro'
copyright = u'2013-2019, Henry Proudhon'

# The project version is extracted from the main __init__.py
def extract_version():
    """
    Extracts version values from the main __init__.py and
    returns them as a dictionary.
    """
    with open('../pymicro/__init__.py') as fd:
        for line in fd.readlines():
            if (line.startswith('__version__')):
                exec (line.strip())
    return locals()["__version__"]

version = '%s' % extract_version()

# 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 = 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 = []

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

# The theme to use for HTML and HTML Help pages.
print(os.environ)
if not 'READTHEDOCS' in os.environ.keys():  # if building locally
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = ["../../sphinx_rtd_theme"] # the theme should be installed aside the pymicro folder

# 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 = {}
html_theme_options['canonical_url'] = 'http://pymicro.readthedocs.io/en/latest/'

# 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 = 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']

# 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 = 'pymicrodoc'

# -- 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 = [
    ('index', 'pymicro.tex', u'pymicro Documentation',
     u'Henry Proudhon', '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

# 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

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'pymicro', u'pymicro Documentation',
     [u'Henry Proudhon'], 1)
]
<commit_msg>updated copyright year<commit_after># -*- coding: utf-8 -*-
#
# pymicro documentation build configuration file, created by
# sphinx-quickstart on Tue Oct 22 11:17:23 2013.
#
# 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
import mock

MOCK_MODULES = ['numpy', 'scipy', 'scipy.special', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.image',
                'matplotlib.cm', 'matplotlib.colors', 'scipy.ndimage', 'wx', 'wx.Panel', 'vtk', 'vtk.util',
                'vtk.util.colors', 'skimage', 'skimage.transform', '_tifffile', 'h5py']  # , 'ImPanel', 'PlotPanel']
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = mock.Mock()
# 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('..'))
sys.path.append(os.path.abspath('sphinxext'))
print(sys.path)
print('content of .')
print(os.listdir('.'))
print('content of ..')
print(os.listdir('..'))
print('content of ../..')
print(os.listdir('../..'))
try:
    import pymicro
    print('** successfully imported pymicro')
    from pymicro.crystal.lattice import Lattice
    print('** successfully imported Lattice')
except:
    print('problem during import')
    pass

try:
    import gen_rst
    print('** successfully imported gen_rst')
except:
    pass

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

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

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '1.1'
# 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.autosummary',
              'sphinx.ext.mathjax',
              'sphinxcontrib.bibtex',
              'gen_rst']
mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'

autodoc_member_order = 'bysource'
autodoc_default_flags = ['members', 'special-members', 'undoc-members', 'show-inheritance']
autosummary_generate = True

# 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'pymicro'
copyright = u'2013-2020, Henry Proudhon'

# The project version is extracted from the main __init__.py
def extract_version():
    """
    Extracts version values from the main __init__.py and
    returns them as a dictionary.
    """
    with open('../pymicro/__init__.py') as fd:
        for line in fd.readlines():
            if (line.startswith('__version__')):
                exec (line.strip())
    return locals()["__version__"]

version = '%s' % extract_version()

# 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 = 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 = []

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

# The theme to use for HTML and HTML Help pages.
print(os.environ)
if not 'READTHEDOCS' in os.environ.keys():  # if building locally
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = ["../../sphinx_rtd_theme"] # the theme should be installed aside the pymicro folder

# 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 = {}
html_theme_options['canonical_url'] = 'http://pymicro.readthedocs.io/en/latest/'

# 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 = 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']

# 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 = 'pymicrodoc'

# -- 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 = [
    ('index', 'pymicro.tex', u'pymicro Documentation',
     u'Henry Proudhon', '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

# 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

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'pymicro', u'pymicro Documentation',
     [u'Henry Proudhon'], 1)
]
<|endoftext|>


<commit_before># Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
An Astropy affiliated package for photometry.
"""

# Affiliated packages may add whatever they like to this file, but
# should keep this content at the top.
# ----------------------------------------------------------------------------
from ._astropy_init import *
# ----------------------------------------------------------------------------

if not _ASTROPY_SETUP_:
    from .aperture import *
    from .background import *
    from .centroids import *
    from .detection import *
    from .morphology import *
    from .psf import *
    from .segmentation import *
<commit_msg>Update package docstring [skip ci]<commit_after># Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Photutils is an Astropy affiliated package to provide tools for
detecting and performing photometry of astronomical sources.  It also
has tools for background estimation, PSF matching, centroiding, and
morphological measurements.
"""

# Affiliated packages may add whatever they like to this file, but
# should keep this content at the top.
# ----------------------------------------------------------------------------
from ._astropy_init import *
# ----------------------------------------------------------------------------

if not _ASTROPY_SETUP_:
    from .aperture import *
    from .background import *
    from .centroids import *
    from .detection import *
    from .morphology import *
    from .psf import *
    from .segmentation import *
<|endoftext|>


<commit_before># -*- coding: utf-8 -*-
#
# boltons documentation build configuration file, created by
# sphinx-quickstart on Sat Mar 21 00:34:18 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 sys
import os

# 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.
CUR_PATH = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, os.path.abspath(CUR_PATH + '/../'))

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

autosummary_generate = True

# 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.autosummary',
    'sphinx.ext.doctest',
    'sphinx.ext.intersphinx',
    'sphinx.ext.coverage',
    'sphinx.ext.viewcode',
]

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

# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'boltons'
copyright = u'2015, Mahmoud Hashemi'
author = u'Mahmoud Hashemi'

version = '0.4'
release = '0.4.3'

exclude_patterns = ['_build']

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

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/2.7', None)}

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

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
if not on_rtd: # only import and set the theme if we're building docs locally
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
    #html_theme = 'alabaster'

# 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 = 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'

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

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

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

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

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

# Latex figure (float) alignment
#'figure_align': 'htbp',
}

# 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 = [
  (master_doc, 'boltons.tex', u'boltons Documentation',
   u'Mahmoud Hashemi', '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).
man_pages = [
    (master_doc, 'boltons', u'boltons Documentation',
     [author], 1)
]

# 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 = [
  (master_doc, 'boltons', u'boltons Documentation',
   author, 'boltons', '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
<commit_msg>Enable napoleon for docstrings.<commit_after># -*- coding: utf-8 -*-
#
# boltons documentation build configuration file, created by
# sphinx-quickstart on Sat Mar 21 00:34:18 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 sys
import os

# 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.
CUR_PATH = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, os.path.abspath(CUR_PATH + '/../'))

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

autosummary_generate = True

# 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.autosummary',
    'sphinx.ext.doctest',
    'sphinx.ext.intersphinx',
    'sphinx.ext.coverage',
    'sphinx.ext.viewcode',
    'sphinx.ext.napoleon',
]

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

# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'boltons'
copyright = u'2015, Mahmoud Hashemi'
author = u'Mahmoud Hashemi'

version = '0.4'
release = '0.4.3'

exclude_patterns = ['_build']

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

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/2.7', None)}

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

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
if not on_rtd: # only import and set the theme if we're building docs locally
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
    #html_theme = 'alabaster'

# 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 = 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'

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

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

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

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

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

# Latex figure (float) alignment
#'figure_align': 'htbp',
}

# 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 = [
  (master_doc, 'boltons.tex', u'boltons Documentation',
   u'Mahmoud Hashemi', '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).
man_pages = [
    (master_doc, 'boltons', u'boltons Documentation',
     [author], 1)
]

# 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 = [
  (master_doc, 'boltons', u'boltons Documentation',
   author, 'boltons', '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
<|endoftext|>


<commit_before>#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# harold documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 19 17:38:48 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 sys
import os
import shlex

# 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.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.todo',
    'sphinx.ext.mathjax',
]

#
autodoc_member_order = 'bysource'

# Napoleon settings
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True

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

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
# source_suffix = ['.rst', '.md']
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 = 'harold'
copyright = '2016, Ilhan Polat'
author = 'Ilhan Polat'

# 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 = '0.1.1'
# The full version, including alpha/beta/rc tags.
release = '0.1.1b1'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
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','setup.py']

# 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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

# -- 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 = 'alabaster'
html_theme = "sphinx_rtd_theme"

# 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 = 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'

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

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

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

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

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

# Latex figure (float) alignment
#'figure_align': 'htbp',
}

# 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 = [
  (master_doc, 'harold.tex', 'harold Documentation',
   'Ilhan Polat', '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).
man_pages = [
    (master_doc, 'harold', 'harold Documentation',
     [author], 1)
]

# 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 = [
  (master_doc, 'harold', 'harold Documentation',
   author, 'harold', '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
<commit_msg>readthedocs doesn't like anything<commit_after>#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# harold documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 19 17:38:48 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 sys
import os
import shlex
from unittest.mock import MagicMock

class Mock(MagicMock):
    @classmethod
    def __getattr__(cls, name):
            return Mock()

MOCK_MODULES = ['tabulate', 'scipy', 'matplotlib', 'numpy']
sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

# 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.
os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))

# -- 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.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.todo',
    'sphinx.ext.mathjax',
]

#
autodoc_member_order = 'bysource'

# Napoleon settings
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True

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

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
# source_suffix = ['.rst', '.md']
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 = 'harold'
copyright = '2016, Ilhan Polat'
author = 'Ilhan Polat'

# 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 = '0.1.1'
# The full version, including alpha/beta/rc tags.
release = '0.1.1b1'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
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','setup.py']

# 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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

# -- 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 = 'alabaster'
html_theme = "sphinx_rtd_theme"

# 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 = 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'

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

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

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

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

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

# Latex figure (float) alignment
#'figure_align': 'htbp',
}

# 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 = [
  (master_doc, 'harold.tex', 'harold Documentation',
   'Ilhan Polat', '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).
man_pages = [
    (master_doc, 'harold', 'harold Documentation',
     [author], 1)
]

# 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 = [
  (master_doc, 'harold', 'harold Documentation',
   author, 'harold', '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
<|endoftext|>


<commit_before>import codecs
import os
import sys

from datetime import datetime

HERE = os.path.dirname(os.path.abspath(__file__))
BASE_DIR = os.path.dirname(HERE)
TT_MODULE_DIR = os.path.join(BASE_DIR, 'tt')
TT_VERSION_FILE = os.path.join(TT_MODULE_DIR, 'version.py')
sys.path.insert(0, BASE_DIR)

with codecs.open(TT_VERSION_FILE, encoding='utf-8') as f:
    exec(f.read())  # loads __version__ and __version_info__

extensions = ['sphinx.ext.autodoc',
              'sphinx.ext.intersphinx',
              'sphinx.ext.viewcode']

intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}

autodoc_default_flags = ['members',
                         'special-members',
                         'show-inheritance']

suppress_warnings = ['image.nonlocal_uri']

html_theme = 'alabaster'
html_sidebars = {
    '**': [
        'about.html',
        'navigation.html',
        'relations.html',
        'searchbox.html'
    ]
}
html_theme_options = {
    'logo': 'logo.png',
    'logo_text_align': 'centered',
    'description': 'the Boolean expression toolbox',

    'github_user': 'welchbj',
    'github_repo': 'tt',
    'github_type': 'star',

    'extra_nav_links': {},
    'sidebar_includehidden': True,
    'fixed_sidebar': True,

    'font_family': "'PT Sans Caption', sans-serif",
    'font_size': '0.9em',
    'head_font_family': "'Cabin', sans-serif"
}

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
templates_path = ['_templates']
html_static_path = ['_static']

project = 'tt'
year = datetime.now().year
author = 'Brian Welch'
copyright = '{}, {}'.format(year, author)
version = '.'.join(str(i) for i in __version_info__[:2])  # noqa
release = __version__  # noqa
master_doc = 'index'
source_suffix = '.rst'
pygments_style = 'sphinx'
<commit_msg>Change note background and border to a light blue pairing<commit_after>import codecs
import os
import sys

from datetime import datetime

HERE = os.path.dirname(os.path.abspath(__file__))
BASE_DIR = os.path.dirname(HERE)
TT_MODULE_DIR = os.path.join(BASE_DIR, 'tt')
TT_VERSION_FILE = os.path.join(TT_MODULE_DIR, 'version.py')
sys.path.insert(0, BASE_DIR)

with codecs.open(TT_VERSION_FILE, encoding='utf-8') as f:
    exec(f.read())  # loads __version__ and __version_info__

extensions = ['sphinx.ext.autodoc',
              'sphinx.ext.intersphinx',
              'sphinx.ext.viewcode']

intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}

autodoc_default_flags = ['members',
                         'special-members',
                         'show-inheritance']

suppress_warnings = ['image.nonlocal_uri']

html_theme = 'alabaster'
html_sidebars = {
    '**': [
        'about.html',
        'navigation.html',
        'relations.html',
        'searchbox.html'
    ]
}
html_theme_options = {
    'logo': 'logo.png',
    'logo_text_align': 'centered',
    'description': 'the Boolean expression toolbox',

    'github_user': 'welchbj',
    'github_repo': 'tt',
    'github_type': 'star',

    'extra_nav_links': {},
    'sidebar_includehidden': True,
    'fixed_sidebar': True,

    'note_bg': '#e8f0fc',
    'note_border': '#c4daff',

    'font_family': "'PT Sans Caption', sans-serif",
    'font_size': '0.9em',
    'head_font_family': "'Cabin', sans-serif"
}

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
templates_path = ['_templates']
html_static_path = ['_static']

project = 'tt'
year = datetime.now().year
author = 'Brian Welch'
copyright = '{}, {}'.format(year, author)
version = '.'.join(str(i) for i in __version_info__[:2])  # noqa
release = __version__  # noqa
master_doc = 'index'
source_suffix = '.rst'
pygments_style = 'sphinx'
<|endoftext|>


<commit_before># -*- coding: utf-8 -*-
#
# 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

# 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('../'))
sys.path.append(os.path.abspath('sphinxext'))
sys.path.append(os.path.abspath('pyplots'))

# -- 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.autodoc', 'sphinx.ext.doctest',
              'sphinx.ext.intersphinx', 'sphinx.ext.todo',
              'sphinx.ext.coverage', 'sphinx.ext.pngmath',
              'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
			        'matplotlib.sphinxext.plot_directive']

# 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'bedtools'
copyright = u'2009 - 2016, Aaron R. Quinlan and Neil Kindlon'

# 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 = '2.26.0'
# The full version, including alpha/beta/rc tags.
release = '2.26.0'

# 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 = 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 = []

# -- 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 = 'rtd'

# 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 = ["themes"]

# 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 = project + " v" + release

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = 'bedtools.swiss.png'

# 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 = 'bedtools.png'

# 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']
html_style = 'labibi.css'

# 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 = {
    'index': ['sidebar-intro.html', 'sourcelink.html', 'searchbox.html']
}

# 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 = False

# 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 = 'bedtools-docs'

# Google analytics
#googleanalytics_id = "UA-24167610-15"

# -- 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 = [
  ('index', 'bedtools.tex', u'Bedtools Documentation',
  u'Quinlan lab @ Univ. of Utah', '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

# 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

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1)
]

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}

class Mock(object):
    def __init__(self, *args, **kwargs):
        pass

    def __call__(self, *args, **kwargs):
        return Mock()

    @classmethod
    def __getattr__(cls, name):
        if name in ('__file__', '__path__'):
            return '/dev/null'
        elif name[0] == name[0].upper():
            return type(name, (), {})
        else:
            return Mock()

MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot',
                'matplotlib.sphinxext', 'matplotlib.sphinxext.plot_directive']
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = Mock()
<commit_msg>Update conf.py<commit_after># -*- coding: utf-8 -*-
#
# 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

# 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('../'))
sys.path.append(os.path.abspath('sphinxext'))
sys.path.append(os.path.abspath('pyplots'))

# -- 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.autodoc', 'sphinx.ext.doctest',
              'sphinx.ext.intersphinx', 'sphinx.ext.todo',
              'sphinx.ext.coverage', 'sphinx.ext.pngmath',
              'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
			        'matplotlib.sphinxext.plot_directive']

# 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'bedtools'
copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon'

# 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 = '2.27.0'
# The full version, including alpha/beta/rc tags.
release = '2.27.0'

# 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 = 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 = []

# -- 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 = 'rtd'

# 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 = ["themes"]

# 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 = project + " v" + release

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = 'bedtools.swiss.png'

# 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 = 'bedtools.png'

# 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']
html_style = 'labibi.css'

# 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 = {
    'index': ['sidebar-intro.html', 'sourcelink.html', 'searchbox.html']
}

# 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 = False

# 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 = 'bedtools-docs'

# Google analytics
#googleanalytics_id = "UA-24167610-15"

# -- 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 = [
  ('index', 'bedtools.tex', u'Bedtools Documentation',
  u'Quinlan lab @ Univ. of Utah', '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

# 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

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1)
]

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}

class Mock(object):
    def __init__(self, *args, **kwargs):
        pass

    def __call__(self, *args, **kwargs):
        return Mock()

    @classmethod
    def __getattr__(cls, name):
        if name in ('__file__', '__path__'):
            return '/dev/null'
        elif name[0] == name[0].upper():
            return type(name, (), {})
        else:
            return Mock()

MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot',
                'matplotlib.sphinxext', 'matplotlib.sphinxext.plot_directive']
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = Mock()
<|endoftext|>


<commit_before># Ensure we get the local copy of tornado instead of what's on the standard path
import os
import sys
import time
sys.path.insert(0, os.path.abspath(".."))
import tornado

master_doc = "index"

project = "Tornado"
copyright = "2009-%s, The Tornado Authors" % time.strftime("%Y")

version = release = tornado.version

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.coverage",
    "sphinx.ext.doctest",
    "sphinx.ext.extlinks",
    "sphinx.ext.intersphinx",
    "sphinx.ext.viewcode",
    ]

primary_domain = 'py'
default_role = 'py:obj'

autodoc_member_order = "bysource"
autoclass_content = "both"

# Without this line sphinx includes a copy of object.__init__'s docstring
# on any class that doesn't define __init__.
# https://bitbucket.org/birkenfeld/sphinx/issue/1337/autoclass_content-both-uses-object__init__
autodoc_docstring_signature = False

coverage_skip_undoc_in_source = True
coverage_ignore_modules = [
    "tornado.platform.asyncio",
    "tornado.platform.caresresolver",
    "tornado.platform.twisted",
    ]
# I wish this could go in a per-module file...
coverage_ignore_classes = [
    # tornado.concurrent
    "TracebackFuture",

    # tornado.gen
    "Runner",

    # tornado.ioloop
    "PollIOLoop",

    # tornado.web
    "ChunkedTransferEncoding",
    "GZipContentEncoding",
    "OutputTransform",
    "TemplateModule",
    "url",

    # tornado.websocket
    "WebSocketProtocol",
    "WebSocketProtocol13",
    "WebSocketProtocol76",
    ]

coverage_ignore_functions = [
    # various modules
    "doctests",
    "main",

    # tornado.escape
    # parse_qs_bytes should probably be documented but it's complicated by
    # having different implementations between py2 and py3.
    "parse_qs_bytes",
]

html_favicon = 'favicon.ico'

latex_documents = [
    ('documentation', 'tornado.tex', 'Tornado Documentation', 'Facebook', 'manual', False),
    ]

# HACK: sphinx has limited support for substitutions with the |version|
# variable, but there doesn't appear to be any way to use this in a link
# target.
# http://stackoverflow.com/questions/1227037/substitutions-inside-links-in-rest-sphinx
# The extlink extension can be used to do link substitutions, but it requires a
# portion of the url to be literally contained in the document.  Therefore,
# this link must be referenced as :current_tarball:`z`
extlinks = {
    'current_tarball': (
'https://pypi.python.org/packages/source/t/tornado/tornado-%s.tar.g%%s' % version,
        'tornado-%s.tar.g' % version),
    }

intersphinx_mapping = {
    'python': ('https://docs.python.org/3.4/', None),
    }

on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

# On RTD we can't import sphinx_rtd_theme, but it will be applied by
# default anyway.  This block will use the same theme when building locally
# as on RTD.
if not on_rtd:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
<commit_msg>Fix PDF doc build.<commit_after># Ensure we get the local copy of tornado instead of what's on the standard path
import os
import sys
import time
sys.path.insert(0, os.path.abspath(".."))
import tornado

master_doc = "index"

project = "Tornado"
copyright = "2009-%s, The Tornado Authors" % time.strftime("%Y")

version = release = tornado.version

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.coverage",
    "sphinx.ext.doctest",
    "sphinx.ext.extlinks",
    "sphinx.ext.intersphinx",
    "sphinx.ext.viewcode",
    ]

primary_domain = 'py'
default_role = 'py:obj'

autodoc_member_order = "bysource"
autoclass_content = "both"

# Without this line sphinx includes a copy of object.__init__'s docstring
# on any class that doesn't define __init__.
# https://bitbucket.org/birkenfeld/sphinx/issue/1337/autoclass_content-both-uses-object__init__
autodoc_docstring_signature = False

coverage_skip_undoc_in_source = True
coverage_ignore_modules = [
    "tornado.platform.asyncio",
    "tornado.platform.caresresolver",
    "tornado.platform.twisted",
    ]
# I wish this could go in a per-module file...
coverage_ignore_classes = [
    # tornado.concurrent
    "TracebackFuture",

    # tornado.gen
    "Runner",

    # tornado.ioloop
    "PollIOLoop",

    # tornado.web
    "ChunkedTransferEncoding",
    "GZipContentEncoding",
    "OutputTransform",
    "TemplateModule",
    "url",

    # tornado.websocket
    "WebSocketProtocol",
    "WebSocketProtocol13",
    "WebSocketProtocol76",
    ]

coverage_ignore_functions = [
    # various modules
    "doctests",
    "main",

    # tornado.escape
    # parse_qs_bytes should probably be documented but it's complicated by
    # having different implementations between py2 and py3.
    "parse_qs_bytes",
]

html_favicon = 'favicon.ico'

latex_documents = [
    ('index', 'tornado.tex', 'Tornado Documentation', 'The Tornado Authors', 'manual', False),
    ]

# HACK: sphinx has limited support for substitutions with the |version|
# variable, but there doesn't appear to be any way to use this in a link
# target.
# http://stackoverflow.com/questions/1227037/substitutions-inside-links-in-rest-sphinx
# The extlink extension can be used to do link substitutions, but it requires a
# portion of the url to be literally contained in the document.  Therefore,
# this link must be referenced as :current_tarball:`z`
extlinks = {
    'current_tarball': (
'https://pypi.python.org/packages/source/t/tornado/tornado-%s.tar.g%%s' % version,
        'tornado-%s.tar.g' % version),
    }

intersphinx_mapping = {
    'python': ('https://docs.python.org/3.4/', None),
    }

on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

# On RTD we can't import sphinx_rtd_theme, but it will be applied by
# default anyway.  This block will use the same theme when building locally
# as on RTD.
if not on_rtd:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
<|endoftext|>