# -*- coding: utf-8 -*-
#
# cobra documentation build configuration file, created by
# sphinx-quickstart on Wed Jun 13 19:17:34 2012.
#
# 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
from os.path import dirname
# 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, dirname(dirname(__file__)))
# In order to build documentation that requires libraries to import
[docs]class Mock(object):
[docs] def __init__(self, *args, **kwargs):
return
[docs] def __call__(self, *args, **kwargs):
return Mock()
[docs] @classmethod
def __getattr__(cls, name):
if name in ('__file__', '__path__'):
return '/dev/null'
else:
return Mock()
# These modules should correspond to the importable Python packages.
MOCK_MODULES = [
'depinfo',
'numpy',
'scipy', 'scipy.optimize', 'scipy.sparse', 'scipy.io', 'scipy.stats',
'pp',
'libsbml',
'pandas',
'tabulate',
'optlang', 'optlang.interface', 'optlang.symbolics',
'optlang.symbolics.core',
'future', 'future.utils',
'ruamel', 'ruamel.yaml'
]
for mod_name in MOCK_MODULES:
sys.modules[mod_name] = Mock()
# -- General configuration ----------------------------------------------------
# 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.intersphinx',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'sphinx.ext.autosummary',
'autoapi.extension',
'nbsphinx'
]
# Document Python Code
autoapi_type = 'python'
autoapi_dirs = ['..']
autoapi_ignore = ['.tox', '.pytest_cache', 'scripts', 'benchmarks']
# Napoleon settings
napoleon_numpy_docstring = True
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'cobra'
copyright = u'2016, The cobrapy core team'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
from cobra import __version__ as release
version = '.'.join(release.split('.')[:2])
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build', '.ipynb_checkpoints']
pygments_style = 'sphinx'
# -- Options for HTML output --------------------------------------------------
mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
# -- Options for LaTeX output --------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
'papersize': 'a4paper',
# The font size ('10pt', '11pt' or '12pt').
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
'preamble': r'\usepackage{amsmath,amssymb}',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'cobra.tex', u'cobra Documentation',
u'The cobrapy core team', 'manual'),
]
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'cobra', u'cobra Documentation',
[u'The cobrapy core team'], 1)
]
# -- Options for Texinfo output ------------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'cobra', u'cobra Documentation',
u'The cobrapy core team', 'cobra',
'A package for constraints-based modeling of biological networks',
'Miscellaneous'),
]
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {"http://docs.python.org/": None,
"http://docs.scipy.org/doc/numpy/": None,
"http://docs.scipy.org/doc/scipy/reference": None}
intersphinx_cache_limit = 10 # days to keep the cached inventories
###########################################################################
# auto-created readthedocs.org specific configuration #
###########################################################################
#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
import sys
import os.path
from six import string_types
from sphinx import version_info
# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
if isinstance(source_suffix, string_types):
SUFFIX = source_suffix
else:
SUFFIX = source_suffix[0]
else:
SUFFIX = '.rst'
# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
html_static_path = []
if os.path.exists('_static'):
html_static_path.append('_static')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static')
# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = False
if 'html_theme' in globals():
if html_theme in ['default']:
# Allow people to bail with a hack of having an html_style
if not 'html_style' in globals():
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
else:
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
using_rtd_theme = True
else:
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
else:
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
using_rtd_theme = True
if globals().get('websupport2_base_url', False):
websupport2_base_url = 'https://readthedocs.org/websupport'
if 'http' not in settings.MEDIA_URL:
websupport2_static_url = 'https://media.readthedocs.org/static/'
else:
websupport2_static_url = 'https://media.readthedocs.org//static'
#Add project information to the template context.
context = {
'using_theme': using_rtd_theme,
'html_theme': html_theme,
'current_version': "0.13.3",
'version_slug': "0.13.3",
'MEDIA_URL': "https://media.readthedocs.org/",
'PRODUCTION_DOMAIN': "readthedocs.org",
'versions': [
("latest", "/en/latest/"),
("stable", "/en/stable/"),
("0.13.3", "/en/0.13.3/"),
("0.13.2", "/en/0.13.2/"),
("0.13.1", "/en/0.13.1/"),
("0.13.0", "/en/0.13.0/"),
("0.12.1", "/en/0.12.1/"),
("0.12.0", "/en/0.12.0/"),
("0.11.3", "/en/0.11.3/"),
("0.11.2", "/en/0.11.2/"),
("0.11.1", "/en/0.11.1/"),
("0.11.0", "/en/0.11.0/"),
("0.10.1", "/en/0.10.1/"),
("0.10.0", "/en/0.10.0/"),
("0.9.1", "/en/0.9.1/"),
("0.9.0", "/en/0.9.0/"),
("0.8.2", "/en/0.8.2/"),
("0.8.1", "/en/0.8.1/"),
("0.8.0", "/en/0.8.0/"),
("0.7.0", "/en/0.7.0/"),
("0.6.2", "/en/0.6.2/"),
("0.6.1", "/en/0.6.1/"),
("0.6.0", "/en/0.6.0/"),
("0.5.11", "/en/0.5.11/"),
("0.5.10", "/en/0.5.10/"),
("0.5.9", "/en/0.5.9/"),
("0.5.8", "/en/0.5.8/"),
("0.5.7", "/en/0.5.7/"),
("0.5.6", "/en/0.5.6/"),
("0.5.4", "/en/0.5.4/"),
("0.5.3", "/en/0.5.3/"),
("0.5.2", "/en/0.5.2/"),
("0.4.1", "/en/0.4.1/"),
("0.4.0", "/en/0.4.0/"),
("0.3.2", "/en/0.3.2/"),
("master", "/en/master/"),
("devel", "/en/devel/"),
],
'downloads': [
],
'subprojects': [
],
'slug': 'cobrapy',
'name': u'cobrapy',
'rtd_language': u'en',
'programming_language': u'py',
'canonical_url': 'https://cobrapy.readthedocs.io/en/latest/',
'analytics_code': '',
'single_version': False,
'conf_py_path': '/documentation_builder/',
'api_host': 'https://readthedocs.org',
'github_user': 'opencobra',
'github_repo': 'cobrapy',
'github_version': '0.13.3',
'display_github': True,
'bitbucket_user': 'None',
'bitbucket_repo': 'None',
'bitbucket_version': '0.13.3',
'display_bitbucket': False,
'gitlab_user': 'None',
'gitlab_repo': 'None',
'gitlab_version': '0.13.3',
'display_gitlab': False,
'READTHEDOCS': True,
'using_theme': (html_theme == "default"),
'new_theme': (html_theme == "sphinx_rtd_theme"),
'source_suffix': SUFFIX,
'ad_free': False,
'user_analytics_code': '',
'global_analytics_code': 'UA-17997319-1',
'commit': '9ab50bc0',
}
if 'html_context' in globals():
html_context.update(context)
else:
html_context = context
# Add custom RTD extension
if 'extensions' in globals():
# Insert at the beginning because it can interfere
# with other extensions.
# See https://github.com/rtfd/readthedocs.org/pull/4054
extensions.insert(0, "readthedocs_ext.readthedocs")
else:
extensions = ["readthedocs_ext.readthedocs"]
# Build the json artifacts with the html build step
rtd_generate_json_artifacts = True