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# -*- 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, join
# 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.
SRC_PATH = join(dirname(dirname(__file__)), "src")
sys.path.insert(0, SRC_PATH)
# -- 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_dirs = [join(SRC_PATH, "cobra")]
autoapi_add_toctree_entry = False
# Enable typehints
autodoc_typehints = "signature"
# Napoleon settings
napoleon_numpy_docstring = True
# The master toctree document.
master_doc = "index"
# General information about the project.
project = "cobra"
copyright = "2016-2022, 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.
# This import has to be here.
from cobra import __version__ as release # noqa: E402
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 = (
'/usr/share/javascript/mathjax/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",
"cobra Documentation",
"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",
"cobra Documentation",
"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
|
