conf.py

# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# 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.

import datetime
import os
import re
import semantic_version
import shutil
import sys
import urllib.request

docssrc_dir = os.path.abspath(os.path.join(__file__, ".."))
project_dir = os.path.dirname(docssrc_dir)

sys.path.insert(0, os.path.abspath(os.path.join(__file__, project_dir)))

# -- Imports -----------------------------------------------------------------

import fastobo

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

# General information
project = fastobo.__name__
author = re.match("(.*) <.*>", fastobo.__author__).group(1)
year = datetime.date.today().year
copyright = "{}, {}".format("2019" if year == 2019 else "2019-{}".format(year), author)


# extract the semantic version
semver = semantic_version.Version.coerce(fastobo.__version__)
version = str(semver.truncate(level="patch"))
release = str(semver)

# patch the docstring so that we don't show the link to redirect
# to the docs (we don't want to see it when reading the docs already, duh!)
doc_lines = fastobo.__doc__.splitlines()
if "See Also:" in doc_lines:
    see_also = doc_lines.index("See Also:")
    fastobo.__doc__ = "\n".join(doc_lines[:see_also])


# -- 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.autosummary",
    "sphinx.ext.intersphinx",
    "sphinx.ext.napoleon",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.todo",
    "sphinx.ext.extlinks",
    "sphinx_design",
    "sphinxcontrib.jquery",
    "recommonmark",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
]

# 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", ".md"]

# The master toctree document.
master_doc = "index"

# 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 = 'en'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = ["_build", "**.ipynb_checkpoints", 'Thumbs.db', '.DS_Store']

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

# The name of the default role for inline references
default_role = "py:obj"


# -- 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 = 'pydata_sphinx_theme'

# 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/js', '_static/json']
html_js_files = ["custom-icon.js"]
html_css_files = ["custom.css"]

# 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 = {
    "external_links": [],
    "show_toc_level": 2,
    "use_edit_page_button": True,
    "icon_links": [
        {
            "name": "GitHub",
            "url": "https://github.com/fastobo/fastobo-py",
            "icon": "fa-brands fa-github",
        },
        {
            "name": "PyPI",
            "url": "https://pypi.org/project/fastobo",
            "icon": "fa-custom fa-pypi",
        },
    ],
    "logo": {
        "text": "FastOBO",
        "image_light": "_images/logo.png",
        "image_dark": "_images/logo.png",
    },
    "navbar_start": ["navbar-logo", "version-switcher"],
    "navbar_align": "left",
    "footer_start": ["copyright"],
    "footer_center": ["sphinx-version"],
    "switcher": {
        "json_url": "https://fastobo.readthedocs.io/en/latest/_static/switcher.json",
        "version_match": version,
    }
}

html_context = {
    "github_user": "fastobo",
    "github_repo": "fastobo-py",
    "github_version": "main",
    "doc_path": "docs",
}

html_favicon = '_images/favicon.ico'

# -- Extension configuration -------------------------------------------------

# -- Options for imgmath extension -------------------------------------------

imgmath_image_format = "svg"

# -- Options for napoleon extension ------------------------------------------

napoleon_include_init_with_doc = True
napoleon_include_special_with_doc = True
napoleon_include_private_with_doc = True
napoleon_use_admonition_for_examples = True
napoleon_use_admonition_for_notes = True
napoleon_use_admonition_for_references = True
napoleon_use_rtype = False

# -- Options for autodoc extension -------------------------------------------

autoclass_content = "class"
autodoc_member_order = "bysource"
autosummary_generate = []

# -- Options for intersphinx extension ---------------------------------------

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
    "python": ("https://docs.python.org/3/", None),
    "biopython": ("https://biopython.org/docs/latest/", None),
    "scoring-matrices": ("https://scoring-matrices.readthedocs.io/en/stable/", None),
}

# -- Options for recommonmark extension --------------------------------------

source_suffix = {
    ".rst": "restructuredtext",
    ".txt": "markdown",
    ".md": "markdown",
}

# -- Options for nbsphinx extension ------------------------------------------

nbsphinx_execute = "auto"
nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc={'figure.dpi': 96}",
]

# -- Options for extlinks extension ------------------------------------------

extlinks = {
    "doi": ("https://doi.org/%s", "doi:%s"),
    "pmid": ("https://pubmed.ncbi.nlm.nih.gov/%s", "PMID:%s"),
    "pmc": ("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s", "PMC%s"),
    "isbn": ("https://www.worldcat.org/isbn/%s", "ISBN:%s"),
    "wiki": ("https://en.wikipedia.org/wiki/%s", "Wikipedia:%s"),
}