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haddock3

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"""Sphinx config file."""

import datetime
import subprocess
from pathlib import Path

from haddock import version as haddock_version

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.autosummary",
    "sphinx.ext.coverage",
    "sphinx.ext.doctest",
    "sphinx.ext.extlinks",
    "sphinx.ext.ifconfig",
    "sphinx.ext.intersphinx",
    "sphinx.ext.napoleon",
    "sphinx.ext.todo",
    "sphinx.ext.viewcode",
    "sphinxarg.ext",
    "sphinx.ext.autosectionlabel",
    "myst_parser",
    "sphinx_rtd_theme",
]

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

master_doc = "pages/index"
project = "haddock3"
year = datetime.date.today().year
author = "BonvinLab"
copyright = "{0}, {1}".format(year, author)
version = release = haddock_version

# docs/ is the Sphinx source root: docs/pages/ holds hand-authored content,
# docs/src/ holds content generated by sphinx-apidoc / build_defaults_rst.py.
# Everything else directly under docs/ (this file, README.md, Makefile,
# build_defaults_rst.py, titles.yaml) is build tooling, not a documentation
# page. Only README.md needs excluding explicitly -- the others don't match
# source_suffix, so Sphinx never treats them as documents.
exclude_patterns = ["README.md"]

todo_include_todos = True
pygments_style = "trac"
templates_path = ["."]
extlinks = {
    "issue": ("https://github.com/haddocking/haddock3/issues/%s", "#"),
    "pr": ("https://github.com/haddocking/haddock3/pull/%s", "PR #"),
}

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

linkcheck_ignore = [r"https://codecov.io/*"]

html_theme = "sphinx_rtd_theme"
html_use_smartypants = True
html_last_updated_fmt = "%b %d, %Y"
html_split_index = False
html_short_title = "%s-%s" % (project, version)

# master_doc lives at pages/index, so it builds to pages/index.html rather
# than index.html at the site root. Static hosts (GitHub Pages included)
# need an index.html at the root to serve the bare site URL, so redirect/
# provides one that forwards to pages/index.html.
html_extra_path = ["redirect"]

autosectionlabel_prefix_document = True

napoleon_use_ivar = True
napoleon_use_rtype = False
napoleon_use_param = False

# myst options
myst_heading_anchors = 3


# prepare default yaml RST
# this procedure is not part of the docs configuration for sphinx.
# it is a quick "hack" to run the script that generates rst files for the
# default parameters


def build_default_rst(*args):
    """Build the RST files for default parameters when Sphinx is initiated."""
    repo_root = Path(__file__).parent.parent
    build_yaml_rst_path = str(Path(__file__).parent / "build_defaults_rst.py")

    subprocess.run(
        ["python", build_yaml_rst_path],
        cwd=str(repo_root),
        timeout=60,
        check=True,
        capture_output=False,
    )


def setup(app):
    app.connect("builder-inited", build_default_rst)

	"""Sphinx config file."""

	import datetime
	import subprocess
	from pathlib import Path

	from haddock import version as haddock_version

	extensions = [
	"sphinx.ext.autodoc",
	"sphinx.ext.autosummary",
	"sphinx.ext.coverage",
	"sphinx.ext.doctest",
	"sphinx.ext.extlinks",
	"sphinx.ext.ifconfig",
	"sphinx.ext.intersphinx",
	"sphinx.ext.napoleon",
	"sphinx.ext.todo",
	"sphinx.ext.viewcode",
	"sphinxarg.ext",
	"sphinx.ext.autosectionlabel",
	"myst_parser",
	"sphinx_rtd_theme",
	]

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

	master_doc = "pages/index"
	project = "haddock3"
	year = datetime.date.today().year
	author = "BonvinLab"
	copyright = "{0}, {1}".format(year, author)
	version = release = haddock_version

	# docs/ is the Sphinx source root: docs/pages/ holds hand-authored content,
	# docs/src/ holds content generated by sphinx-apidoc / build_defaults_rst.py.
	# Everything else directly under docs/ (this file, README.md, Makefile,
	# build_defaults_rst.py, titles.yaml) is build tooling, not a documentation
	# page. Only README.md needs excluding explicitly -- the others don't match
	# source_suffix, so Sphinx never treats them as documents.
	exclude_patterns = ["README.md"]

	todo_include_todos = True
	pygments_style = "trac"
	templates_path = ["."]
	extlinks = {
	"issue": ("https://github.com/haddocking/haddock3/issues/%s", "#"),
	"pr": ("https://github.com/haddocking/haddock3/pull/%s", "PR #"),
	}

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

	linkcheck_ignore = [r"https://codecov.io/*"]

	html_theme = "sphinx_rtd_theme"
	html_use_smartypants = True
	html_last_updated_fmt = "%b %d, %Y"
	html_split_index = False
	html_short_title = "%s-%s" % (project, version)

	# master_doc lives at pages/index, so it builds to pages/index.html rather
	# than index.html at the site root. Static hosts (GitHub Pages included)
	# need an index.html at the root to serve the bare site URL, so redirect/
	# provides one that forwards to pages/index.html.
	html_extra_path = ["redirect"]

	autosectionlabel_prefix_document = True

	napoleon_use_ivar = True
	napoleon_use_rtype = False
	napoleon_use_param = False

	# myst options
	myst_heading_anchors = 3


	# prepare default yaml RST
	# this procedure is not part of the docs configuration for sphinx.
	# it is a quick "hack" to run the script that generates rst files for the
	# default parameters


	def build_default_rst(*args):
	"""Build the RST files for default parameters when Sphinx is initiated."""
	repo_root = Path(__file__).parent.parent
	build_yaml_rst_path = str(Path(__file__).parent / "build_defaults_rst.py")

	subprocess.run(
	["python", build_yaml_rst_path],
	cwd=str(repo_root),
	timeout=60,
	check=True,
	capture_output=False,
	)


	def setup(app):
	app.connect("builder-inited", build_default_rst)