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docs: separate api docs
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johanneskoester committed Mar 15, 2022
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Snakemake documentation build configuration file, created by
# sphinx-quickstart on Sat Feb 1 16:01:02 2014.
#
# 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
from datetime import datetime


# 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.mathjax",
"sphinx.ext.viewcode",
"sphinx.ext.napoleon",
"sphinxarg.ext",
"sphinx.ext.autosectionlabel",
"myst_parser",
]

# skip internal class that Sphinx can't process (#296)
autodoc_default_options = {"exclude-members": "lazy_property"}

# Snakemake theme (made by SciAni).
html_css_files = ["theme.css"]

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

# The suffix of source filenames.
source_suffix = [".rst", ".md"]

# The encoding of source files.
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = "index-api"

# General information about the project.
project = "Snakemake"
date = datetime.now()
copyright = "2014-{year}, Johannes Koester".format(year=date.timetuple()[0])

import snakemake

# 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 = snakemake.__version__

if os.environ.get("READTHEDOCS") == "True":
# Because Read The Docs modifies conf.py, versioneer gives a "dirty"
# version like "5.10.0+0.g28674b1.dirty" that is cleaned here.
version = version.partition("+0.g")[0]

# 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 = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False


# -- 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 = "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 = sphinx_bootstrap_theme.get_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 = ["_static/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 = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
# html_additional_pages = {"index": "index.html"}

# 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 = "Snakemakedoc"


# -- 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': '',
}

# 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 = [
("index", "Snakemake.tex", "Snakemake Documentation", "Johannes Koester", "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 = [("index", "snakemake", "Snakemake Documentation", ["Johannes Koester"], 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 = [
(
"index",
"Snakemake",
"Snakemake Documentation",
"Johannes Koester",
"Snakemake",
"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


def setup(app):
app.add_css_file("sphinx-argparse.css")
@@ -0,0 +1,63 @@
.. _manual-main:

=========
Snakemake
=========

.. image:: https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod
:target: https://gitpod.io/#https://github.com/snakemake/snakemake

.. image:: https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda
:target: https://bioconda.github.io/recipes/snakemake/README.html

.. image:: https://img.shields.io/pypi/pyversions/snakemake.svg
:target: https://www.python.org

.. image:: https://img.shields.io/pypi/v/snakemake.svg
:target: https://pypi.python.org/pypi/snakemake

.. image:: https://img.shields.io/github/workflow/status/snakemake/snakemake/Publish%20to%20Docker%20Hub?color=blue&label=docker%20container&branch=main
:target: https://hub.docker.com/r/snakemake/snakemake

.. image:: https://github.com/snakemake/snakemake/workflows/CI/badge.svg?branch=main&label=tests
:target: https://github.com/snakemake/snakemake/actions?query=branch%3Amain+workflow%3ACI

.. image:: https://img.shields.io/badge/stack-overflow-orange.svg
:target: https://stackoverflow.com/questions/tagged/snakemake

.. image:: https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow
:target: https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester

.. image:: https://img.shields.io/discord/753690260830945390?label=discord%20chat
:alt: Discord
:target: https://discord.gg/NUdMtmr

.. image:: https://img.shields.io/github/stars/snakemake/snakemake?style=social
:alt: GitHub stars
:target: https://github.com/snakemake/snakemake/stargazers

.. .. raw:: html
<span class="__dimensions_badge_embed__" data-doi="https://doi.org/10.1093/bioinformatics/bts480" data-legend="always" data-style="large_rectangle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
The Snakemake workflow management system is a tool to create **reproducible and scalable** data analyses.
Workflows are described via a human readable, Python based language.
They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition.
Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

Snakemake is **highly popular**, with `>7 new citations per week <https://badge.dimensions.ai/details/id/pub.1018944052>`_.
For an introduction, please visit https://snakemake.github.io.

This is the home of the **Snakemake API documentation**, which is meant **purely for developers**.
If you are looking for the Snakemake user documentation, please visit https://snakemake.readthedocs.io.



.. toctree::
:caption: API Reference
:name: api-reference
:hidden:
:maxdepth: 1

api_reference/snakemake
api_reference/snakemake_utils
api_reference/internal/modules
@@ -44,7 +44,7 @@ Workflows are described via a human readable, Python based language.
They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition.
Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

Snakemake is **highly popular**, with `>5 new citations per week <https://badge.dimensions.ai/details/id/pub.1018944052>`_.
Snakemake is **highly popular**, with `>7 new citations per week <https://badge.dimensions.ai/details/id/pub.1018944052>`_.
For an introduction, please visit https://snakemake.github.io.


@@ -160,9 +160,7 @@ Resources
:hidden:
:maxdepth: 1

api_reference/snakemake
api_reference/snakemake_utils
api_reference/internal/modules


.. toctree::

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