From ded7da90258284f06d4e9263e667cd632cdc12ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 15 Mar 2022 16:36:26 +0100 Subject: [PATCH] docs: separate api docs --- docs/conf-api.py | 288 +++++++++++++++++++++++++++++++++++++++++++++ docs/index-api.rst | 63 ++++++++++ docs/index.rst | 4 +- 3 files changed, 352 insertions(+), 3 deletions(-) create mode 100644 docs/conf-api.py create mode 100644 docs/index-api.rst diff --git a/docs/conf-api.py b/docs/conf-api.py new file mode 100644 index 000000000..e8c25d744 --- /dev/null +++ b/docs/conf-api.py @@ -0,0 +1,288 @@ +#!/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 +# " v 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 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") diff --git a/docs/index-api.rst b/docs/index-api.rst new file mode 100644 index 000000000..b3d4a7712 --- /dev/null +++ b/docs/index-api.rst @@ -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 + + +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 `_. +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 \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index ce878d9d3..bd2d1edca 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -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 `_. +Snakemake is **highly popular**, with `>7 new citations per week `_. 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::