425 lines
14 KiB
Python
425 lines
14 KiB
Python
# -*- coding: utf-8 -*-
|
|
#
|
|
# Nextflow documentation build configuration file, created by
|
|
# sphinx-quickstart on Sat May 5 16:57:28 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, os
|
|
import sphinx_rtd_theme
|
|
import datetime
|
|
import subprocess
|
|
import shlex
|
|
|
|
# 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.mathjax',
|
|
'sphinxcontrib.mermaid',
|
|
'sphinxext.rediraffe',
|
|
'sphinx_rtd_theme',
|
|
'myst_parser',
|
|
'sphinx_tabs.tabs',
|
|
'sphinx_copybutton'
|
|
]
|
|
|
|
myst_enable_extensions = ['colon_fence', 'deflist', 'dollarmath']
|
|
|
|
myst_heading_anchors = 3
|
|
|
|
rediraffe_redirects = {
|
|
'getstarted.md': 'install.md',
|
|
'basic.md': 'overview.md',
|
|
'tracing.md': 'reports.md',
|
|
'mail.md': 'notifications.md',
|
|
'operator.md': 'reference/operator.md',
|
|
'dsl1.md': 'migrations/dsl1.md',
|
|
'updating-syntax.md': 'strict-syntax.md',
|
|
'updating-spot-retries.md': 'guides/updating-spot-retries.md',
|
|
'metrics.md': 'tutorials/metrics.md',
|
|
'data-lineage.md' : 'tutorials/data-lineage.md',
|
|
'workflow-outputs.md': 'tutorials/workflow-outputs.md',
|
|
'flux.md': 'tutorials/flux.md',
|
|
'developer/plugins.md': 'plugins/developing-plugins.md',
|
|
'plugins.md': 'plugins/plugins.md',
|
|
'channel.md': 'workflow.md',
|
|
'module.md': 'modules/modules.md'
|
|
}
|
|
|
|
# Add any paths that contain templates here, relative to this directory.
|
|
templates_path = ['_templates']
|
|
|
|
# The suffix of source filenames.
|
|
source_suffix = '.md'
|
|
|
|
# The encoding of source files.
|
|
#source_encoding = 'utf-8-sig'
|
|
|
|
# The master toctree document.
|
|
master_doc = 'index'
|
|
|
|
# General information about the project.
|
|
project = u'Nextflow'
|
|
copyright = str(datetime.date.today().year) + u', Seqera Labs, S.L'
|
|
|
|
# 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.
|
|
|
|
# AUTO-GENERATED BY GIT
|
|
# Check if we are checked out at a specific version or not
|
|
process = subprocess.Popen(shlex.split("git tag --points-at HEAD"), stdout=subprocess.PIPE)
|
|
|
|
# The full version, including alpha/beta/rc tags.
|
|
release = process.communicate()[0].decode("utf-8").strip()
|
|
|
|
# The short X.Y version.
|
|
version = release.replace("-edge", "")
|
|
|
|
# The name for this set of Sphinx documents. If None, it defaults to
|
|
# "<project> v<release> documentation".
|
|
html_title = f"Nextflow {release} documentation"
|
|
|
|
# Get the current sha if not checked out at a specific version
|
|
if len(release) == 0:
|
|
process = subprocess.Popen(shlex.split("git rev-parse --short HEAD"), stdout=subprocess.PIPE)
|
|
current_sha = process.communicate()[0].decode("utf-8").strip()
|
|
release = f"dev <samp>({current_sha})</samp>"
|
|
html_title = "Nextflow documentation"
|
|
|
|
|
|
# A shorter title for the navigation bar. Default is the same as html_title.
|
|
#html_short_title = None
|
|
|
|
# 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', '**README.md']
|
|
|
|
# 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 = 'default'
|
|
|
|
# A list of ignored prefixes for module index sorting.
|
|
#modindex_common_prefix = []
|
|
|
|
# Add copyable selector
|
|
copybutton_selector = ".copyable pre"
|
|
|
|
# -- 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 = {
|
|
'logo_only': True,
|
|
'display_version': False
|
|
}
|
|
|
|
html_context = {
|
|
"display_github": True,
|
|
"github_user": "nextflow-io",
|
|
"github_repo": "nextflow",
|
|
"github_version": "master",
|
|
"conf_py_path": "/docs/"
|
|
}
|
|
|
|
# Nextflow theme
|
|
html_css_files = ['theme.css']
|
|
|
|
# Add any paths that contain custom themes here, relative to this directory.
|
|
#html_theme_path = []
|
|
|
|
# The name of an image file (relative to this directory) to place at the top
|
|
# of the sidebar.
|
|
html_logo = '_static/nextflow-logo.png'
|
|
|
|
# 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 = '_static/favicon.ico'
|
|
|
|
# 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']
|
|
|
|
# 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 = False
|
|
|
|
# Custom sidebar templates, maps document names to template names.
|
|
html_sidebars = {
|
|
'**': ['globaltoc.html']
|
|
}
|
|
|
|
# Additional templates that should be rendered to pages, maps page names to
|
|
# template names.
|
|
#html_additional_pages = {}
|
|
|
|
# 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 = False
|
|
|
|
# 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 = 'Nextflowdoc'
|
|
|
|
|
|
# -- 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]).
|
|
latex_documents = [
|
|
('index', 'Nextflow.tex', u'Nextflow Documentation',
|
|
u'Paolo Di Tommaso', 'manual'),
|
|
]
|
|
|
|
# The name of an image file (relative to this directory) to place at the top of
|
|
# the title page.
|
|
latex_logo = '_static/nextflow-logo.png'
|
|
|
|
# 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', 'nextflow', u'Nextflow Documentation',
|
|
[u'Paolo Di Tommaso'], 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', 'Nextflow', u'Nextflow Documentation',
|
|
u'Paolo Di Tommaso', 'Nextflow', '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'
|
|
|
|
|
|
# -- Options for Epub output ---------------------------------------------------
|
|
|
|
# Bibliographic Dublin Core info.
|
|
epub_title = u'Nextflow'
|
|
epub_author = u'Paolo Di Tommaso'
|
|
epub_publisher = u'Paolo Di Tommaso'
|
|
epub_copyright = u'Copyright 2013-2024, Seqera Labs'
|
|
|
|
# The language of the text. It defaults to the language option
|
|
# or en if the language is not set.
|
|
#epub_language = ''
|
|
|
|
# The scheme of the identifier. Typical schemes are ISBN or URL.
|
|
#epub_scheme = ''
|
|
|
|
# The unique identifier of the text. This can be a ISBN number
|
|
# or the project homepage.
|
|
#epub_identifier = ''
|
|
|
|
# A unique identification for the text.
|
|
#epub_uid = ''
|
|
|
|
# A tuple containing the cover image and cover page html template filenames.
|
|
#epub_cover = ()
|
|
|
|
# HTML files that should be inserted before the pages created by sphinx.
|
|
# The format is a list of tuples containing the path and title.
|
|
#epub_pre_files = []
|
|
|
|
# HTML files that should be inserted after the pages created by sphinx.
|
|
# The format is a list of tuples containing the path and title.
|
|
#epub_post_files = []
|
|
|
|
# A list of files that should not be packed into the epub file.
|
|
#epub_exclude_files = []
|
|
|
|
# The depth of the table of contents in toc.ncx.
|
|
#epub_tocdepth = 3
|
|
|
|
# Allow duplicate toc entries.
|
|
#epub_tocdup = True
|
|
|
|
# see also: https://github.com/pygments/pygments/blob/master/pygments/lexers/jvm.py
|
|
from pygments.lexer import RegexLexer
|
|
from sphinx.highlighting import lexers
|
|
|
|
class NextflowLexer(RegexLexer):
|
|
"""
|
|
For Nextflow source code.
|
|
"""
|
|
|
|
import re
|
|
from pygments.lexer import bygroups, using, this, default
|
|
from pygments.token import Comment, Operator, Keyword, Name, String, Number, Whitespace
|
|
from pygments.util import shebang_matches
|
|
|
|
name = 'Nextflow'
|
|
url = 'https://nextflow.io/'
|
|
aliases = ['nextflow', 'nf']
|
|
filenames = ['*.nf']
|
|
mimetypes = ['text/x-nextflow']
|
|
# version_added = '1.5'
|
|
|
|
flags = re.MULTILINE | re.DOTALL
|
|
|
|
tokens = {
|
|
'root': [
|
|
# Nextflow allows a file to start with a shebang
|
|
(r'#!(.*?)$', Comment.Preproc, 'base'),
|
|
default('base'),
|
|
],
|
|
'base': [
|
|
(r'[^\S\n]+', Whitespace),
|
|
(r'(//.*?)(\n)', bygroups(Comment.Single, Whitespace)),
|
|
(r'/\*.*?\*/', Comment.Multiline),
|
|
# keywords: go before method names to avoid lexing "throw new XYZ"
|
|
# as a method signature
|
|
(r'(assert|catch|else|if|instanceof|new|return|throw|try|in|as)\b', Keyword),
|
|
(r'(channel|log)', Name.Namespace),
|
|
# method names
|
|
(r'^(\s*(?:[a-zA-Z_][\w.\[\]]*\s+)+?)' # return arguments
|
|
r'('
|
|
r'[a-zA-Z_]\w*' # method name
|
|
r'|"(?:\\\\|\\[^\\]|[^"\\])*"' # or double-quoted method name
|
|
r"|'(?:\\\\|\\[^\\]|[^'\\])*'" # or single-quoted method name
|
|
r')'
|
|
r'(\s*)(\()', # signature start
|
|
bygroups(using(this), Name.Function, Whitespace, Operator)),
|
|
(r'@[a-zA-Z_][\w.]*', Name.Decorator),
|
|
(r'(def|enum|include|from|output|params|process|workflow)\b', Keyword.Declaration),
|
|
(r'(boolean|byte|char|double|float|int|long|short|void)\b', Keyword.Type),
|
|
(r'(true|false|null)\b', Keyword.Constant),
|
|
(r'""".*?"""', String.Double),
|
|
(r"'''.*?'''", String.Single),
|
|
(r'"(\\\\|\\[^\\]|[^"\\])*"', String.Double),
|
|
(r"'(\\\\|\\[^\\]|[^'\\])*'", String.Single),
|
|
(r'/(\\\\|\\[^\\]|[^/\\])*/', String),
|
|
(r"'\\.'|'[^\\]'|'\\u[0-9a-fA-F]{4}'", String.Char),
|
|
(r'(\.)([a-zA-Z_]\w*)', bygroups(Operator, Name.Attribute)),
|
|
(r'[a-zA-Z_]\w*:', Name.Label),
|
|
(r'[a-zA-Z_$]\w*', Name),
|
|
(r'[~^*!%&\[\](){}<>|+=:;,./?-]', Operator),
|
|
(r'[0-9][0-9]*\.[0-9]+([eE][0-9]+)?[fd]?', Number.Float),
|
|
(r'0x[0-9a-fA-F]+', Number.Hex),
|
|
(r'[0-9]+L?', Number.Integer),
|
|
(r'\n', Whitespace)
|
|
],
|
|
}
|
|
|
|
def analyse_text(text):
|
|
return shebang_matches(text, r'nextflow')
|
|
|
|
lexers['nextflow'] = NextflowLexer()
|