add nextflow d30e48d
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424
nextflow/docs/conf.py
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424
nextflow/docs/conf.py
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# -*- coding: utf-8 -*-
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#
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# Nextflow documentation build configuration file, created by
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# sphinx-quickstart on Sat May 5 16:57:28 2012.
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#
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# This file is execfile()d with the current directory set to its containing dir.
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#
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# Note that not all possible configuration values are present in this
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# autogenerated file.
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#
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# All configuration values have a default; values that are commented out
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# serve to show the default.
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import sys, os
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import sphinx_rtd_theme
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import datetime
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import subprocess
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import shlex
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#sys.path.insert(0, os.path.abspath('.'))
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# -- General configuration -----------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be extensions
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# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = [
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'sphinx.ext.mathjax',
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'sphinxcontrib.mermaid',
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'sphinxext.rediraffe',
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'sphinx_rtd_theme',
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'myst_parser',
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'sphinx_tabs.tabs',
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'sphinx_copybutton'
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]
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myst_enable_extensions = ['colon_fence', 'deflist', 'dollarmath']
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myst_heading_anchors = 3
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rediraffe_redirects = {
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'getstarted.md': 'install.md',
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'basic.md': 'overview.md',
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'tracing.md': 'reports.md',
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'mail.md': 'notifications.md',
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'operator.md': 'reference/operator.md',
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'dsl1.md': 'migrations/dsl1.md',
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'updating-syntax.md': 'strict-syntax.md',
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'updating-spot-retries.md': 'guides/updating-spot-retries.md',
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'metrics.md': 'tutorials/metrics.md',
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'data-lineage.md' : 'tutorials/data-lineage.md',
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'workflow-outputs.md': 'tutorials/workflow-outputs.md',
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'flux.md': 'tutorials/flux.md',
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'developer/plugins.md': 'plugins/developing-plugins.md',
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'plugins.md': 'plugins/plugins.md',
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'channel.md': 'workflow.md',
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'module.md': 'modules/modules.md'
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}
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix of source filenames.
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source_suffix = '.md'
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# The encoding of source files.
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#source_encoding = 'utf-8-sig'
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# The master toctree document.
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master_doc = 'index'
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# General information about the project.
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project = u'Nextflow'
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copyright = str(datetime.date.today().year) + u', Seqera Labs, S.L'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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# AUTO-GENERATED BY GIT
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# Check if we are checked out at a specific version or not
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process = subprocess.Popen(shlex.split("git tag --points-at HEAD"), stdout=subprocess.PIPE)
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# The full version, including alpha/beta/rc tags.
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release = process.communicate()[0].decode("utf-8").strip()
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# The short X.Y version.
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version = release.replace("-edge", "")
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# The name for this set of Sphinx documents. If None, it defaults to
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# "<project> v<release> documentation".
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html_title = f"Nextflow {release} documentation"
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# Get the current sha if not checked out at a specific version
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if len(release) == 0:
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process = subprocess.Popen(shlex.split("git rev-parse --short HEAD"), stdout=subprocess.PIPE)
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current_sha = process.communicate()[0].decode("utf-8").strip()
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release = f"dev <samp>({current_sha})</samp>"
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html_title = "Nextflow documentation"
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# A shorter title for the navigation bar. Default is the same as html_title.
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#html_short_title = None
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#language = None
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# There are two options for replacing |today|: either, you set today to some
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# non-false value, then it is used:
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#today = ''
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# Else, today_fmt is used as the format for a strftime call.
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#today_fmt = '%B %d, %Y'
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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exclude_patterns = ['_build', '**README.md']
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# The reST default role (used for this markup: `text`) to use for all documents.
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#default_role = None
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# If true, '()' will be appended to :func: etc. cross-reference text.
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#add_function_parentheses = True
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# If true, the current module name will be prepended to all description
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# unit titles (such as .. function::).
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#add_module_names = True
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# If true, sectionauthor and moduleauthor directives will be shown in the
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# output. They are ignored by default.
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#show_authors = False
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'default'
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# A list of ignored prefixes for module index sorting.
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#modindex_common_prefix = []
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# Add copyable selector
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copybutton_selector = ".copyable pre"
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# -- Options for HTML output ---------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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html_theme = "sphinx_rtd_theme"
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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html_theme_options = {
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'logo_only': True,
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'display_version': False
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}
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html_context = {
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"display_github": True,
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"github_user": "nextflow-io",
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"github_repo": "nextflow",
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"github_version": "master",
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"conf_py_path": "/docs/"
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}
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# Nextflow theme
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html_css_files = ['theme.css']
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# Add any paths that contain custom themes here, relative to this directory.
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#html_theme_path = []
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# The name of an image file (relative to this directory) to place at the top
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# of the sidebar.
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html_logo = '_static/nextflow-logo.png'
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# The name of an image file (within the static path) to use as favicon of the
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# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
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# pixels large.
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html_favicon = '_static/favicon.ico'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
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# using the given strftime format.
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#html_last_updated_fmt = '%b %d, %Y'
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# If true, SmartyPants will be used to convert quotes and dashes to
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# typographically correct entities.
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html_use_smartypants = False
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# Custom sidebar templates, maps document names to template names.
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html_sidebars = {
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'**': ['globaltoc.html']
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}
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# Additional templates that should be rendered to pages, maps page names to
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# template names.
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#html_additional_pages = {}
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# If false, no module index is generated.
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#html_domain_indices = True
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# If false, no index is generated.
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#html_use_index = True
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# If true, the index is split into individual pages for each letter.
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#html_split_index = False
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# If true, links to the reST sources are added to the pages.
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html_show_sourcelink = False
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# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
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#html_show_sphinx = True
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# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
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#html_show_copyright = True
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# If true, an OpenSearch description file will be output, and all pages will
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# contain a <link> tag referring to it. The value of this option must be the
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# base URL from which the finished HTML is served.
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#html_use_opensearch = ''
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# This is the file name suffix for HTML files (e.g. ".xhtml").
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#html_file_suffix = None
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'Nextflowdoc'
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# -- Options for LaTeX output --------------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#'preamble': '',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title, author, documentclass [howto/manual]).
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latex_documents = [
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('index', 'Nextflow.tex', u'Nextflow Documentation',
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u'Paolo Di Tommaso', 'manual'),
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]
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# The name of an image file (relative to this directory) to place at the top of
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# the title page.
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latex_logo = '_static/nextflow-logo.png'
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# For "manual" documents, if this is true, then toplevel headings are parts,
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# not chapters.
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#latex_use_parts = False
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# If true, show page references after internal links.
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#latex_show_pagerefs = False
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# If true, show URL addresses after external links.
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#latex_show_urls = False
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# Documents to append as an appendix to all manuals.
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#latex_appendices = []
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# If false, no module index is generated.
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#latex_domain_indices = True
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# -- Options for manual page output --------------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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('index', 'nextflow', u'Nextflow Documentation',
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[u'Paolo Di Tommaso'], 1)
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]
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# If true, show URL addresses after external links.
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#man_show_urls = False
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# -- Options for Texinfo output ------------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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('index', 'Nextflow', u'Nextflow Documentation',
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u'Paolo Di Tommaso', 'Nextflow', 'One line description of project.',
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'Miscellaneous'),
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]
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# Documents to append as an appendix to all manuals.
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#texinfo_appendices = []
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# If false, no module index is generated.
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#texinfo_domain_indices = True
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# How to display URL addresses: 'footnote', 'no', or 'inline'.
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#texinfo_show_urls = 'footnote'
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# -- Options for Epub output ---------------------------------------------------
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# Bibliographic Dublin Core info.
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epub_title = u'Nextflow'
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epub_author = u'Paolo Di Tommaso'
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epub_publisher = u'Paolo Di Tommaso'
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epub_copyright = u'Copyright 2013-2024, Seqera Labs'
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# The language of the text. It defaults to the language option
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# or en if the language is not set.
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#epub_language = ''
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# The scheme of the identifier. Typical schemes are ISBN or URL.
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#epub_scheme = ''
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# The unique identifier of the text. This can be a ISBN number
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# or the project homepage.
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#epub_identifier = ''
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# A unique identification for the text.
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#epub_uid = ''
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# A tuple containing the cover image and cover page html template filenames.
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#epub_cover = ()
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# HTML files that should be inserted before the pages created by sphinx.
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# The format is a list of tuples containing the path and title.
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#epub_pre_files = []
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# HTML files that should be inserted after the pages created by sphinx.
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# The format is a list of tuples containing the path and title.
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#epub_post_files = []
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# A list of files that should not be packed into the epub file.
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#epub_exclude_files = []
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# The depth of the table of contents in toc.ncx.
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#epub_tocdepth = 3
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# Allow duplicate toc entries.
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#epub_tocdup = True
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# see also: https://github.com/pygments/pygments/blob/master/pygments/lexers/jvm.py
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from pygments.lexer import RegexLexer
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from sphinx.highlighting import lexers
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class NextflowLexer(RegexLexer):
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"""
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For Nextflow source code.
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"""
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import re
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from pygments.lexer import bygroups, using, this, default
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from pygments.token import Comment, Operator, Keyword, Name, String, Number, Whitespace
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from pygments.util import shebang_matches
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name = 'Nextflow'
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url = 'https://nextflow.io/'
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aliases = ['nextflow', 'nf']
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filenames = ['*.nf']
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mimetypes = ['text/x-nextflow']
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# version_added = '1.5'
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flags = re.MULTILINE | re.DOTALL
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tokens = {
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'root': [
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# Nextflow allows a file to start with a shebang
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(r'#!(.*?)$', Comment.Preproc, 'base'),
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default('base'),
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],
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'base': [
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(r'[^\S\n]+', Whitespace),
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(r'(//.*?)(\n)', bygroups(Comment.Single, Whitespace)),
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(r'/\*.*?\*/', Comment.Multiline),
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# keywords: go before method names to avoid lexing "throw new XYZ"
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# as a method signature
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(r'(assert|catch|else|if|instanceof|new|return|throw|try|in|as)\b', Keyword),
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(r'(channel|log)', Name.Namespace),
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# method names
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(r'^(\s*(?:[a-zA-Z_][\w.\[\]]*\s+)+?)' # return arguments
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r'('
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r'[a-zA-Z_]\w*' # method name
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r'|"(?:\\\\|\\[^\\]|[^"\\])*"' # or double-quoted method name
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r"|'(?:\\\\|\\[^\\]|[^'\\])*'" # or single-quoted method name
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r')'
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r'(\s*)(\()', # signature start
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bygroups(using(this), Name.Function, Whitespace, Operator)),
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(r'@[a-zA-Z_][\w.]*', Name.Decorator),
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(r'(def|enum|include|from|output|params|process|workflow)\b', Keyword.Declaration),
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(r'(boolean|byte|char|double|float|int|long|short|void)\b', Keyword.Type),
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(r'(true|false|null)\b', Keyword.Constant),
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(r'""".*?"""', String.Double),
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(r"'''.*?'''", String.Single),
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(r'"(\\\\|\\[^\\]|[^"\\])*"', String.Double),
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(r"'(\\\\|\\[^\\]|[^'\\])*'", String.Single),
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(r'/(\\\\|\\[^\\]|[^/\\])*/', String),
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(r"'\\.'|'[^\\]'|'\\u[0-9a-fA-F]{4}'", String.Char),
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(r'(\.)([a-zA-Z_]\w*)', bygroups(Operator, Name.Attribute)),
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(r'[a-zA-Z_]\w*:', Name.Label),
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(r'[a-zA-Z_$]\w*', Name),
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(r'[~^*!%&\[\](){}<>|+=:;,./?-]', Operator),
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(r'[0-9][0-9]*\.[0-9]+([eE][0-9]+)?[fd]?', Number.Float),
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(r'0x[0-9a-fA-F]+', Number.Hex),
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(r'[0-9]+L?', Number.Integer),
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(r'\n', Whitespace)
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],
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}
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def analyse_text(text):
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return shebang_matches(text, r'nextflow')
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lexers['nextflow'] = NextflowLexer()
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