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switch to sphinx-favicon from deprecated "favicons" config (#388)
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-114
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‎setup.cfg

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@@ -40,6 +40,7 @@ install_requires =
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sphinx==5.*
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sphinx-reredirects==0.1.*
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sphinxcontrib-runcmd==0.2.*
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sphinx-favicon
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python-Levenshtein
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sphinx-intl
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‎src/conf.py

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@@ -20,12 +20,12 @@
2020

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# -- Project information -----------------------------------------------------
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project = 'Common Workflow Language User Guide'
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copyright = '2013, CWL Project Team'
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author = 'CWL Project Team'
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project = "Common Workflow Language User Guide"
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copyright = "2013, CWL Project Team"
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author = "CWL Project Team"
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# The full version, including alpha/beta/rc tags
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release = '0.1'
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release = "0.1"
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# Define the version we use for matching in the version switcher.
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version_match = os.environ.get("READTHEDOCS_VERSION")
@@ -37,142 +37,163 @@
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'myst_parser',
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'sphinx.ext.graphviz',
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'sphinx_reredirects',
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'cwl.sphinx.runcmd'
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"myst_parser",
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"sphinx.ext.graphviz",
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"sphinx_reredirects",
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"sphinx_favicon",
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"cwl.sphinx.runcmd",
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]
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# myst-parser settings
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myst_heading_anchors = 4
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myst_enable_extensions = [
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'colon_fence',
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'deflist',
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'substitution',
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'replacements',
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"colon_fence",
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"deflist",
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"substitution",
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"replacements",
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]
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CWL_VERSION = 'v1.2'
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CWL_VERSION = "v1.2"
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myst_substitutions = {
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'repo_url': 'https://github.com/common-workflow-language/user_guide/',
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'source_branch': 'main',
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'cwl_version': f'`{CWL_VERSION}`',
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'cwl_version_text': f'{CWL_VERSION}'
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"repo_url": "https://github.com/common-workflow-language/user_guide/",
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"source_branch": "main",
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"cwl_version": f"`{CWL_VERSION}`",
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"cwl_version_text": f"{CWL_VERSION}",
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}
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master_doc = 'index'
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master_doc = "index"
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# Set the default role so we can use `foo` instead of ``foo``
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default_role = 'literal'
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default_role = "literal"
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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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templates_path = ["_templates"]
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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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# This pattern also affects html_static_path and html_extra_path.
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# CONTRIBUTING.md is referenced in the footer, but not linked via Sphinx
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# aio.md is also referenced in one page, but not directly via Sphinx, hence the exclusions here.
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exclude_patterns = [
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'**/Thumbs.db',
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'**/.DS_Store',
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'**/.git',
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'.idea',
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'.github',
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'**/_build',
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'**/_includes',
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'cwl',
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'venv',
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'README.md',
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'CODE_OF_CONDUCT.md',
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'CONTRIBUTING.md'
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"**/Thumbs.db",
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"**/.DS_Store",
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"**/.git",
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".idea",
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".github",
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"**/_build",
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"**/_includes",
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"cwl",
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"venv",
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"README.md",
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"CODE_OF_CONDUCT.md",
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"CONTRIBUTING.md",
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]
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source_suffix = ['.rst', '.md']
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source_suffix = [".rst", ".md"]
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# -- Options for URL redirects -----------------------------------------------
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redirects = {
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'01-introduction/index.md': '../introduction/quick-start.html',
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'02-1st-example/index.md': '../introduction/quick-start.html',
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'03-input/index.md': '../topics/inputs.html',
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'04-output/index.md': '../topics/outputs.html',
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'05-stdout/index.md': '../topics/outputs.html',
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'06-params/index.md': '../topics/parameter-references.html',
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'07-containers/index.md': '../topics/using-containers.html',
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'08-arguments/index.md': '../topics/additional-arguments-and-parameters.html',
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'09-array-inputs/index.md': '../topics/inputs.html',
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'10-array-outputs/index.md': '../topics/outputs.html',
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'11-records/index.md': '../topics/inputs.html',
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'12-env/index.md': '../topics/environment-variables.html',
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'13-expressions/index.md': '../topics/expressions.html',
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'14-runtime/index.md': '../topics/creating-files-at-runtime.html',
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'15-staging/index.md': '../topics/staging-input-files.html',
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'16-file-formats/index.md': '../topics/file-formats.html',
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'17-metadata/index.md': '../topics/metadata-and-authorship.html',
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'19-custom-types/index.md': '../topics/custom-types.html',
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'20-software-requirements/index.md': '../topics/specifying-software-requirements.html',
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'21-1st-workflow/index.md': '../topics/workflows.html',
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'22-nested-workflows/index.md': '../topics/workflows.html#nested-workflows',
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'23-scatter-workflow/index.md': '../topics/workflows.html#scattering-workflows',
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'24_conditional-workflow/index.md': '../topics/workflows.html#conditional-workflows',
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'rec-practices/index.md': '../topics/best-practices.html',
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'misc/index.md': '../faq.html',
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'episodes.md': 'index.html#table-of-contents',
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'setup.md': 'introduction/prerequisites.html',
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'extras.md': '/index.html',
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'yaml/index.md': '../topics/yaml-guide.html',
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'CODE_OF_CONDUCT.html': 'https://github.com/common-workflow-language/user_guide/blob/main/CODE_OF_CONDUCT.md'
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"01-introduction/index.md": "../introduction/quick-start.html",
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"02-1st-example/index.md": "../introduction/quick-start.html",
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"03-input/index.md": "../topics/inputs.html",
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"04-output/index.md": "../topics/outputs.html",
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"05-stdout/index.md": "../topics/outputs.html",
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"06-params/index.md": "../topics/parameter-references.html",
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"07-containers/index.md": "../topics/using-containers.html",
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"08-arguments/index.md": "../topics/additional-arguments-and-parameters.html",
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"09-array-inputs/index.md": "../topics/inputs.html",
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"10-array-outputs/index.md": "../topics/outputs.html",
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"11-records/index.md": "../topics/inputs.html",
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"12-env/index.md": "../topics/environment-variables.html",
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"13-expressions/index.md": "../topics/expressions.html",
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"14-runtime/index.md": "../topics/creating-files-at-runtime.html",
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"15-staging/index.md": "../topics/staging-input-files.html",
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"16-file-formats/index.md": "../topics/file-formats.html",
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"17-metadata/index.md": "../topics/metadata-and-authorship.html",
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"19-custom-types/index.md": "../topics/custom-types.html",
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"20-software-requirements/index.md": "../topics/specifying-software-requirements.html",
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"21-1st-workflow/index.md": "../topics/workflows.html",
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"22-nested-workflows/index.md": "../topics/workflows.html#nested-workflows",
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"23-scatter-workflow/index.md": "../topics/workflows.html#scattering-workflows",
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"24_conditional-workflow/index.md": "../topics/workflows.html#conditional-workflows",
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"rec-practices/index.md": "../topics/best-practices.html",
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"misc/index.md": "../faq.html",
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"episodes.md": "index.html#table-of-contents",
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"setup.md": "introduction/prerequisites.html",
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"extras.md": "/index.html",
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"yaml/index.md": "../topics/yaml-guide.html",
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"CODE_OF_CONDUCT.html": "https://github.com/common-workflow-language/user_guide/blob/main/CODE_OF_CONDUCT.md",
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}
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# -- Options for Pygments ----------------------------------------------------
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pygments_style = 'default'
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pygments_style = "default"
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# TODO: maybe write our own lexer to customize tokens, keywords, etc?
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lexers['cwl'] = YamlLexer()
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lexers["cwl"] = YamlLexer()
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highlight_options = {
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'default': {
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'stripall': True
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}
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}
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highlight_options = {"default": {"stripall": True}}
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# -- GraphViz configuration --------------------------------------------------
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from cwl.doc.graphs import create_processing_units_graph
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graphviz_output_format = 'svg'
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graphviz_output_format = "svg"
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myst_substitutions['CWL_PROCESSING_UNITS_GRAPH'] = create_processing_units_graph()
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myst_substitutions["CWL_PROCESSING_UNITS_GRAPH"] = create_processing_units_graph()
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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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#
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html_theme = 'pydata_sphinx_theme'
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html_theme = "pydata_sphinx_theme"
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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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html_static_path = ["_static"]
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favicons = [
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{
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"rel": "icon",
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"sizes": "16x16",
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"href": "images/favicons/cwl/favicon-16x16.png",
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},
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{
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"rel": "icon",
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"sizes": "32x32",
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"href": "images/favicons/cwl/favicon-32x32.png",
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},
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{
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"rel": "icon",
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"sizes": "96x96",
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"href": "images/favicons/cwl/favicon-96x96.png",
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},
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{
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"rel": "icon",
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"sizes": "128x128",
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"href": "images/favicons/cwl/favicon-128.png",
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},
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{
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"rel": "icon",
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"sizes": "196x196",
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"href": "images/favicons/cwl/favicon-196x196.png",
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},
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]
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html_css_files = [
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'css/custom.css',
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"css/custom.css",
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]
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html_logo = '_static/images/logos/cwl/CWL-Logo-HD-cropped2.png'
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html_favicon = '_static/images/favicons/cwl/favicon.ico'
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html_logo = "_static/images/logos/cwl/CWL-Logo-HD-cropped2.png"
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html_favicon = "_static/images/favicons/cwl/favicon.ico"
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html_extra_path = [
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'browserconfig.xml',
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'favicon.ico',
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'manifest.json'
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]
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html_extra_path = ["browserconfig.xml", "favicon.ico", "manifest.json"]
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html_theme_options = {
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"external_links": [
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{"name": "Community", "url": "https://www.commonwl.org/community/"},
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{"name": "Community", "url": "https://www.commonwl.org/community/"},
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],
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"header_links_before_dropdown": 6,
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"icon_links": [
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"navbar_end": [
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# "version-switcher",
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"theme-switcher",
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"navbar-icon-links"
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"navbar-icon-links",
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],
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"show_nav_level": 2,
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"navigation_depth": 2,
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"collapse_navigation": True,
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"show_prev_next": True,
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"favicons": [
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{
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"rel": "icon",
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"sizes": "16x16",
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"href": "images/favicons/cwl/favicon-16x16.png"
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},
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{
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"rel": "icon",
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"sizes": "32x32",
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"href": "images/favicons/cwl/favicon-32x32.png"
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},
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{
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"rel": "icon",
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"sizes": "96x96",
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"href": "images/favicons/cwl/favicon-96x96.png"
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},
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{
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"rel": "icon",
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"sizes": "128x128",
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"href": "images/favicons/cwl/favicon-128.png"
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},
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{
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"rel": "icon",
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"sizes": "196x196",
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"href": "images/favicons/cwl/favicon-196x196.png"
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}
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],
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"footer_items": ["copyright"],
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}
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232226
"github_repo": "user_guide",
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"github_version": "main",
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"doc_path": "src",
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"default_mode": "light"
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"default_mode": "light",
236230
}
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gettext_uuid = True
239233
gettext_compact = "user_guide"
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locale_dirs = ['../locales/']
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locale_dirs = ["../locales/"]
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# Patched MyST parser
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SPHINX_LOGGER = logging.getLogger(__name__)
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263258
class MystParser(SphinxParser):
264259
"""Sphinx parser for Markedly Structured Text (MyST)."""
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@@ -309,7 +304,9 @@ def parse(self, inputstring: str, document: nodes.document) -> None:
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# gives you the translation without resolving the links. Here we just re-use the
310305
# ``md_env`` dictionary that contains the ``.references`` populated in the first
311306
# pass, fixing i18n with MyST Parser.
312-
env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env
307+
env = (
308+
{} if not hasattr(document.settings, "md_env") else document.settings.md_env
309+
)
313310
parser.options["document"] = document
314311
parser.render(inputstring, env)
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document.settings.md_env = parser.renderer.md_env

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