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Gallery (#328)
* Remove language specification to get rid of 404 error. * Initial version of gallery using nbsphinx with a hack to make it work with myst_nb. * Add gallery. * Run black. * Add all dirs to gallery. * WIP: Trying to get thumbnails to work. * Remove sphinxext stuff
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‎examples/conf.py

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import os
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from sphinx.application import Sphinx
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# -- Project information -----------------------------------------------------
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project = "PyMC"
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copyright = "2021, PyMC Community"
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copyright = "2022, PyMC Community"
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author = "PyMC Community"
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# -- General configuration ---------------------------------------------------
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"sphinxcontrib.bibtex",
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"sphinx_codeautolink",
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"notfound.extension",
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"sphinx_gallery.load_style",
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]
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# List of patterns, relative to source directory, that match files and
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]
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def hack_nbsphinx(app: Sphinx) -> None:
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from nbsphinx import (
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depart_gallery_html,
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doctree_resolved,
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GalleryNode,
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NbGallery,
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patched_toctree_resolve,
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NotebookParser,
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NbInput,
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NbOutput,
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NbInfo,
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NbWarning,
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CodeAreaNode,
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depart_codearea_html,
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visit_codearea_latex,
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depart_codearea_latex,
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GetSizeFromImages,
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)
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from sphinx.environment.adapters import toctree
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nbsphinx_thumbnails = {
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"case_studies/stochastic_volatility": "_static/stochastic_volatility.png",
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}
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def builder_inited(app: Sphinx):
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if not hasattr(app.env, "nbsphinx_thumbnails"):
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app.env.nbsphinx_thumbnails = {}
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def do_nothing(*node):
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pass
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app.add_source_parser(NotebookParser)
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# app.add_config_value('nbsphinx_execute', 'auto', rebuild='env')
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app.add_config_value("nbsphinx_kernel_name", "", rebuild="env")
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app.add_config_value("nbsphinx_execute_arguments", [], rebuild="env")
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app.add_config_value("nbsphinx_allow_errors", False, rebuild="")
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app.add_config_value("nbsphinx_timeout", None, rebuild="")
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app.add_config_value("nbsphinx_codecell_lexer", "none", rebuild="env")
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app.add_config_value("nbsphinx_prompt_width", "4.5ex", rebuild="html")
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app.add_config_value("nbsphinx_responsive_width", "540px", rebuild="html")
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app.add_config_value("nbsphinx_prolog", None, rebuild="env")
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app.add_config_value("nbsphinx_epilog", None, rebuild="env")
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app.add_config_value("nbsphinx_input_prompt", "[%s]:", rebuild="env")
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app.add_config_value("nbsphinx_output_prompt", "[%s]:", rebuild="env")
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app.add_config_value("nbsphinx_custom_formats", {}, rebuild="env")
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# Default value is set in config_inited():
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app.add_config_value("nbsphinx_requirejs_path", None, rebuild="html")
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# Default value is set in config_inited():
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app.add_config_value("nbsphinx_requirejs_options", None, rebuild="html")
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# This will be updated in env_updated():
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app.add_config_value("nbsphinx_widgets_path", None, rebuild="html")
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app.add_config_value("nbsphinx_widgets_options", {}, rebuild="html")
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# app.add_config_value('nbsphinx_thumbnails', {}, rebuild='html')
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app.add_config_value("nbsphinx_assume_equations", True, rebuild="env")
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app.add_directive("nbinput", NbInput)
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app.add_directive("nboutput", NbOutput)
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app.add_directive("nbinfo", NbInfo)
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app.add_directive("nbwarning", NbWarning)
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app.add_directive("nbgallery", NbGallery)
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app.add_node(
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CodeAreaNode,
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html=(do_nothing, depart_codearea_html),
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latex=(visit_codearea_latex, depart_codearea_latex),
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text=(do_nothing, do_nothing),
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)
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app.connect("builder-inited", builder_inited)
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app.connect("doctree-resolved", doctree_resolved)
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app.add_post_transform(GetSizeFromImages)
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app.add_config_value("nbsphinx_execute", "auto", rebuild="env")
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app.add_config_value("nbsphinx_thumbnails", nbsphinx_thumbnails, rebuild="html")
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app.add_directive("nbgallery", NbGallery)
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app.add_node(
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GalleryNode,
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html=(do_nothing, depart_gallery_html),
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latex=(do_nothing, do_nothing),
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text=(do_nothing, do_nothing),
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)
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app.connect("builder-inited", builder_inited)
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app.connect("doctree-resolved", doctree_resolved)
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# Monkey-patch Sphinx TocTree adapter
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toctree.TocTree.resolve = patched_toctree_resolve
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def setup(app: Sphinx):
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hack_nbsphinx(app)
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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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# 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", "../thumbnails"]
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html_css_files = ["custom.css"]
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templates_path = ["../_templates"]
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html_sidebars = {

‎examples/gallery.rst

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Gallery
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=======
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(Generalized) Linear and Hierarchical Linear Models
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-------------------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: generalized_linear_models
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:glob:
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:reversed:
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generalized_linear_models/*
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Case Studies
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------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: case_studies
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:glob:
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:reversed:
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case_studies/*
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Diagnostics and Model Criticism
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-------------------------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: diagnostics_and_criticism
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:glob:
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:reversed:
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diagnostics_and_criticism/*
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Gaussian Processes
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------------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: gaussian_processes
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:glob:
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:reversed:
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gaussian_processes/*
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Inference in ODE models
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-----------------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: ode_models
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:glob:
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:reversed:
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ode_models/*
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MCMC
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----
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: samplers
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:glob:
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:reversed:
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samplers/*
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Mixture Models
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--------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: mixture_models
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:glob:
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:reversed:
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mixture_models/*
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Survival Analysis
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-----------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: survival_analysis
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:glob:
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:reversed:
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survival_analysis/*
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Time Series
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-----------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: time_series
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:glob:
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:reversed:
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time_series/*
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Variational Inference
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---------------------
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.. nbgallery::
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:caption: This is a thumbnail gallery:
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:name: variational_inference
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:glob:
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:reversed:
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variational_inference/*

‎examples/index.md

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:::{toctree}
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:maxdepth: 1
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:hidden:
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gallery
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blog
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object_index/index
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:::

‎requirements-docs.txt

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sphinxext-opengraph
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sphinx-codeautolink
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sphinx-notfound-page
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nbsphinx
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sphinx-gallery

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