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docs/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# Users are expected to override these values in their own `_config.yml` file.
+# This is also the "master list" of all allowed keys and values.
+
+#######################################################################################
+# Book settings
+title                       : serena Documentation  # The title of the book. Will be placed in the left navbar.
+author                      : serena contributors  # The author of the book
+copyright                   : ""  # Copyright year to be placed in the footer
+logo                        : "" # A path to the book logo
+# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
+exclude_patterns            : ['**.ipynb_checkpoints', '.DS_Store', 'Thumbs.db', '_build', 'jupyter_execute', '.jupyter_cache', '.pytest_cache', 'docs/autogen_rst.py', 'docs/create_toc.py']
+# Auto-exclude files not in the toc
+only_build_toc_files        : false
+
+#######################################################################################
+# Execution settings
+execute:
+  execute_notebooks         : cache  # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
+  cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
+  exclude_patterns          : []    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
+  timeout                   : -1    # The maximum time (in seconds) each notebook cell is allowed to run.
+  run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),
+                                    # otherwise the notebook's parent directory will be the cwd.
+  allow_errors              : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run.
+  stderr_output             : show  # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe'
+
+#######################################################################################
+# Parse and render settings
+parse:
+  myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html
+    - amsmath
+    - colon_fence
+    # - deflist
+    - dollarmath
+    # - html_admonition
+    # - html_image
+    - linkify
+    # - replacements
+    # - smartquotes
+    - substitution
+    - tasklist
+  myst_url_schemes: [ mailto, http, https ] # URI schemes that will be recognised as external URLs in Markdown links
+  myst_dmath_double_inline: true  # Allow display math ($$) within an inline context
+
+#######################################################################################
+# HTML-specific settings
+html:
+  favicon                   : ""  # A path to a favicon image
+  use_edit_page_button      : false  # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
+  use_repository_button     : false  # Whether to add a link to your repository button
+  use_issues_button         : false  # Whether to add an "open an issue" button
+  use_multitoc_numbering    : true   # Continuous numbering across parts/chapters
+  extra_footer              : ""
+  google_analytics_id       : ""  # A GA id that can be used to track book views.
+  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
+  baseurl                   : "https://github.com/oraios/serena"
+  analytics:
+
+  comments:
+    hypothesis              : false
+    utterances              : false
+  announcement              : "" # A banner announcement at the top of the site.
+
+#######################################################################################
+# LaTeX-specific settings
+latex:
+  latex_engine              : pdflatex  # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex'
+  use_jupyterbook_latex     : true # use sphinx-jupyterbook-latex for pdf builds as default
+  targetname                : book.tex
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - refs.bib
+
+#######################################################################################
+# Launch button settings
+launch_buttons:
+  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
+  binderhub_url             : ""  # The URL of the BinderHub (e.g., https://mybinder.org)
+  jupyterhub_url            : ""  # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu)
+  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)
+  colab_url                 : "https://colab.research.google.com"
+
+repository:
+  url                       : https://github.com/oraios/serena  # The URL to your book's repository
+  path_to_book              : docs  # A path to your book's folder, relative to the repository root.
+  branch                    : main  # Which branch of the repository should be used when creating links
+
+#######################################################################################
+# Advanced and power-user settings
+sphinx:
+  extra_extensions          :
+    - sphinx.ext.autodoc
+    - sphinx.ext.viewcode
+    - sphinx_toolbox.more_autodoc.sourcelink
+    - sphinxcontrib.spelling
+  local_extensions          :   # A list of local extensions to load by sphinx specified by "name: path" items
+  recursive_update          : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update (false)
+  config                    :   # key-value pairs to directly over-ride the Sphinx configuration
+    autodoc_typehints_format: "short"
+    autodoc_member_order: "bysource"
+    autoclass_content: "both"
+    autodoc_default_options:
+      show-inheritance: True
+    suppress_warnings: ["mystnb.unknown_mime_type"]  # needed for plotly rendering
+    autodoc_show_sourcelink: True
+    add_module_names: False
+    github_username: oraios
+    github_repository: https://github.com/oraios/serena
+    python_use_unqualified_type_names: True
+    nb_mime_priority_overrides: [
+      [ 'html', 'application/vnd.jupyter.widget-view+json', 10 ],
+      [ 'html', 'application/javascript', 20 ],
+      [ 'html', 'text/html', 30 ],
+      [ 'html', 'text/latex', 40 ],
+      [ 'html', 'image/svg+xml', 50 ],
+      [ 'html', 'image/png', 60 ],
+      [ 'html', 'image/jpeg', 70 ],
+      [ 'html', 'text/markdown', 80 ],
+      [ 'html', 'text/plain', 90 ],
+      [ 'spelling', 'application/vnd.jupyter.widget-view+json', 10 ],
+      [ 'spelling', 'application/javascript', 20 ],
+      [ 'spelling', 'text/html', 30 ],
+      [ 'spelling', 'text/latex', 40 ],
+      [ 'spelling', 'image/svg+xml', 50 ],
+      [ 'spelling', 'image/png', 60 ],
+      [ 'spelling', 'image/jpeg', 70 ],
+      [ 'spelling', 'text/markdown', 80 ],
+      [ 'spelling', 'text/plain', 90 ],
+    ]
+    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+    mathjax3_config:
+      loader: { load: [ '[tex]/configmacros' ] }
+      tex:
+        packages: { '[+]': [ 'configmacros' ] }
+        macros:
+          vect: ["{\\mathbf{\\boldsymbol{#1}} }", 1]
+          E: "{\\mathbb{E}}"
+          P: "{\\mathbb{P}}"
+          R: "{\\mathbb{R}}"
+          abs: ["{\\left| #1 \\right|}", 1]
+          simpl: ["{\\Delta^{#1} }", 1]
+          amax: "{\\text{argmax}}"