Serena

# 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 : Oraios AI & Oraios Software # The author of the book copyright : "2025 by Serena contributors" # Copyright year to be placed in the footer # 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 : true ####################################################################################### # Execution settings execute: # NOTE: Notebooks are not executed, because test_notebooks.py executes them and stores them with outputs in the docs/ folder # NOTE: If changed, repeat below in `nb_execution_mode`. execute_notebooks : "off" # 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 : 1000 # 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 : true # 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 - html_admonition - html_image 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 use_darkmode_button : false extra_footer : "" home_page_in_navbar : true # Whether to include your home page in the left Navigation Bar baseurl : "https://oraios.github.io/serena/" 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 master_doc: "01-about/000_intro.md" html_theme_options: logo: image_light: ../resources/serena-logo.svg image_dark: ../resources/serena-logo-dark-mode.svg autodoc_typehints_format: "short" autodoc_member_order: "bysource" autoclass_content: "both" autodoc_default_options: show-inheritance: True autodoc_show_sourcelink: True add_module_names: False github_username: oraios github_repository: serena nb_execution_mode: "off" nb_merge_streams: True # This is important for cell outputs to appear as single blocks rather than one block per line 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}}"