mkdocs.yml

site_name: BlackBIRDS
site_description: Documentation for the BlackBIRDS library.
site_url: https://arnauqb.github.io/blackbirds
site_author: Arnau Quera-Bofarull

repo_url: https://github.com/arnauqb/blackbirds

extra_javascript: 
  - _static/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

theme:
  name: "material"
  features:
      - navigation.sections  # Sections are included in the navigation on the left.
      - toc.integrate  # Table of contents is integrated on the left; does not appear separately on the right.
      - header.autohide  # header disappears as you scroll
  palette:
      # Light mode / dark mode
      # We deliberately don't automatically use `media` to check a user's preferences. We default to light mode as
      # (a) it looks more professional, and (b) is more obvious about the fact that it offers a (dark mode) toggle.
      - scheme: default
        primary: white
        accent: amber
        toggle:
           icon: material/weather-night
           name: Switch to dark mode
      - scheme: slate
        primary: black
        accent: amber
        toggle:
           icon: material/weather-sunny
           name: Switch to light mode
  icon:
      repo: fontawesome/brands/github  # GitHub logo in top right
      logo: fontawesome/solid/crow # birds icon
        #logo: "material/math-integral-box"
  favicon: "_static/logo.jpg"
    #custom_dir: "docs/_overrides"  # Overriding part of the HTML

markdown_extensions:
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences  # Seems to enable syntax highlighting when used with the Material theme.
  - pymdownx.details  # Allowing hidden expandable regions denoted by ???
  - pymdownx.snippets:  # Include one Markdown file into another
      base_path: docs
  - admonition
  - toc:
      permalink: "¤"  # Adds a clickable permalink to each section heading
      toc_depth: 4  # Prevents h5, h6 (i.e. methods) from showing up in the TOC.

extra_javascript:
  - javascripts/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
    
extra_css:
    - _static/custom_css.css

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          setup_commands:
            - import pytkdocs_tweaks
            - pytkdocs_tweaks.main()
          selection:
            inherited_members: true  # Allow looking up inherited methods
          rendering:
            show_root_heading: true  # actually display anything at all...
            show_root_full_path: true  # display "diffrax.asdf" not just "asdf"
            show_if_no_docstring: true
            show_signature_annotations: true
            show_source: false  # don't include source code
            members_order: source  # order methods according to their order of definition in the source code, not alphabetical order
            heading_level: 4  #
  -  mkdocs-jupyter

nav:
  - index.md
  - Examples:
    - Variational Inference:
      - examples/variational_inference/01-random_walk.ipynb
      - examples/variational_inference/02-SIR.ipynb
      - examples/variational_inference/03-brock_hommes.ipynb
      - examples/variational_inference/04-score_vs_pathwise_gradient.ipynb
      - examples/variational_inference/05-gpu_parallelisation.py
      - examples/variational_inference/06-classical_posterior.ipynb
    - MCMC:
      - examples/mcmc/01-mala-mcmc_conjugate_prior_likelihood_pairs.ipynb
    - Simulated Minimum Distance:
      - examples/smd/01-random_walk.ipynb
    - examples/gpu_parallelization.md
  - API:
    - Inference:
      - api/infer/mcmc.md
      - api/infer/smd.md
      - api/infer/vi.md
    - api/jacfwd.md
    - api/losses.md
    - api/mpi_setup.md
    - Models:
      - api/models/random_walk.md
      - api/models/sir.md
      - api/models/brock_hommes.md
      - api/models/rama_cont.md
    - api/posterior_estimators.md
    - api/simulate.md
    - api/utils.md