mkdocs.yml

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.
        - media: "(prefers-color-scheme: default)"
          scheme: default
          primary: white
          accent: orange
          toggle:
             icon: material/weather-night
             name: Switch to dark mode
        - media: "(prefers-color-scheme: slate)"
          scheme: slate
          primary: black
          accent: orange
          toggle:
             icon: material/weather-sunny
             name: Switch to light mode
    icon:
        repo: fontawesome/brands/github  # GitHub logo in top right
    logo_light_mode: "_static/logo-light.svg"  # jpc logo in top left
    logo_dark_mode: "_static/logo-dark.svg"  # jpc logo in top left
    favicon: "_static/favicon.png"
    custom_dir: "docs/_overrides"  # Overriding part of the HTML

site_name: jpc
site_description: The documentation for the jpc software library.
site_author: Francesco Innocenti

repo_url: https://github.com/thebuckleylab/jpc
repo_name: thebuckleylab/jpc
edit_uri: ""  # No edit button, as some of our pages are in /docs and some in /examples via symlink, so it's impossible for them all to be accurate

strict: true  # Don't allow warnings during the build process

extra_javascript:
    # The below three make MathJax work, see https://squidfunk.github.io/mkdocs-material/reference/mathjax/
    - _static/mathjax.js
    - https://polyfill.io/v3/polyfill.min.js?features=es6
    - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

extra_css:
    - _static/custom_css.css

markdown_extensions:
    - pymdownx.arithmatex:  # Render LaTeX via MathJax
        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
    - attr_list

plugins:
    - search  # default search plugin; needs manually re-enabling when using any other plugins
    - autorefs  # Cross-links to headings
    - include_exclude_files:
        include:
            - ".htaccess"
        exclude:
            - "_overrides"

    - mknotebooks  # Jupyter examples
    - mkdocstrings:
        handlers:
            python:
                setup_commands:
                    - import pytkdocs_tweaks
                    - pytkdocs_tweaks.main()
                    - import jaxtyping
                    - jaxtyping.set_array_name_format("array")
                    - import jax
                    - jax.ShapeDtypeStruct.__module__ = "jax"
                    - jax.core.ClosedJaxpr.__module__ = "jax.core"

                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 "jpc.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

nav:
    - 'index.md'
    - ⚙️ How it works:
        - Basic usage: 'basic_usage.md'
        - Advanced usage: 'advanced_usage.md'
    - 📚 Examples:
        - Introductory:
            - Discriminative PC: 'examples/discriminative_pc.ipynb'
            - Supervised generative PC: 'examples/supervised_generative_pc.ipynb'
            - Unsupervised generative PC: 'examples/unsupervised_generative_pc.ipynb'
        - Advanced:
            - Hybrid PC: 'examples/hybrid_pc.ipynb'
            - Linear theoretical energy: 'examples/linear_net_theoretical_energy.ipynb'
    - 🌱 Basic API:
          - 'api/Training.md'
          - 'api/Testing.md'
          - 'api/Utils.md'
    - 🚀 Advanced API:
        - 'api/Initialisation.md'
        - 'api/Energy functions.md'
        - 'api/Inference.md'
        - 'api/Gradients.md'
        - 'api/Updates.md'
        - 'api/Analytical tools.md'

copyright: |
  &copy; 2024 <a href="https://github.com/thebuckleylab"  target="_blank" rel="noopener">thebuckleylab</a>