mkdocs.yml

site_name: GPJax
site_description: The documentation for the GPJax software library.
site_url: https://docs.jaxgaussianprocesses.com/
repo_url: https://github.com/JaxGaussianProcesses/GPJax
repo_name: JaxGaussianProcesses/GPJax

edit_uri: ""

nav:
  - 🏡 Home: index.md
  - Getting started:
    - 🛠️ Installation: installation.md
    - 🎨 Design principles: design.md
    - 🤝 Contributing: contributing.md
    - 🔪 Sharp bits: sharp_bits.md
    - 🌳 GPJax PyTrees: examples/pytrees.md
    - 📎 JAX 101 [External]: https://jax.readthedocs.io/en/latest/jax-101/index.html
  - 💡 Background:
    - Intro to GPs: examples/intro_to_gps.py
    - Intro to Kernels: examples/intro_to_kernels.py
  - 🎓 Tutorials:
    - Regression: examples/regression.py
    - Classification: examples/classification.py
    - Poisson regression: examples/poisson.py
    - Barycentres: examples/barycentres.py
    - Deep kernel learning: examples/deep_kernels.py
    - Graph kernels: examples/graph_kernels.py
    - Sparse GPs: examples/uncollapsed_vi.py
    - Stochastic sparse GPs: examples/collapsed_vi.py
    - Bayesian Optimisation: examples/bayesian_optimisation.py
    - Decision Making: examples/decision_making.py
    - Multi-output GPs for Ocean Modelling: examples/oceanmodelling.py
  - 📖 Guides for customisation:
    - Kernels: examples/constructing_new_kernels.py
    - Likelihoods: examples/likelihoods_guide.py
    - UCI regression: examples/yacht.py
  - 💻 Raw tutorial code: give_me_the_code.md
  - Community:
    - 👥 Code of conduct: CODE_OF_CONDUCT.md
    - 📜 Governance: GOVERNANCE.md
    - 📨 Contact: https://jaxgaussianprocesses.com/contact/
  - 📕 Reference: api/


theme:
  name: material
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.expand
    - navigation.top # Show a back to top button
    - content.code.copy
    - search.suggest # Show search suggestions
    - search.highlight # Highlight search results in results
    - content.code.annotate # Allow individual lines of code to be annotated
  icon:
    repo: fontawesome/brands/github
  logo: _static/favicon.ico
  favicon: _static/favicon.ico

markdown_extensions:
  - admonition
  - pymdownx.details # Enhance admonitions with collapse/expand
  - markdown_katex:
      no_inline_svg: True
      insert_fonts_css: True
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.superfences
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.tabbed
  - toc:
      permalink: ''
      toc_depth: 4
  - footnotes
  # - pymdownx.arithmatex:
  #     generic: true
  - attr_list
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg

plugins:
  - search
  - gen-files:
      scripts:
        - docs/scripts/gen_pages.py  # or any other name or path
        - docs/scripts/notebook_converter.py  # or any other name or path
  - literate-nav:
      nav_file: SUMMARY.md
  - bibtex:
      bib_file: "docs/refs.bib"
      csl_file: "https://raw.githubusercontent.com/citation-style-language/styles/af38aba0e9b08406c8827abfc888e5f3e3fa1d65/journal-of-the-royal-statistical-society.csl"
      cite_inline: true
  - mkdocs-jupyter:
      execute: true
      allow_errors: false
      include: ["examples/*.py"]
      ignore: ["examples/utils.py", "_statch/*.py", "scripts/*.py"]
    # binder: true
    # binder_service_name: "gh"
#     binder_branch: "main"
  - mkdocstrings:
      watch:
        - gpjax
      default_handler: python
      handlers:
        python:
          rendering:
            show_root_heading: true
            show_root_full_path: true
            show_if_no_docstring: true
            show_signature_annotations: true
            show_source: false
            members_order: source  # order methods according to their order of definition in the source code, not alphabetical order
            heading_level: 4
          options:
            inherited_members: true  # Allow looking up inherited methods
            docstring_style: "google"

  - git-authors:
      show_contribution: false
      show_line_count: true
      show_email_address: false
      count_empty_lines: true
      fallback_to_empty: false
      sort_authors_by: contribution
      enabled: true

extra:
  analytics:
    provider: google
    property: G-L15440C0N0

extra_css:
  - stylesheets/extra.css
  - stylesheets/permalinks.css
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css

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
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.js
  - javascripts/katex.js