mkdocs.yml

site_name: Diffid
site_description: High-performance time-series inference and optimisation toolkit with Rust core and ergonomic Python bindings
site_author: Brady Planden
site_url: https://diffid.bradyplanden.com
repo_name: bradyplanden/diffid
repo_url: https://github.com/bradyplanden/diffid
edit_uri: edit/main/docs/

theme:
  name: material
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: blue
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: blue
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Roboto
    code: Roboto Mono
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.expand
    - navigation.path
    - navigation.indexes
    - navigation.top
    - navigation.footer
    - search.suggest
    - search.highlight
    - search.share
    - toc.follow
    - content.code.copy
    - content.code.annotate
    - content.tabs.link

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
  - git-revision-date-localized:
      enable_creation_date: true
      type: date
      fallback_to_build_date: true
      strict: false
  - minify:
      minify_html: true
  - mkdocstrings:
      handlers:
        python:
          paths: [python/src]
          options:
            docstring_style: numpy
            docstring_section_style: table
            members_order: source
            show_source: false
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            signature_crossrefs: true
            separate_signature: true
            line_length: 80
            merge_init_into_class: true
            docstring_options:
              ignore_init_summary: true
  - mkdocs-jupyter:
      include_source: true
      execute: false
      allow_errors: false
      kernel_name: python3

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
      toc_depth: 3
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde
  - pymdownx.snippets
  - pymdownx.emoji:
        emoji_index: !!python/name:material.extensions.emoji.twemoji
        emoji_generator: !!python/name:material.extensions.emoji.to_svg

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/bradyplanden/diffid
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/diffid/
  version:
    provider: mike
    default: latest

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

nav:
  - Home: index.md
  - Getting Started:
      - getting-started/index.md
      - Installation: getting-started/installation.md
      - 5-Minute Quickstart: getting-started/quickstart.md
      - First ODE Fit: getting-started/first-ode-fit.md
      - Core Concepts: getting-started/concepts.md
  - Tutorials:
      - tutorials/index.md
      - Notebooks:
          - Optimisation Basics: tutorials/notebooks/optimisation_basics.ipynb
          - ODE Fitting with DiffSL: tutorials/notebooks/ode_fitting_diffsol.ipynb
          - Parameter Uncertainty: tutorials/notebooks/parameter_uncertainty.ipynb
          - Model Comparison: tutorials/notebooks/model_comparison.ipynb
          - Predator-Prey Models: tutorials/notebooks/advanced_predator_prey.ipynb
          - Parallel Optimisation: tutorials/notebooks/parallel_optimisation.ipynb
          - Advanced Cost Functions: tutorials/notebooks/advanced_cost_functions.ipynb
  - User Guides:
      - guides/index.md
      - Choosing an Optimiser: guides/choosing-optimiser.md
      - Tuning Optimisers: guides/tuning-optimisers.md
      - Choosing a Sampler: guides/choosing-sampler.md
      - Cost Metrics: guides/cost-metrics.md
      - DiffSL Backend: guides/diffsol-backend.md
      - Parallel Execution: guides/parallel-execution.md
      - Custom Solvers: guides/custom-solvers.md
      - Troubleshooting: guides/troubleshooting.md
  - Algorithms:
      - algorithms/index.md
      - Optimisers:
          - Nelder-Mead: algorithms/optimisers/nelder-mead.md
          - CMA-ES: algorithms/optimisers/cmaes.md
          - Adam: algorithms/optimisers/adam.md
      - Samplers:
          - Metropolis-Hastings: algorithms/samplers/metropolis-hastings.md
          - Dynamic Nested Sampling: algorithms/samplers/dynamic-nested-sampling.md
  - API Reference:
      - api-reference/index.md
      - Python:
          - Builders: api-reference/python/builders.md
          - Optimisers: api-reference/python/optimisers.md
          - Samplers: api-reference/python/samplers.md
          - Cost Metrics: api-reference/python/cost-metrics.md
          - Results: api-reference/python/results.md
      - Rust:
          - api-reference/rust/index.md
  - Examples:
      - examples/gallery.md
  - Development:
      - development/index.md
      - Contributing: development/contributing.md
      - Architecture: development/architecture.md
  - Changelog: changelog.md

strict: true  # Fail on warnings

watch:
  - python/src/diffid
  - docs