mkdocs.yml

site_name: Feedbax
site_author: Matt Laporte
site_url: https://docs.lprt.ca/feedbax

repo_url: https://github.com/mlprt/feedbax
repo_name: mlprt/feedbax
edit_uri: ""  # No edit buttons

theme:
  name: material
  features:
    - navigation.sections
    - toc.integrate
    - header.autohide
  custom_dir: docs/_overrides
  icon:
    logo: material/tibia-alt
    # logo: material/arm-flex
    annotation: material/info-twotone
  palette:
    scheme: fbx

# strict: true  # Build fails on warnings

watch:
  - feedbax  # automatically update docs when running `mkdocs serve` and source files change

markdown_extensions:
  - pymdownx.snippets:
      check_paths: true
      base_path: ["docs/embeds/"]
  - pymdownx.arithmatex:  # Render LaTeX via MathJax
      generic: true
  - pymdownx.details  # Enables collapsible admonitions
  - attr_list
  - md_in_html
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.superfences:  # Enables syntax highlighting
      custom_fences:
        - name: plotly
          class: mkdocs-plotly
          format: !!python/name:mkdocs_plotly_plugin.fences.fence_plotly
  - pymdownx.inlinehilite
  - admonition
  - toc:
      toc_depth: 4  # Only show root objects; i.e. no methods, properties...
      permalink: ¤

extra_css:
  - _static/custom.css

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

plugins:
  - plotly:
      template_default: "plotly_white"
      template_slate: "plotly_dark"
  - search
  - mknotebooks:  # Jupyter notebooks
      # write_markdown: true  # Write markdown files for notebooks
      # execute: true
      # allow_errors: true
      # binder: true  # Enable Binder integration
      # binder_service_name: "gh"
      # binder_branch: "main"
      # binder_ui: "lab"
      preamble: docs/notebook_preamble.py
      regex_remove_patterns: ["^###REMOVE_CELL"]
  - mkdocstrings:
      enable_inventory: true
      custom_templates: docs/_templates
      handlers:
          python:
              options:
                  show_root_toc_entry: true
                  heading_level: 4  # Heading level for the object name
                  show_root_heading: true  # Show the object name
                  show_root_full_path: true  # Show the full path of the object
                  show_bases: true
                  # show_symbol_type_toc: true
                  annotations_path: brief
                  # merge_init_into_class: true
                  # separate_signature: true    # This and `merge_init_into_class` go together
                  show_signature_annotations: true
                  # signature_crossrefs: true  # This doesn't appear to do anything
                  docstring_section_style: table
                  filters: [
                      "!^_",
                      "__init__",
                      "__call__",
                      "model_spec",
                      "dynamics_spec",
                  ]  # Exclude private but not dunder methods
                  inherited_members: ["__call__"]
                  show_source: false
                  members_order: source  # Same member ordering as in source code
                  # all_members: true
                  extensions:
                  - griffe_inherited_method_crossrefs


nav:
  - 'index.md'
  - Why JAX?: 'examples/pytrees.ipynb'
  - Top-down view of Feedbax: 'structure.md'
  - Examples:
    - Feedbax 101:
      - 1. Training a pre-built model: 'examples/0_train_simple.ipynb'
      - 2. From automatic to manual: 'examples/1_train.ipynb'
      - 3. Intervening on a model: 'examples/3_intervening.ipynb'
      - 4. Training ensembles of models: 'examples/4_vmap.ipynb'
      - 5. Models with stages: 'examples/5_model_stages.ipynb'
      - 6. Advanced interventions: 'examples/6_intervening_2.ipynb'
      - 7. Designing custom tasks: 'examples/7_custom_tasks.ipynb'
      # - 8. Advanced analyses: 'examples/8_advanced.ipynb'
    - Features:
      - Composable loss functions: 'examples/losses.ipynb'
      - Biomechanical simulations: 'examples/biomechanics.ipynb'
      - Saving and loading: 'examples/saving_and_loading.ipynb'
      - Debugging: 'examples/debugging.ipynb'
      # - Tracking training progress with tensorboard: 'examples/tensorboard.ipynb'
  - API:
    - Prebuilt models: 'api/xabdeef.md'
    - Models:
      - Base classes: 'api/model.md'
      - 'api/staged.md'
      - 'api/intervene.md'
      - 'api/iterate.md'
      - 'api/bodies.md'
      - 'api/channel.md'
      - 'api/networks.md'
      - 'api/mechanics.md'
      - 'api/plant.md'
      - 'api/dynamics.md'
      - 'api/skeleton.md'
      - 'api/muscle.md'
    - 'api/task.md'
    - 'api/loss.md'
    - 'api/trainer.md'
    - 'api/state.md'
    - 'api/tree.md'
    - 'api/serialisation.md'
    - Analysis and visualisation:
      - 'api/plot.md'
      - 'api/dimred.md'