TwinWeaver/mkdocs.yml at main · MendenLab/TwinWeaver · GitHub

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site_name: TwinWeaver
site_description: TwinWeaver is a Python framework for longitudinal Patient Digital Twins using LLMs.
site_url: https://example.com/twinweaver/

# 1. Source Code Link (Adds a nice GitHub icon to the header)
repo_name: TwinWeaver
repo_url: https://github.com/MendenLab/TwinWeaver
edit_uri: edit/main/docs/

extra_css:
  - stylesheets/extra.css

theme:
  name: material
  custom_dir: docs/overrides
  # 2. Custom Logo/Favicon
  icon:
    logo: material/dna
  favicon: images/favicon.png

  features:
    - navigation.tabs           # Top-level tabs
    - navigation.sections       # Sidebar sections
    - navigation.instant        # Instant loading (SPA feel)
    - navigation.tracking       # Scroll tracking
    - navigation.top            # Back to top button
    - content.code.copy         # Copy code button
    - content.code.annotate     # Allow inline code annotations (+)
    - content.tooltips
    - search.suggest
    - search.highlight

  # 3. Light/Dark Mode Toggle
  palette:
    - scheme: default
      primary: slate            # Professional grey/blue tone
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: slate
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  # 4. Modern Typography
  font:
    text: Inter
    code: JetBrains Mono

# 5. Social Links (Footer)
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/MendenLab/TwinWeaver
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/twinweaver/
  analytics:
    provider: google
    property: G-RHFJVCCEDM

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          options:
            docstring_style: numpy
            show_source: true
            show_root_heading: true   # Shows the class/function name in bold
            # Moves arguments out of the header line to a block below
            separate_signature: true
            show_category_heading: true
  - mkdocs-jupyter:
      execute_ignore: ["*"]

markdown_extensions:
  - admonition
  - attr_list                   # Essential for styling images/buttons
  - md_in_html
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.inlinehilite
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.tabbed:
      alternate_style: true
  # 6. Math Support
  - pymdownx.arithmatex:
      generic: true
  # 7. Enhanced Code Blocks (Mermaid + Annotations)
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - toc:
      permalink: true

# 8. MathJax Configuration (Required for Arithmatex)
extra_javascript:
  - javascript/mathjax.js
  - javascript/toc-emoji-remover.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home:
      - index.md
      - Installation: installation.md
      - Tutorials: tutorials.md
      - Quick Start: quickstart.md
      - Framework Overview: framework.md
      - Dataset Format: dataset-format.md
      - Data Splitting: data-splitting.md
      - TTE Probability Inference: tte-inference.md
      - Pro Tips: pro-tips.md
      - API Index: api-index.md
      - Contributing: contributing.md
      - Citation: citation.md
  - Examples:
      - Overview: examples/README.md
      - Data Preparation: examples/01_data_preparation_for_training.ipynb
      - Inference Prompt Prep: examples/02_inference_prompt_preparation.ipynb
      - End-to-End Finetuning: examples/03_end_to_end_llm_finetuning.ipynb
      - Data Preprocessing:
          - Raw Data Preprocessing: examples/data_preprocessing/raw_data_preprocessing.ipynb
      - Advanced:
          - Custom Splitting:
              - Training (Individual Splitters): examples/advanced/custom_splitting/training_individual_splitters.ipynb
              - Training (Custom Split Events): examples/advanced/custom_splitting/training_custom_split_events.ipynb
              - Training (Forecasting QA): examples/advanced/custom_splitting/training_forecasting_qa.ipynb
              - Training (Forecasting-Only Splitter): examples/advanced/custom_splitting/training_forecasting_splitter_only.ipynb
              - Inference (Individual Splitters): examples/advanced/custom_splitting/inference_individual_splitters.md
          - Custom Output:
              - Custom Text Generation: examples/advanced/custom_output/customizing_text_generation.ipynb
              - Custom Summarized Row: examples/advanced/custom_output/custom_summarized_row.ipynb
          - Pretraining:
              - Prepare Pretraining Data: examples/advanced/pretraining/prepare_pretraining_data.md
              - End-to-End Training with Pretrain: examples/advanced/pretraining/end_to_end_llm_training_with_pretrain.ipynb
          - TTE Probability Inference: examples/advanced/tte_inference/tte_probability_inference.ipynb
          - Forecasting Inference: examples/advanced/forecasting_inference/forecasting_vllm_inference.ipynb
      - Integrations:
          - MEDS Import: examples/integrations/meds_data_import.ipynb
      - Hackathon:
          - Overview: examples/hackathon/README.md
          - Data Preparation Challenge: examples/hackathon/01_data_preparation_challenge.ipynb
          - LLM Finetuning Challenge: examples/hackathon/02_llm_finetuning_challenge.ipynb
  - API Reference:
      - Common:
          - Config: reference/common/config.md
          - Data Manager: reference/common/data_manager.md
          - Converter Base: reference/common/converter_base.md
      - Instruction:
          - Converter Instruction: reference/instruction/converter_instruction.md
          - Converter Forecasting: reference/instruction/converter_forecasting.md
          - Converter Forecasting QA: reference/instruction/converter_forecasting_qa.md
          - Converter Events: reference/instruction/converter_events.md
          - Main Data Splitter: reference/instruction/data_splitter.md
          - All Data Splitters: reference/instruction/data_splitters.md
      - Pretrain:
          - Converter Pretrain: reference/pretrain/converter_pretrain.md
      - Utils:
          - MEDS Importer: reference/utils/meds_importer.md
          - Preprocessing Helpers: reference/utils/preprocessing_helpers.md
          - TTE Inference: reference/utils/tte_inference.md
          - Forecasting Inference: reference/utils/forecasting_inference.md