mkdocs.yml

site_name: LZGraphs
site_url: https://MuteJester.github.io/LZGraphs/
site_description: High-performance LZ76-based graph representations for immune receptor repertoire analysis
site_author: Thomas Konstantinovsky
repo_url: https://github.com/MuteJester/LZGraphs
repo_name: MuteJester/LZGraphs
edit_uri: edit/master/docs/

copyright: Copyright © 2024-2026 Thomas Konstantinovsky

# Internal design specs live under docs/ for convenience but must not be
# published to the public site (they are not in the nav and have no git history).
exclude_docs: |
  superpowers/

theme:
  name: material
  custom_dir: docs/overrides
  logo: images/lzglogo2.png
  favicon: images/lzglogo2.png
  font:
    text: Inter
    code: JetBrains Mono
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: deep purple
      accent: cyan
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: deep purple
      accent: cyan
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.top
    - navigation.indexes
    - navigation.path
    - navigation.footer
    - navigation.instant
    - navigation.instant.prefetch
    - search.suggest
    - search.highlight
    - search.share
    - content.code.copy
    - content.code.annotate
    - content.action.edit
    - content.tabs.link
    - content.tooltips
    - toc.follow
    - announce.dismiss
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil
    annotation: material/plus-circle

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
  - social
  - tags
  - redirects:
      redirect_maps:
        getting-started/first-steps.md: getting-started/core-ideas.md
        getting-started/quickstart.md: getting-started/quickstart-lzgraph.md
  - mkdocs-jupyter:
      execute: false
      include_source: true
  - glightbox
  - git-revision-date-localized:
      enable_creation_date: true
      type: timeago
      fallback_to_build_date: true

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      toc_depth: 3
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
      linenums_style: pymdownx-inline
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.snippets:
      auto_append:
        - docs/.overrides/abbreviations.md
  - 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

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/MuteJester/LZGraphs
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/LZGraphs/
  generator: false
  tags:
    Diversity: diversity
    Simulation: simulation
    Genes: genes
    Construction: construction
    Comparison: comparison
    ML: ml
    CLI: cli
    IO: io
    LZGraph: lzgraph
    FlashBackGraph: flashbackgraph
  analytics:
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/thumb-up-outline
          name: This page was helpful
          data: 1
          note: Thanks for your feedback!
        - icon: material/thumb-down-outline
          name: This page could be improved
          data: 0
          note: Thanks — we'll work on improving this page.

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home: index.md
  - Start Here:
    - getting-started/index.md
    - Install: getting-started/installation.md
    - Core Ideas: getting-started/core-ideas.md
    - Which Graph Should I Use?: getting-started/choose-your-graph.md
    - LZGraph Quickstart: getting-started/quickstart-lzgraph.md
    - FlashBackGraph Quickstart: getting-started/quickstart-flashback.md
  - Learn by Family:
    - tutorials/index.md
    - 'LZGraph: Graph Construction': tutorials/graph-construction.md
    - 'LZGraph: Sequence Analysis': tutorials/sequence-analysis.md
    - 'LZGraph: Diversity Metrics': tutorials/diversity-metrics.md
    - 'FlashBack: Exact Diversity': tutorials/flashback-diversity.md
    - 'FlashBack: Anomaly Detection': tutorials/flashback-anomaly.md
    - 'FlashBack: Personalization & Algebra': tutorials/flashback-algebra.md
    - Examples:
      - examples/index.md
      - 'LZGraph: Getting Started': examples/lzgraph/01_Getting_Started.ipynb
      - 'LZGraph: Analytics & Diversity': examples/lzgraph/02_Analytics_and_Diversity.ipynb
      - 'LZGraph: Advanced Usage': examples/lzgraph/03_Advanced_Usage.ipynb
      - 'FlashBack: Getting Started': examples/flashback/01_Getting_Started.ipynb
      - 'FlashBack: Analytics & Diversity': examples/flashback/02_Analytics_and_Diversity.ipynb
      - 'FlashBack: Advanced Usage': examples/flashback/03_Advanced_Usage.ipynb
      - 'FlashBack: SCALE Anomaly Detection': examples/flashback/04_SCALE_Anomaly_Detection.ipynb
  - How-To Guides:
    - how-to/index.md
    - Prepare Your Data: how-to/data-preparation.md
    - Save & Load Graphs: how-to/serialization.md
    - Generate Sequences: how-to/sequence-generation.md
    - Compare Repertoires: how-to/repertoire-comparison.md
    - Personalize Graphs: how-to/posterior-personalization.md
    - Distribution Analytics: how-to/distribution-analytics.md
    - Graph Algebra: how-to/graph-algebra.md
    - Feature Extraction for ML: how-to/feature-extraction.md
  - Concepts:
    - concepts/index.md
    - LZ76 Algorithm: concepts/lz76-algorithm.md
    - Graph Variants: concepts/graph-types.md
    - FlashBack Exact Model: concepts/flashback-model.md
    - Probability Model: concepts/probability-model.md
    - Distribution Analytics: concepts/distribution-analytics.md
    - vs. IGoR, OLGA, SONIA: concepts/comparison.md
  - Reference:
    - api/index.md
    - LZGraph: api/lzgraph.md
    - FlashBackGraph: api/flashback-graph.md
    - FlashBackGrammar: api/flashback-grammar.md
    - SimulationResult: api/simulation-result.md
    - PgenDistribution: api/pgen-distribution.md
    - Module Functions: api/functions.md
    - CLI Tool: api/cli.md
    - Exceptions: api/exceptions.md
  - Resources:
    - Glossary: resources/glossary.md
    - FAQ: resources/faq.md
    - Benchmarks: resources/benchmarks.md
    - Changelog: resources/changelog.md
    - Citation: resources/citation.md
    - Architecture: architecture/c-reimplementation.md
  - Tags: tags.md