OptiMHC/mkdocs.yml at main · 5h4ng/OptiMHC · GitHub

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site_name: OptiMHC
site_description: A high-performance rescoring pipeline for immunopeptidomics data to significantly enhance peptide identification performance
site_author: Zixiang Shang
repo_url: https://github.com/5h4ng/OptiMHC
repo_name: 5h4ng/OptiMHC

theme:
  name: material
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - search.suggest
    - search.highlight
    - content.code.copy

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          options:
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            members_order: source
            docstring_style: numpy
            merge_init_into_class: true
            show_if_no_docstring: false

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.tabbed:
      alternate_style: true
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true

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

nav:
  - Home: index.md
  - Getting Started:
    - Installation: getting-started/installation.md
    - Quick Start: getting-started/quickstart.md
  - Tutorial:
    - Overview: tutorial/index.md
    - Examples: tutorial/examples.md
    - Pipeline Workflow: tutorial/workflow.md
    - Features:
      - Overview: tutorial/features/index.md
      - Original Features: tutorial/features/original.md
      - Basic Features: tutorial/features/basic.md
      - Spectral Similarity: tutorial/features/spectral-similarity.md
      - Retention Time Deviation: tutorial/features/rt-deviation.md
      - Antigen Presentation Scores: tutorial/features/antigen-presentation.md
      - PWM Score: tutorial/features/pwm.md
      - Overlapping Peptide Score: tutorial/features/overlapping.md
  - API Reference:
    - Overview: api/index.md
    - Core: api/core.md
    - I/O: api/io.md
    - Feature Generators: api/features.md
    - Rescoring: api/rescore.md
    - Visualization: api/visualization.md
    - CLI: api/cli.md
  - Development:
    - development/index.md