synth-nmr/mkdocs.yml at master · elkins-lab/synth-nmr · GitHub

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site_name: synth-nmr
site_url: https://elkins-lab.github.io/synth-nmr
repo_url: https://github.com/elkins/synth-nmr
repo_name: elkins/synth-nmr
site_description: NMR spectroscopy calculations for protein structures
site_author: George Elkins
copyright: Copyright &copy; 2026 George Elkins

theme:
  name: material
  custom_dir: docs/overrides
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.expand
    - navigation.top
    - navigation.footer
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: deep purple
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: teal
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

# Enhanced navigation structure
nav:
  - Home: index.md
  - Getting Started:
    - Installation & CLI: getting_started.md
  - Scientific Background:
    - Introduction & Theory: science/index.md
    - Chemical Shifts: science/chemical_shifts.md
    - SHIFTX2 Integration: science/shiftx2.md
    - Relaxation (Dynamics): science/relaxation.md
    - NOEs (Distances): science/noes.md
    - J-Couplings (Dihedrals): science/j_couplings.md
    - RDCs (Orientations): science/rdcs.md
    - Ensemble NMR & MD: science/trajectory.md
  - Tutorials:
    - Basic Predictions: tutorials/basic_nmr_prediction.ipynb
    - Advanced Observables: tutorials/advanced_observables.ipynb
    - Relaxation Analysis: tutorials/relaxation_analysis.ipynb
    - Ensemble NMR Analysis: tutorials/ensemble_nmr_analysis.ipynb
  - API Reference:
    - Overview: api/index.md
    - Chemical Shifts: api/chemical_shifts.md
    - Relaxation: api/relaxation.md
    - NOEs: api/nmr.md
    - J-Coupling: api/j_coupling.md
    - RDCs: api/rdc.md
    - Data Pipeline: api/data_pipeline.md
    - NEF IO: api/nef_io.md
    - Neural Shifts: api/neural_shifts.md
    - Trajectory: api/trajectory.md
    - Validation: api/validation.md
    - Structure Utils: api/structure_utils.md
  - Developer Guide:
    - Overview: development/index.md
    - Architecture: development/architecture.md
    - Testing & CI: development/testing.md
    - Release Process: development/release_process.md

# Plugins
plugins:
  - mkdocs-jupyter:
      theme: material
      include_source: true
      execute: false
      allow_errors: false
      kernel_name: python3
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
  - mkdocstrings:
      handlers:
        python:
          paths: ["."]
          options:
            docstring_style: google
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            members_order: source
            group_by_category: true
            show_category_heading: true
            show_if_no_docstring: false
            inherited_members: false
            filters:
              - "!^_"  # Exclude private members

# Markdown extensions
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets:
      base_path: [docs]
  - pymdownx.superfences:
      custom_fences:
        - name: math
          class: arithmatex
          format: !!python/name:pymdownx.arithmatex.fence_mathjax_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.arithmatex:
      generic: true
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - def_list
  - footnotes
  - tables
  - abbr
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

# Extra javascript for MathJax
extra_javascript:
  - javascripts/mathjax.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js