SAXSShell/mkdocs.yml at main · KWWyatt/SAXSShell · GitHub

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site_name: SAXSShell
site_description: >-
  Workflow-oriented documentation for SAXSShell, focused on comparing
  molecular-dynamics-derived solvation structures against small-angle X-ray
  scattering data.
site_url: https://kewh5868.github.io/SAXSShell/
repo_url: https://github.com/kewh5868/SAXSShell
repo_name: kewh5868/SAXSShell

theme:
  name: material
  logo: source/img/saxshell_icon.svg
  favicon: source/img/saxshell_favicon.png
  features:
    - navigation.sections
    - navigation.expand
    - navigation.top
    - navigation.path
    - content.code.copy
    - search.suggest
    - search.highlight
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: blue grey
      accent: blue
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: blue grey
      accent: blue
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode

plugins:
  - search

hooks:
  - docs/hooks.py

markdown_extensions:
  - admonition
  - attr_list
  - def_list
  - footnotes
  - tables
  - pymdownx.arithmatex:
      generic: true
  - toc:
      permalink: true
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: 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
      - Quickstart: getting-started/quickstart.md
      - Project Setup: getting-started/project-setup.md
  - User Guide:
      - Main UI Workflow Elements:
          - GUI Overview: user-guide/gui-overview.md
          - Project Configuration: user-guide/project-configuration.md
          - Template System: user-guide/template-system.md
          - Pre-loaded SAXS Models: user-guide/preloaded-saxs-models.md
          - SAXS Contrast Mode: user-guide/saxs-contrast-mode.md
          - SAXS Prefit: user-guide/saxs-prefit.md
          - LMFit Workflow: user-guide/lmfit-workflow.md
          - pyDREAM Workflow: user-guide/pydream-workflow.md
          - Results and Export: user-guide/results-and-export.md
      - Supporting Applications:
          - MD Extraction:
              - MD Extraction and Cluster Preparation: user-guide/cluster-extraction.md
              - XYZ to PDB Conversion: user-guide/xyz2pdb-conversion.md
          - Structure Analysis:
              - Bond Analysis: user-guide/bond-analysis.md
              - Cluster Dynamics: user-guide/cluster-dynamics-ml.md
          - PDF:
              - PDF Calculation: user-guide/pdf-calculation.md
              - fullrmc Packmol Docker Link: user-guide/fullrmc-packmol-docker.md
          - Visualization:
              - Blender Structure Renderer: user-guide/blender-structure-renderer.md
          - SAXS Calculation Preview:
              - SAXS Contrast Mode: user-guide/saxs-contrast-mode.md
              - 1D Born Approximation (Average): user-guide/electron-density-mapping.md
              - 3D FFT Born Approximation: user-guide/fft-born-approximation.md
          - X-ray Toolkit:
              - X-ray Toolkit: user-guide/xray-toolkit.md
          - (beta):
              - Representative Structure CLI: user-guide/representative-structure-cli.md
              - Cluster Dynamics Time-Binned: user-guide/cluster-dynamics.md
              - Debye-Waller Analysis: user-guide/debye-waller-analysis.md
  - Tutorials:
      - Example Workflow: tutorials/example-workflow.md
      - MD to SAXS Pipeline: tutorials/md-to-saxs-pipeline.md
  - API:
      - Overview: api/overview.md
  - Development:
      - Repo Structure: development/repo-structure.md
      - SAXS Contrast Mode: development/saxs-contrast-mode.md
      - Contributing: development/contributing.md