mkdocs.yml

site_name: MPACT
site_description: Documentation for MPACT, a desktop tool for mass-spectrometry / natural-products metabolomics data analysis
repo_url: https://github.com/robertsamples/mpact
edit_uri: edit/main/docs/

theme:
  name: material
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.top
    - navigation.indexes
    - content.code.copy
    - search.suggest

markdown_extensions:
  - admonition
  - tables
  - toc:
      permalink: true
  - pymdownx.highlight
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true

nav:
  - Home: index.md
  - Installation: installation.md
  - Getting Started: getting-started.md
  - User Guide:
      - File Selection: user-guide/file-selection.md
      - Filtering Settings: user-guide/filtering-settings.md
      - Analysis Settings & Plot Feature Sets: user-guide/analysis-settings.md
      - Running an Analysis: user-guide/running-analysis.md
      - Outputs: user-guide/outputs.md
  - Plots & Results:
      - Data Review: plots/data-review.md
      - Group Analysis: plots/group-analysis.md
      - Multivariate Analysis: plots/multivariate.md
      - m/z vs RT: plots/mz-rt.md
      - Mass Defect: plots/mass-defect.md
      - 3D Fold Change: plots/3d.md
      - Volcano Plot: plots/volcano.md
      - Heatmap: plots/heatmap.md
  - Feature Info: feature-info.md
  - Troubleshooting: troubleshooting.md
  - Changelog: changelog.md