mkdocs.yml

site_name: 'ESIIL Postdoctoral Researcher OASIS'
site_description: 'Central resource for ESIIL postdoctoral researchers'
site_author: Rob Ramos
site_url: https://cu-esiil.github.io/biotic_niche_modeling/

# Repository
repo_name: biotic_niche_modeling
repo_url: https://github.com/CU-ESIIL/biotic_niche_modeling
edit_uri: edit/main/docs/
# Copyright
copyright: 'Copyright © 2023 University of Colorado Boulder'

# Page tree
nav:
  - Home: index.md
  - Meeting notes:
       - meetings/index.md  
  - Resources:
       - Code of Conduct: resources/code-of-conduct.md
       - Participant agreement: resources/participant_agreement.md
       - R and Python bilingualism: resources/bilingualism_md.md
       - STAC: resources/stac_mount_save.md
       - Sentinal 2 STAC example: resources/Pull_Sentinal2_l2_data.md
       - Markdown: resources/markdown_basics.md
       - Cyverse basics: resources/cyverse_basics.md
       - Github basics: resources/github_basics.md
       - Cyverse hacks: resources/cyverse_hacks.md
       - Docker: resources/docker_basics.md
       - Working groups: resources/working_groups_and_postdocs.md
  - Notes:
       - OASIS orientation: resources/pre_meeting_notes.md
  - Code documentation:
       - Data processing: resources/data_processing.md
       - Data analysis: resources/data_analysis.md
       - Visualizations: resources/visualizations.md 
  - Manuscript drafts:
       - Manuscript: resources/manuscript.md
  - References:
       - Notes from readings: resources/notes_from_readings.md
       - Citations: resources/citations.md

# Configuration
theme:
  highlightjs: true
  name: material
  font:
    text: 'Open Sans'
    code: 'Roboto Mono'
  logo: 'assets/esiil_content/ESIIL_logo.png'
  favicon: 'assets/esiil_content/favicon.ico'
  # setting features for the navigation tab
  features:
    - navigation.sections
    - navigation.instant
    - navigation.tracking
    - navigation.indexes
    - navigation.top
    - toc.integrate
    - toc.follow
    - content.code.copy
  # Default values, taken from mkdocs_theme.yml
  language: en
  palette:
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: white)"
      primary: 'white'
      toggle:
        icon: material/weather-night
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/weather-sunny
        name: Switch to system preference

# Options
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/cu-esiil/

extra_css:
  - stylesheets/extra.css

plugins:
  - search
  - mkdocstrings
  - git-revision-date
  - mkdocs-jupyter:
      include_source: true
      ignore_h1_titles: true
  - blog:
      blog_dir: meetings
      post_dir: meetings/notes
      archive: false
      categories: false

markdown_extensions:
  - admonition
  - def_list
  - footnotes
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem
  - pymdownx.caret
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji 
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.snippets:
      base_path:
        - docs
        - README.md
      check_paths: true
  - pymdownx.tasklist:
      custom_checkbox: true

extra_javascript:
  - javascripts/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js