mkdocs.yaml

site_name: "Collaborative Distributed Science Guide"  # Update guide name here
site_description: "A guide to collaborative work (originally for Imageomics), including GitHub and Hugging Face workflows."  # Update description
site_author: "Imageomics Institute"    # Update organization/author name
site_url: "https://Imageomics.github.io/Collaborative-distributed-science-guide/"  # Update your site URL

repo_url: https://github.com/Imageomics/Collaborative-distributed-science-guide  # Update your repository URL
edit_uri: edit/main/docs/

theme:
  name: material
  icon:
    view: material/eye
  logo: logos/Imageomics_ABC.png    # Set your logo
  favicon: logos/Imageomics_ABC.png    # Set your logo or favicon of choice
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference
  features:
    - content.action.view
    - content.code.copy
    - navigation.tabs
    - navigation.tabs.sticky

extra_css:
  - stylesheets/extra.css

extra:
  social:
  # Switch to your socials, more info from MkDocs: 
  # https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#social-links
    - icon: fontawesome/brands/github
      link: https://github.com/Imageomics
    - icon: simple/huggingface
      link: https://huggingface.co/imageomics
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/imageomics-institute
    - icon: fontawesome/brands/bluesky
      link: https://bsky.app/profile/imageomics.bsky.social
    - icon: fontawesome/brands/x-twitter
      link: https://twitter.com/imageomics
    - icon: fontawesome/brands/instagram
      link: https://www.instagram.com/imageomics/
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/@ImageomicsInstitute/videos
    - icon: octicons/link-16
      link: https://imageomics.org

# Add your own copyright notice, but please include the note 
# "This guide was generated from the <a href="https://github.com/Imageomics/Collaborative-distributed-science-guide" target="_blank"><u>Collaborative Distributed Science Guide</u></a>, developed by the <a href="https://imageomics.org" target="_blank"><u>Imageomics Institute</u></a> and the <a href="http://abcresearchcenter.org/" target="_blank"><u>AI and Biodiversity Change (ABC) Global Center</u></a>."
copyright: >
  This work was supported by both the <a href="https://imageomics.org" target="_blank"><u>Imageomics Institute</u></a> and the <a href="http://abcresearchcenter.org/" target="_blank"><u>AI and Biodiversity Change (ABC) Global Center</u></a>. 

  The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240" target="_blank"><u>Award #2118240</u></a> (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning).

  The ABC Global Center is funded by the US National Science Foundation under <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330423&HistoricalAwards=false" target="_blank"><u>Award No. 2330423</u></a> and the Natural Sciences and Engineering Research Council of Canada under <a href="https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=782440" target="_blank"><u>Award No. 585136</u></a>.
  This guide draws on research funded by the Social Sciences and Humanities Research Council.

  Any opinions, findings, conclusions, or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, the Natural Sciences and Engineering Research Council of Canada, or the Social Sciences and Humanities Research Council.

plugins:
  - glightbox
  - macros
  - search

markdown_extensions:
  - admonition
  - attr_list
  - footnotes
  - md_in_html
  - pymdownx.betterem
  - pymdownx.blocks.caption
  - pymdownx.details
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tasklist
  - pymdownx.tilde
  - pymdownx.keys
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - toc:
      permalink: true
      title: 📖 On This Page

nav:
# These are all relative links within the repo, only update if adding or deleting pages
  - Home: index.md
  - GitHub Guide:
      - "Repo Guide": wiki-guide/GitHub-Repo-Guide.md
      - "Workflow": wiki-guide/The-GitHub-Workflow.md
      - "Pull Request Guide": wiki-guide/The-GitHub-Pull-Request-Guide.md
      - "Projects Guide": wiki-guide/Guide-to-GitHub-Projects.md
      - "Branch Protections": wiki-guide/When-to-think-about-branch-protections.md
      - "Two Repo Problem": wiki-guide/Two-Repo-Problem.md
      - "Git Cherry-Pick Guide": wiki-guide/Git-Cherry-Pick-Guide.md
      # May want to personalize (on page as well): Why use the <organization/group> GitHub
      - "Why Use the Organization GitHub": wiki-guide/Why-use-the-organization-GitHub.md
  - Hugging Face Guide:
      - "Repo Guide": wiki-guide/Hugging-Face-Repo-Guide.md
      - "Workflow": wiki-guide/The-Hugging-Face-Workflow.md
      - "Dataset Upload Guide": wiki-guide/The-Hugging-Face-Dataset-Upload-Guide.md
      # May want to personalize (on page as well): Why use the <organization/group> Hugging Face
      - "Why Use the Organization Hugging Face": wiki-guide/Why-use-the-organization-Hugging-Face.md
  - FAIR Guide:
      - "About FAIR Principles": wiki-guide/FAIR-Guide.md
      - "Metadata Checklist": wiki-guide/Metadata-Checklist.md
      - "Code Repo Checklist": wiki-guide/Code-Checklist.md
      - "Data Card Checklist": wiki-guide/Data-Checklist.md
      - "Model Card Checklist": wiki-guide/Model-Checklist.md
      - "DOI Generation": wiki-guide/DOI-Generation.md
  - Templates:
      - "About Templates": wiki-guide/About-Templates.md
      - "Dataset Card Template": wiki-guide/HF_DatasetCard_Template_mkdocs.md
      - "Model Card Template": wiki-guide/HF_ModelCard_Template_mkdocs.md
  - Command Line Cheat Sheet: wiki-guide/Command-Line-Cheat-Sheet.md
  - Code of Conduct: CODE_OF_CONDUCT.md
  - Digital Product Policy: 
      - "About Digital Product Policies": wiki-guide/About-Digital-Product-Policies.md
      - "Release and Licensing Policy": wiki-guide/Digital-products-release-licensing-policy.md
      - "Digital Product Life Cycle": wiki-guide/Digital-Product-Lifecycle.md
  - Other Resources:
      - "Technical Infrastructure": wiki-guide/Technical-Infrastructure.md
      - "Virtual Environments": wiki-guide/Virtual-Environments.md
      - "Helpful Tools": wiki-guide/Helpful-Tools-for-your-Workflow.md
      - "Handling API Keys": wiki-guide/Handling-API-Keys.md
      - "Glossary for Imageomics": wiki-guide/Glossary-for-Imageomics.md