mkdocs.yml

site_name: Neurobagel
theme:
  name: material
  custom_dir: docs/overrides
  features:
  - navigation.footer
  - navigation.tabs
  - navigation.tabs.sticky
  - navigation.indexes
  - navigation.expand
  - content.tabs.link
  - content.code.copy  # allow user to copy a code block's contents to the clipboard
  logo: "imgs/logo/neurobagel_logo.png"
  favicon: "imgs/logo/neurobagel_favicon.png"
  palette:
    primary: deep purple
    accent: amber
  font:
    text: Roboto
    code: Roboto Mono
repo_url: https://github.com/neurobagel/documentation

# Page Navigation
nav:
  - Welcome: "index.md"
  - User guide:
    - "user_guide/index.md"
    - Running cohort queries:
        - Search the public nodes: "user_guide/public_nodes.md"
        - How to use the query tool: "user_guide/query_tool.md"
        - Querying the API directly: "user_guide/api.md"
    - Setting up your own Neurobagel node:
        - Getting started: "user_guide/getting_started.md"
        - Configuring a node: "user_guide/config.md"
        - Maintaining a node: "user_guide/maintaining.md"
    - Annotating your data:
        - Preparing data for annotation: "user_guide/data_prep.md"
        - Annotation tool guide: "user_guide/annotation_tool.md"
        - Generating harmonized subject-level metadata: "user_guide/cli.md"
  - Data models:
    - Harmonized variables: "data_models/variables.md"
    - Augmented BIDS data dictionaries: "data_models/dictionaries.md"
    - Data files for Neurobagel graphs: "data_models/graph_data.md"
    - Naming conventions for terms: "data_models/term_naming_standards.md"
  - Contributing:
    - How to contribute: "contributing/CONTRIBUTING.md"
    - Our team: "contributing/team.md"
  - Getting help: "getting_help.md"
  - Glossary: "glossary.md"
  - Citing Neurobagel: "cite.md"

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - md_in_html  # for annotations
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true 
  - tables
  

plugins:
  - search
  - table-reader
  - yamp:
    # directory within docs dir to add content
      temp_dir: "repos"
      # delete docs/{temp_dir} after build||serve?
      #  default: true
      cleanup: true
      # delete docs/{temp_dir} at the beginning of the
      # mkdocs invocation.
      start_fresh: true
      # declare a list of repositories or directories to add
      # to docs/{temp_dir}
      #   default: []
      repos:
        # the git repository URL to clone
      - url: "https://github.com/neurobagel/recipes"
        # a list of globs to checkout
        # if empty or not provided, the entire repository is cloned
        # default: [ ]
        include: [ "docs/neurobagel_environment_variables.tsv"]
        # the branch of the repository to clone
        branch: "main"
      - url: "https://github.com/neurobagel/neurobagel_examples"
        include: [ "query-tool-results" ]
        branch: "main"
  - include-markdown
  - open-in-new-tab

extra:
  analytics:
    provider: plausible