mkdocs.yml

site_name: Neurobagel Developer Documentation
site_description: Internal docs on topics relevant for developing and maintaining Neurobagel
theme:
  name: material
  features:
    - navigation.footer
    - navigation.tabs
  palette:
    primary: cyan
    accent: deep purple
  logo: "assets/images/logo/neurobagel_logo.png"
  favicon: "assets/images/logo/neurobagel_favicon.png"
repo_url: https://github.com/neurobagel/dev-docs

nav:
  - Home: "index.md"
  - "How we work":
      - "Process": "sections/How we work.md"
      - "Release": "sections/Neurobagel Release process.md"
      - "Code of Conduct": "sections/Neurobagel Code of Conduct.md"
  - Tools:
      - "Query tool": "sections/Query Tool.md"
  - Deployment:
      - "PATs": "sections/Neurobagel PATs.md"
      - "Compatibility": "sections/Version compatibility.md"
      - "Dockerized NGINX": "sections/Dockerized NGINX deployment.md"
      - "Add public key for users": "sections/Setting up SSH keys.md"
      - "Docker": "sections/Docker.md"
      - "Old Stardog setup": "sections/Legacy Stardog graph backend deployment instructions.md"
      - "API": "sections/API.md"
      - "APache Jena deploy": "sections/Apache Jena Fuseki Deployment.md"
  - "Concepts":
      - "Security": "sections/Keycloak.md"
      - "OAuth": "sections/OAuth _ OIDC dump.md"
      - "Cypress Vue testing": "sections/Cypress Vue Testing.md"
      - "Cypress snippets": "sections/Cypress Snippets.md"
      - "Cypress Tasks": "sections/Cypress Tasks.md"
  - "MISC":
      - "HC query issues": "sections/Troubleshooting erroneous HC_Diagnosis query results.md"
      - "vGPU issues": "sections/Fabrique (vGPU prep and other issues).md"
      - "Git tricks": "sections/Git Tricks.md"
      - "MNI node issues": "sections/BIC node federation.md"
      - "Vite tricks": "sections/Vite tricks.md"
      - "Vue JS devtools": "sections/Tools.md"
      - "Nuxt tricks": "sections/Nuxt Tricks.md"
      - "Neurobagel data model limitations": "sections/Limitations of Neurobagel data model.md"
      - "CSS" : "CSS.md"


markdown_extensions:
  - admonition
  - pymdownx.magiclink