hbcd-docs-internal/mkdocs.yml at main · DCAN-Labs/hbcd-docs-internal · GitHub

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site_name: HBCD DCC Docs

use_directory_urls: true

theme:
  name: readthedocs
  custom_dir: docs/overrides # for template overrides, used in this case for addition of "Page Last Updated: <DATE>" to pages
  features:
    - toc.integrate
    - navigation.expand
    - toc.follow
    - navigation.sections
    - header.autohide
    - content.code.annotate

markdown_extensions:
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.snippets
  - pymdownx.details
  - attr_list
  - admonition
  - toc:
      permalink: '🔗'

extra_javascript:
  - https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js
  - js/mermaid-init.js
  - js/extra.js
  - https://www.googletagmanager.com/gtag/js?id=G-95CHYYTVHC
  - js/ga.js

extra:
  analytics:
    provider: google
    property: G-95CHYYTVHC

extra_css:
  - css/custom.css
  - css/banners.css
  - css/hide-sidebar.css
  - css/mermaid.css
  - css/tables.css
  - overrides/styles.css # to add styling for date of last update to top of pages
  - https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css
  - https://cdn.jsdelivr.net/npm/bootstrap-icons/font/bootstrap-icons.css
  - css/reduce-righthand-whitespace.css
  - css/qc-wf-banners.css

plugins:
  - search
  - mermaid2:
      arguments:
        startOnLoad: true
        flowchart:
          htmlLabels: true
        theme: base  # "default" or "base"
        themeVariables:
          primaryColor: "#ffffff"
          primaryTextColor: "#000000"
          tertiaryColor: "#f0f0f0"
        layout: elk
  - git-revision-date-localized:
      type: date

docs_dir: docs

nav:
  - HDCC Data Release Framework: overview.md
  - Workflows & SOPs:
    - HDCC Structure: orgcharts.md
    - Quality Control Procedures: workflows/qc.md
    - Data Processing Workflows:
        - Overview: workflows/data-proc-wf.md
        - Tabulated Data: workflows/tab-wf.md
        - File-Based Data: workflows/fb-data-proc-wf.md
        - Clinical Data Validation: workflows/clinical-wf.md
        - Genomics: workflows/genomics.md
    - Release SOP: workflows/release-wf.md
    - MRI Workflows:
        - MR Radiology: workflows/mri/mri-issue-wf.md
        - Post-Processing QC: workflows/mri/mri-postproc-qc.md
  - Standards & Curation:
    - Software & Analytic Standards: standards/software.md
    - Data Curation Procedures: standards/curation.md
  - Beta Release Notes:
    - Exclusions & Filtering: changelog/exclusions.md
    - Known Issues & Pending Updates: changelog/knownissues.md
        # - Current: changelog/knownissues.md
        # - Resolved Issues Archive: changelog/resolved.md
    - Release Notes:
        - Release 2.1 Archive:
            - BR 21.2: changelog/versions/BR21.2.md
            - BR 21.1: changelog/versions/BR21.1.md
            - BR 21.0: changelog/versions/BR21.0.md
        - Release 2.0 Archive:
            - BR 20.2.3: changelog/versions/BR2X/BR20.2.3.md
            - BR 20.2.2: changelog/versions/BR2X/BR20.2.2.md
            - BR 20.2: changelog/versions/BR2X/BR20.2.md
            - BR 20.1: changelog/versions/BR2X/BR20.1.md
            - BR 20.0: changelog/versions/BR2X/BR20.0.md
        - Release 1 Archive:
            - BR 15.2: changelog/versions/BR1X/BR15.2.md
            - BR 15.1: changelog/versions/BR1X/BR15.1.md
            - BR 15.0: changelog/versions/BR1X/BR15.md
            - BR 14.8: changelog/versions/BR1X/BR14.8.md
            - BR 14.7: changelog/versions/BR1X/BR14.7.md
            - BR 14.6: changelog/versions/BR1X/BR14.6.md
            - BR 14.5: changelog/versions/BR1X/BR14.5.md
            - BR 14.0: changelog/versions/BR1X/BR14.md
            - BR 13.0: changelog/versions/BR1X/BR13.md
            - BR 12.0: changelog/versions/BR1X/BR12.md
            - BR 11.0: changelog/versions/BR1X/BR11.md
            - BR 10.0: changelog/versions/BR1X/BR10.md
            - BR 9.0: changelog/versions/BR1X/BR9.md
            - BR 8.0: changelog/versions/BR1X/BR8.md
            - BR 7.5: changelog/versions/BR1X/BR7.5.md
            - BR 7.0: changelog/versions/BR1X/BR7.md
            - BR 6.5: changelog/versions/BR1X/BR6.5.md
            - BR 6.0: changelog/versions/BR1X/BR6.md
            - BR 5.0: changelog/versions/BR1X/BR5.0.md
            - BR 4.0: changelog/versions/BR1X/BR4.0.md
            - BR 3.0: changelog/versions/BR1X/BR3.0.md
            - BR 2.0: changelog/versions/BR1X/BR2.0.md
            - BR 1.0: changelog/versions/BR1X/BR1.0.md
  - Workgroup Instructions:
      - Access BR Data: internal/br-review.md
      - Report Issues: internal/reportissues.md
      - Measure Documentation ("READMEs"): internal/readmes.md
  - Resources:
      - General: resources/index.md
      - HBCD & SCE Governance: resources/hst-sce-governance.md