handbook/mkdocs.yml at master · dbic/handbook · GitHub

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site_name: Dartmouth Brain Imaging Center Handbook
site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://dbic-handbook.readthedocs.io/en/latest/']
site_description: Documentation for users of the Dartmouth Brain Imaging Center
repo_url: https://github.com/dbic/handbook
repo_name: dbic/handbook
copyright: See the source code and discussion pages on <a href="https://github.com/dbic/handbook">GitHub</a>.
theme:
    name: material
    favicon: images/favicon.png
    logo: images/logo.png
    features:
        - navigation.footer
        - content.code.copy
    palette:
        - media: "(prefers-color-scheme: light)"
          scheme: default
          primary: light green
          accent: light green
          toggle:
              icon: material/weather-night
              name: Switch to dark mode
        - media: "(prefers-color-scheme: dark)"
          scheme: slate
          primary: light green
          accent: light green
          toggle:
              icon: material/weather-sunny
              name: Switch to light mode
markdown_extensions:
    - pymdownx.highlight:
        anchor_linenums: true
    - pymdownx.inlinehilite
    - toc:
        anchorlink: true
    - pymdownx.superfences:
        custom_fences:
          - name: mermaid
            class: mermaid
            format: !!python/name:pymdownx.superfences.fence_code_format
plugins:
    # Downloads and self-hosts the mermaid bundle and web fonts that Material
    # would otherwise pull from unpkg.com / Google Fonts at page-load time.
    - privacy:
        # A failed fetch is a warning, and --strict / fail_on_warning turn that
        # into a failed build, so keep third-party decoration out of the build's
        # critical path: these appear on one page and stay ordinary remote
        # images, as they were before self-hosting was enabled.
        assets_exclude:
          - img.shields.io/*
          - i.imgur.com/*
    - search
validation:
    nav:
        omitted_files: warn
        not_found: warn
    links:
        not_found: warn
        anchors: warn
        unrecognized_links: warn
docs_dir: 'src'
use_directory_urls: false
nav:
    - Home: index.md
    - Fundamentals:
      - Shell: basics/shell.md
      - Containers: basics/containers.md
      - DataLad: basics/datalad.md
      - PyBIDS: todo/pybids.md
    - A new study:
        - Policies & procedures: https://www.dartmouth.edu/dbic/
        - JEDCap: todo/jedcap.md
        - Experimental design: todo/experimental-design.md
        - Pre-registration: todo/pre-registration.md
    - Stimuli/Behavioral: stimuli.md
    - MRI:
        - Overview: mri/overview.md
        - ReproIn naming convention: mri/reproin.md
        - ReproIn naming helper: https://npacore.github.io/reproin-namer/#
        - Siemens Console Walkthrough: mri/walkthrough-1.md
        - Peripherals: mri/peripherals.md
        - MR Safety: mri/safety.md
        - Data access: mri/dataaccess.md
        - Data processing:
            - QA: todo/qa.md
            - Preprocessing: todo/preprocessing.md
            - Analysis: todo/analysis.md
    - EEG: todo/eeg.md
    - MRS: todo/mrs.md
    - Computing resources:
      - Discovery HPC: computing/discovery.md
      - Jupyter on Discovery: computing/discovery-jupyter.md
      - Passwordless SSH: computing/kerberos.md
      - Troubleshooting: computing/troubleshooting.md
    - Publishing:
        - Datasets: todo/datasets.md
        - Data papers: publishing/data-paper.md
        - Study papers: todo/study-papers.md
    - Appendix:
        - Contributors: 99-appendices/01-contributors.md
        - Licenses: 99-appendices/02-licenses.md
    - Additional resources: additional_resources.md
    - Changelog: CHANGES.md
    - Contributing: CONTRIBUTING.md