lab-manual/_quarto.yml at main · UCD-SERG/lab-manual · GitHub

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# affiliations:
#   - id: ucdphs-epi
#     name: Division of Epidemiology, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, United States
#     department: Division of Epidemiology, Department of Public Health Sciences
#     city: Davis
#     state: CA
#     country: United States
#   - id: ucdphs-biostats
#     name: Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, United States
#     department: Division of Biostatistics, Department of Public Health Sciences
#     city: Davis
#     state: CA
#     country: United States

project:
  type: book
  output-dir: docs

book:
  title: "UCD-SeRG Lab Manual"
  # author:
  #   - name: Kristen Aiemjoy
  #     affiliations:
  #       - ref: ucdphs-epi
  #     email: kaiemjoy@health.ucdavis.edu
  #
  #   - name: Ezra Morrison
  #     affiliations:
  #       - ref: ucdphs-biostats
  #     email: demorrison@ucdavis.edu
  date: last-modified
  date-format: "[Last updated:] YYYY-MM-DD"
  repo-url: https://github.com/UCD-SERG/lab-manual
  repo-actions: [edit, source, issue]
  downloads: [pdf, epub, docx]
  chapters:
    - index.qmd
    - culture-and-conduct.qmd
    - communication.qmd
    - reproducibility.qmd
    - code-repositories.qmd
    - coding-practices.qmd
    - coding-style.qmd
    - big-data.qmd
    - data-masking.qmd
    - quarto.qmd
    - github.qmd
    - collaborative-software-development.qmd
    - continuous-integration.qmd
    - unix.qmd
    - reproducible-environments.qmd
    - code-publication.qmd
    - data-publication.qmd
    - slurm.qmd
    - ai-tools.qmd
    - checklists.qmd
    - resources.qmd
    - professional-development.qmd
    - writing.qmd
    - manuscript-preparation.qmd
    - references.qmd
  appendices:
    - appendix-copilot-instructions.qmd
    - appendix-copilot-setup-steps.qmd
    - appendix-document-metadata.qmd
  page-navigation: true

bibliography: [book.bib, packages.bib]

format:
  html:
    theme:
      light: cosmo
      dark: darkly
    css: styles.css
    toc: true
    number-sections: true
    embed-resources: false
    filters:
      - _extensions/preview-highlight.lua
  pdf:
    geometry:
      - top=15mm
      - bottom=20mm
    keep-md: false
    keep-tex: false
    toc: true
    fig-pos: "H"
    hyperrefoptions:
    - bookmarksnumbered=true
    toc-title: Contents
    df-print: tibble
    links-as-notes: true
    documentclass: scrbook
    classoption: [twoside=off]
    shift-heading-level-by: 0
    toc-depth: 2
    number-sections: true
    number-depth: 3
    colorlinks: true
    filters:
      - _extensions/chapter-pagebreak.lua
  docx:
    toc: false
    number-sections: true
    highlight-style: github
    filters:
      - _extensions/chapter-pagebreak.lua
  epub:
    toc: true
    number-sections: true

editor: source