_quarto-shared-defaults.yml

# Shared defaults for all Quarto configs in this project
# =========================================================
# These settings are automatically applied to all paper/site configs
# by the quarto_config_sync.py generator module.
#
# Per-site overrides are specified in each _quarto-*.yml file.
# The sync process merges: DEFAULTS + PER-SITE OVERRIDES
#
# DO NOT EDIT per-site configs for shared settings - edit THIS file instead!
# Then run: python scripts/generate-everything-parameters-variables-calculations-references.py

# Author information (shared across all papers)
author:
  - name: Mike P. Sinn
    email: m@warondisease.org
    orcid: 0009-0006-0212-1094
    affiliations:
      - name: "Institute for Accelerated Medicine"
        url: https://acceleratedmedicine.org

# Environment profiles
profiles:
  default:
    dotenv:
      allowEmptyValues: true

# Execution settings
execute:
  fig-path: "knowledge/figures/"
  cache: false
  freeze: auto
  daemon: 300
  daemon-restart: false
  env:
    PYTHONPATH: "."

# Jupyter kernel (shared virtual environment)
jupyter: dih-project-kernel

# Bibliography (single source of truth)
bibliography: references.bib
csl: nature-annotated.csl

# Language settings (remove "Appendix" prefix)
language:
  crossref-apx-prefix: ""
  section-title-appendices: ""

# Shared metadata (author, legal, contact)
metadata:
  # Author identification
  creator: "Mike P. Sinn"
  orcid: "0009-0006-0212-1094"
  orcid-url: "https://orcid.org/0009-0006-0212-1094"
  primary-author: "Mike P. Sinn"
  byline: "Mike P. Sinn"
  human-author: "Mike P. Sinn"

  # Contact information
  author-email: "mike@warondisease.org"
  author-url: "https://mikesinn.com"
  author-website: "https://mikesinn.com"
  contact: "mike@warondisease.org"

  # Academic profiles
  github-profile: "https://github.com/mikepsinn"
  google-scholar: "https://scholar.google.com/citations?user=RjDd_qcAAAAJ"
  # researchgate: ""    # Add if available

  # Social profiles
  linkedin: "https://www.linkedin.com/in/mikesinn"
  youtube: "https://www.youtube.com/%40WarOnDisease"
  # bluesky: ""         # Add if available

  # Language
  language: "en-US"

  # Version (for working drafts)
  version: "0.9"
  edition: "Working Draft"

  # Copyright and licensing
  copyright: "© 2025 Mike P. Sinn"
  copyright-year: "2025"
  license: "CC BY-NC 4.0"
  license-url: "https://creativecommons.org/licenses/by-nc/4.0/"
  rights: "Creative Commons Attribution-NonCommercial 4.0 International License"

  # Publisher
  publisher: "Institute for Accelerated Medicine"
  publisher-url: "https://acceleratedmedicine.org"
  publisher-name: "Mike P. Sinn"
  publisher-email: "mike@warondisease.org"

  # Repository (default - can be overridden per project)
  repo-url: "https://github.com/wishonia/earth-optimization-protocol"
  issue-url: "https://github.com/wishonia/earth-optimization-protocol/issues"
  source-url: "https://github.com/wishonia/earth-optimization-protocol"

  # Geographic coverage
  geographic-coverage: "Global"

  # Format metadata
  format: "Working Paper"
  type: "Academic"
  medium: "Digital"

  # Social media
  twitter-site: "https://x.com/warondisease"
  twitter-creator: "https://x.com/warondisease"
  vote-url: "https://WarOnDisease.org"

  # Open Graph
  open-graph: true

# External links (single source of truth for footer, links page, etc.)
# Generated into: knowledge/links.qmd, generated-footer.html
# Run: npm run generate:everything
links:
  follow:
    - label: "YouTube"
      url: "https://www.youtube.com/%40WarOnDisease?sub_confirmation=1"
      subtitle: "\\@WarOnDisease"
      icon: "fa-brands fa-youtube"
      footer-label: "▶ YouTube"
    - label: "X / Twitter"
      url: "https://x.com/warondisease"
      subtitle: "\\@warondisease"
      icon: "fa-brands fa-x-twitter"
      footer-label: "𝕏 / Twitter"
    - label: "LinkedIn"
      url: "https://www.linkedin.com/in/mikesinn"
      subtitle: "Mike P. Sinn"
      icon: "fa-brands fa-linkedin"
    - label: "GitHub"
      url: "https://github.com/wishonia/earth-optimization-protocol"
      subtitle: "Source code, data, and all papers"
      icon: "fa-brands fa-github"
    - label: "Google Scholar"
      url: "https://scholar.google.com/citations?user=RjDd_qcAAAAJ"
      subtitle: "Publications"
      icon: "fa-brands fa-google-scholar"
    - label: "ORCID"
      url: "https://orcid.org/0009-0006-0212-1094"
      subtitle: "0009-0006-0212-1094"
      icon: "fa-brands fa-orcid"
  action:
    - label: "Vote"
      url: "https://WarOnDisease.org"
      subtitle: "15 seconds. 38 lives saved."
      icon: "fa-solid fa-check-to-slot"
      primary: true
  support:
    - label: "Support the War on Disease"
      url: "https://github.com/sponsors/wishonia"
      subtitle: "Fund the mission to end war and disease"
      icon: "fa-solid fa-heart"
      primary: true

  # Academic statements (for journal submissions)
  funding: "No funding was received. The author notes the irony of writing extensively about optimal resource allocation while being, himself, sub-optimally resourced."
  data-availability: "All data and code used in this analysis are publicly available at https://github.com/wishonia/earth-optimization-protocol"
  coi-statement: "The author declares no competing interests, beyond a preference for being alive and for arithmetic, which may bias conclusions toward 'fewer people should die' and 'money should be spent on things that work.'"
  ethics-statement: "This research did not involve human experimentation. The policies it examines, however, arguably do."

# HTML format defaults (for papers/websites)
format:
  html:
    lightbox: auto
    theme:
      - cosmo
    filters:
      - assets/filters/live-version-note.lua
    mermaid:
      theme: neutral
    echo: false
    toc: true
    toc-depth: 3
    # Citation features
    link-citations: true    # Make citations clickable links to references
    citation-hover: true    # Show citation preview on hover
    # UX enhancements
    smooth-scroll: true     # Smooth scrolling for anchor links
    code-fold: true         # Collapsible code blocks (show/hide)
    code-tools: false       # Disable "Code" button in navbar
    # reader-mode: true     # Distraction-free reading (disabled - breaks some layouts)
    css:
      - styles.css
      - economics-overrides.css
    include-before-body:
      - file: assets/html/page-loader.html
    include-after-body:
      - file: assets/html/site-enhancements-loader.html
    include-in-footer:
      - file: assets/html/generated-footer.html
    # Note: include-in-header has per-site icons, so not included here

  pdf:
    documentclass: article
    institute: "Institute for Accelerated Medicine"
    filters:
      - assets/filters/live-version-note.lua
    echo: false
    toc: true
    toc-depth: 3
    colorlinks: true
    link-citations: true
    include-in-header:
      - callout-bw.tex
      - institute-header.tex
    geometry:
      - top=1in
      - bottom=1in
      - left=1in
      - right=1in
    fontsize: 11pt
    date: ""