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Introduction to Ancient Metagenomics Book

DOI

This is the source material for the Introduction to Ancient Metagenomics text book developed for the SPAAM Summer School: Introduction to Ancient Metagenomics.

Development notes

This text book has been developed as a Quarto Book, allowing for both website and PDF formats.

If running locally, I highly recommend installing VS Code (or your preferred text editor/IDE) and the corresponding Quarto extension for development. This allows rendering prior to pushing to GitHub, and debugging of any issues of the website view. Make sure you also install all the dependincy requirements as described in the Dockerfile

Locally

If adding a new section chapter:

  1. Clone this repository

  2. Make a new branch e.g. git switch -c new-chapter

  3. Make a new .qmd file in the root directory

  4. Images for the chapter should go into assets/images/chapters/

    • Do not place in docs/assets/images/chapters/!

  5. References in BibTex for the chapter should go a references.bib file into assets/references/chapters/<chapter>

  6. Add the .qmd file to the _quarto.yml config file in the chapters: scope

  7. Render the book the extensions' Quarto: Render Book command, or run the following while inside the reposiroty directory

    quarto preview . --render all --no-browser --no-watch-inputs

  8. Commit, push to GitHub, and open a PR against the main branch [^2]

Warning

Only push .qmd, images, .bib files etc! Do not push html json files etc., from the rendering!

General tips:

  • Use the native markdown syntax for images (![](assets/images/chapters/<your_image>.png))
  • For note blocks see the Quarto docs

Release procedure

Before

  • Check for any major TODOs in the book
  • Make sure authors updated
    • On authors.qmd
    • In citations.cff
    • In citing-this-book.qmd (set DOI to root DOI)
  • Make sure cover images updated
    • Stating (Edition 202X)
    • Update contributors on jacket back
  • Make sure all software installation instructions/conda yaml files are up to date
  • Make sure all data files uploaded, and if necessary Zenodo DOI updated
    • Update from previous upload
    • Make sure to bump year to title
    • Version system: YYYY.point release (2024.0, 2024.1)
    • Make sure to update authors if required
  • Update Zenodo DOI for in each chapter DOI
  • Make sure footnotes year fixed everywhere (_quarto.yml)
  • Update release date in citations.cff

After

  • In citing-this-book.qmd set DOI to release DOI and in CITATIONS.cff

Notes
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