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PUBLICATIONS_MAINTENANCE.md

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Publications Maintenance Notes

This repo uses an older Hugo/theme setup. For publications updates, a few gotchas needed fixing:

  • rmarkdown::render() default output creates a full standalone HTML page and breaks Hugo page styling. Use output_format = "blogdown::html_page" for content/publications/index.Rmd.
  • Publications are now rendered directly from the bib file into year-grouped lists with custom numbering (earliest paper is number 1).
  • bibtex::read.bib() can ignore malformed @article entries missing required fields (e.g. journal), so updates rely on raw bib parsing.
  • Some preprint/publisher records in natverse-papers.bib needed journal backfilling:
    • DOI starts with 10.1101/ -> journal={bioRxiv}
    • DOI starts with 10.7554/eLife -> journal={eLife}

One-command maintenance

Run:

Rscript scripts/update_publications.R

This script will:

  1. patch missing journal for the DOI rules above,
  2. sort bib entries by year in content/publications/natverse-papers.bib,
  3. render grouped publications in content/publications/index.html with blogdown::html_page.