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@mdales mdales commented Jan 30, 2026

This project started out using the experimental "shark" build system, which never reached maturity, and at some point I moved it to using a shell script to run the pipeline. That worked for ad-hoc use, as I could comment out bits I didn't need to run, but as we want to make this more of a CI ran metric for the IUCN team, it needs something more appropriate. To that end I've migrated to using Snakemake, a popular Python data-science pipeline running tool.

This PR:

  • Adds snakemake files required to run the pipeline
  • Removes littlejohn as a dependancy and the scripts that were needed to set it up
  • Removes the now not-needed shell script runner
  • Updates some of the docs

@mdales mdales mentioned this pull request Jan 30, 2026
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2 participants