pdiakumis
commented
3 years ago This is a nice write-up of issues with reproducibility and upgradability of conda environments (suggestion is to use conda-lock): https://pythonspeed.com/articles/conda-dependency-management/
To address (3) in https://github.com/populationgenomics/team-docs/blob/main/reproducible_analyses.md ("Pin all dependencies of your code to a specific version"), it would be great to have a linter that works with our standard Conda / R environment package specifications. There's likely already something that we could reuse.