How is Biology Research handling new Tech?

>Submit paper on ML algorithm for spatial transcriptomics :marseysnappy:

>One reviewer insists we benchmark it against his two year old methodology with like 2 citations that no one knows or cares about :marseysmug2:

>Since scientists can't make repeatable or documented code the entire thing is hard coded to his one training dataset meaning I have to rewrite it :marseygigaretard:

>Rather then provide a GUIX archive or pack or a docker image they just have a list of pip packages :marseyboardcode:

>they are all so outdated they refuse to install the right version :marseytabletired:

:marseyeyelidpulling: I ofc have to finish this in 30 days while I also have two class projects due in 20 days plus studying for my finals. I love having to do the same work as PHD and post grad students for less pay :marseywagie:

TLDR; !linuxchads !fosstards !biology Despite having cowtools to create instantly deployable exact decency loaders via docker or GUIX scientists can apparently pass unreplicatable and hardcoded code past reviewers. :marseythumbsup:

Pip3 download speeds are prob butt (like 600 kb/s) because there is one gorillion AWS and Azure vms for ML trying to set up at the same time and amazon and Microsoft cant arsed to use their billions of dollars to make their own mirrors so they just leach off FOSS projects

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they just have a list of pip packages

Most research scientists aren't even enlightened enough to do this!

Pip3 download speeds are prob butt (like 600 kb/s)

If you can keep your dependencies managed entirely by Pip (and don't have to shoot yourself by touching Conda), definitely use one of the dependency managers with a lockfile like PDM (best) or Poetry. Installs go like 5-10x faster because you're not fighting dependency resolution at every step, and you have a reference of every version of every dependency in the lockfile. Also works really well if you're building a Docker image.

But yeah you can't truly hate Python until you read researcher code. I'm convinced many of them don't even understand data types; total dynamic typing death please.

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If you want a package manager try uv. It came out recently and blows everything else out of the water for performance and ease of use

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Oh nice, will have to look at uv. They made ruff too, which also blows all of the other linters/formatters out of the water in both performance and usability. The Python Packaging Authority should kill themselves for being outdone by another group of randos for the THIRD time.

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