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use artifacts from NCBI directly #4

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@jonalm jonalm commented Oct 11, 2024

add Artifact.toml generating script and Artifact.toml for blast 2.16.0

@jonalm jonalm mentioned this pull request Oct 11, 2024
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@jonalm jonalm changed the title WIP use artifacts from NCBI directly use artifacts from NCBI directly Oct 11, 2024
kescobo
kescobo reviewed Oct 11, 2024
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I agree this is nicer than using Conda - thanks for putting in the effort!

Just need to address the artifacts version thing - since it's a stdlib, I actually don't think it needs compat, but if you keep it, you need to relax the constraint a bit.

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Artifacts.toml
Comment on lines +9 to +12
[[ncbi-blast]]
arch = "x86_64"
git-tree-sha1 = "690abc170201bc029d0e7386da0791d7a76d98ff"
os = "macos"
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Is this valid TOML? looks like it would overwrite the entries above...

Though I assume this was auto-generated by Artifacts.jl, so maybe I'm misunderstanding

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Yeah, it is not obvious, but the double brackets is toml syntax for "array of tables" https://toml.io/en/v1.0.0#array-of-tables

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kescobo commented Oct 11, 2024

As discussed on Slack, using a JLL is still better, but I'd still accept this as an incremental improvement over Conda

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jonalm commented Oct 11, 2024

What system are you on @kescobo, would be nice to test on windows? Maybe the CI supports that?

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kescobo commented Oct 11, 2024

There is definitely a way to add Windows to CI, might have to find another package to copy from.

I use Linux myself, but agree it would be nice to check

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jonalm commented Oct 11, 2024

I added some options to the github workflow, but don't know if I got it right. In any case, it looks like you need to approve running the workflows.

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