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use artifacts from NCBI directly #4

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jonalm
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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 changed the title WIP use artifacts from NCBI directly use artifacts from NCBI directly 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.

Project.toml Outdated Show resolved Hide resolved
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.

@kescobo kescobo merged commit 5695b95 into BioJulia:main Oct 15, 2024
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kescobo commented Oct 15, 2024

Someone on slack reported an error on Windows (https://julialang.slack.com/archives/CAKKFNYLD/p1728896761497669?thread_ts=1728401460.511029&cid=CAKKFNYLD if you get in before slack eats it), but they were getting an error with the Conda version too, and said it might be their work firewall settings.

Given that windows CI here passes, I'm gonna merge and just see what comes of it.

@jonalm jonalm mentioned this pull request Oct 17, 2024
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2 participants