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Update pysam to 0.22.0 #26

Merged
merged 5 commits into from
Nov 29, 2023
Merged

Update pysam to 0.22.0 #26

merged 5 commits into from
Nov 29, 2023

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natefoo
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@natefoo natefoo commented Nov 29, 2023

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@natefoo
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natefoo commented Nov 29, 2023

htslib/hts_probe_cc.sh is in the repo but not the sdist, so the sdist can't be built with cibuildwheel even with the fix for {project}.

@natefoo natefoo merged commit 5bf9725 into galaxyproject:main Nov 29, 2023
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@nsoranzo
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Thanks @natefoo ! I've opened pysam-developers/pysam#1247 , which should fix the first issue in the next release. I think the testing issue can be instead workaround in env.sh, I'll open a follow-up PR here.

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I think the testing issue can be instead workaround in env.sh, I'll open a follow-up PR here.

cf3dfa2

@natefoo
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natefoo commented Dec 1, 2023

Thanks! Sorry for the hacky fixes I used here.

@nsoranzo
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nsoranzo commented Dec 1, 2023

No problem!

@jmarshall
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Can you say more about the problem underlying the “fix for {project}” referred to?

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nsoranzo commented Jan 5, 2024

Can you say more about the problem underlying the “fix for {project}” referred to?

@jmarshall I think we needed to expand the pysam tarball and cd into it in order to support https://github.com/pysam-developers/pysam/blob/master/pyproject.toml#L25-L27

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3 participants