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cov-lineages / pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.
GNU General Public License v3.0
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Workaround for setup-miniconda failing to install mamba on ubuntu #506

Closed AngieHinrichs closed 6 months ago

AngieHinrichs commented 1 year ago

pangolin github action tests have been failing on ubuntu for about a week now (?) not because of anything in pangolin, but because the conda-incubator/setup-miniconda action's conda command to install mamba fails with a ton of cryptic conflict errors. I found that removing mamba-version: "*" from pangolin.yml would prevent the crash, but it would be nice to keep mamba in the CI too. I found a nice report of this issue, including suggested workarounds: conda-incubator/setup-miniconda#274 and indeed the first suggested workaround (replacing mamba-version: "*" with miniforge-variant: Mambaforge) worked.

AngieHinrichs commented 1 year ago

@pvanheus I think you were the original author of .github/workflows/pangolin.yml a couple years ago including the mamba-version: "*". Does this change look OK to you? I don't know much about github actions or the various flavors of condas and forges, I'm just following what I saw in conda-incubator/setup-miniconda#274 because it works. Thanks! [I tried to add you as a reviewer but it didn't accept 'pvanheus']

AngieHinrichs commented 1 year ago

If I don't hear any objections in the next day I'll just merge this. 🙂