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Add nextclade3 via direct download #50

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merged 3 commits into from
Dec 22, 2023
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@victorlin victorlin commented Dec 22, 2023

Description of proposed changes

Nextclade v3 is not yet released in Bioconda. Add it as a direct download so that users of Nextstrain's Conda runtime can transition to using nextclade3.

Related issue(s)

Checklist

  • Checks pass Failing because of unmerged Biopython pin
  • test-pathogen-repo-ci (rsv) gets past the nextclade3 step

@victorlin victorlin self-assigned this Dec 22, 2023
@victorlin victorlin changed the title 🚧 Add nextclade3 Add nextclade3 Dec 22, 2023
Nextclade v3 is not yet released in Bioconda. Add it as a direct
download so that users of Nextstrain's Conda runtime can transition to
using nextclade3.
@victorlin victorlin changed the title Add nextclade3 Add nextclade3 via direct download Dec 22, 2023
Issue linked in changes. Pin to an exact version which is known to be
compatible.
@victorlin victorlin marked this pull request as ready for review December 22, 2023 21:49
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Merging this PR before #51 would mean building a version of the package that exposes the effects of nextstrain/augur#1373, so I won't do that. I also don't want to base this PR on #51 since that ordering doesn't allow showing proof of fixes in each PR.

Plan:

  1. Base #51 on this PR and merge it into here first.
  2. Merge this PR as a bundle of changes described here and in #51.

@victorlin victorlin mentioned this pull request Dec 22, 2023
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@victorlin victorlin merged commit c85a27d into main Dec 22, 2023
20 checks passed
@victorlin victorlin deleted the victorlin/add-nextclade3 branch December 22, 2023 22:24
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CI failure: nextclade3 command not found
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