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There's a weird issue with the Conda runtime where the inital setup uses an older version.¹ Do an update of the default runtime after setup to ensure we are using the latest version. We could remove this extra step after we rework `nextstrain setup` to use the same logic as `nextstrain update`. ¹ nextstrain/mpox#177
We could start using the workflow-context action like the pathogen-repo-build workflow, but that will require all uses of the pathogen-repo-ci to be updated to give id-token write permissions. That's a bigger change that I think can be done separately.
victorlin
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Sep 1, 2023
joverlee521
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Sep 5, 2023
I missed in #48 that the command `nextstrain update` will exit with error for aws-batch and ambient runtimes. Instead of maintaining a list of runtime to run the update command, just allow it to continue-on-error.
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Description of proposed changes
There's a weird issue with the Conda runtime where the inital setup
uses an older version.¹ Do an update of the default runtime after setup
to ensure we are using the latest version.
We could remove this extra step after we rework
nextstrain setuptouse the same logic as
nextstrain update.¹ nextstrain/mpox#177
Checklist