Update pangolin-data to v1.13 (it's at v1.12 right now)

[robert-koch-institut]

Update pangolin-data to v1.13 (it's at v1.12 right now)

[matthuska]

Hi @corneliusroemer , we use the conda packages for pangolin and its dependencies. Currently the current conda package for pangolin-data says it is 1.13, but pangolin --all-versions reports 1.12:

$ conda list | grep pangolin-data
pangolin-data             1.13               pyh5e36f6f_0    bioconda
$ pangolin --all-versions | grep pangolin-data
pangolin-data: 1.12

This is a known issue and has been reported to the pangolin-data issue tracker: cov-lineages/pangolin-data#22 (comment)

As soon as that is resolved and an updated conda package for pangolin-data is released we will automatically start using it.

[mg14]

This seems relevant as BF.7 (and other BA.5* variants with S:346T) seem to be rising, but are missed by v.1.12:

[matthuska]

Thanks @corneliusroemer , there are some technical reasons why we have to stick to conda for all updates. It can lead to delayed updates but we have some internal processes that require us to be able to exactly recreate older pangolin environments, and for that we rely on conda. Thanks for your patience.

[mg14]

Hi Matt - problem solved, thanks!

https://mobile.twitter.com/MoritzGerstung/status/1560864142952730624

[mg14]

Hi Matt I think this is fixed now, see

cov-lineages/pangolin-data#22 (comment)

[matthuska]

Yes I noticed, thanks! The new version should be automatically used in tonight's batch run and the upload to GitHub tomorrow should reflect that. I'll check tomorrow to be sure, and resolve any issues if it's not working as expected.

Thanks again, the online SC2/open-source/conda communities are amazing :)

[corneliusroemer]

Thanks @matthuska for explaining!

I think for the future: you can update the data yourself simply by running pangolin --update-data - not relying on bioconda to update the data first.