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Shorten author name list #290

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corneliusroemer opened this issue Nov 16, 2024 · 4 comments · Fixed by #295
Closed

Shorten author name list #290

corneliusroemer opened this issue Nov 16, 2024 · 4 comments · Fixed by #295
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enhancement New feature or request

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@corneliusroemer
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corneliusroemer commented Nov 16, 2024

Right now the author name list is very long, causing deteriorated functionality:
Brave Browser 2024-11-16 15 06 08

We should shorten with e.g. augur curate's functionality for shortening author names.

@corneliusroemer corneliusroemer added the enhancement New feature or request label Nov 16, 2024
@joverlee521
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@genehack asked a similar question for yellow fever on Slack, so summarizing discussion here

We already abbreviate authors as part of the ingest curate rule and output as the abbr_authors column. However, the full authors list is being used in the final Auspice output because augur export v2 is hard-coded to check for the author or authors field (ref).

Outside of updating augur export, the best path forward would be to switch authors to full_authors and abbr_authors to authors. Example in pathogen-repo-guide

@joverlee521 joverlee521 self-assigned this Nov 19, 2024
joverlee521 added a commit that referenced this issue Nov 20, 2024
Switch `authors` to `full_authors` and `abbr_authors` to `authors` so
that the abbreviated author field is used by `augur export` in the
phylogenetic workflow.

Resolves <#290>
@joverlee521 joverlee521 mentioned this issue Nov 20, 2024
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@corneliusroemer
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Switching sounds good to me.

We should probably unhardcode authors in export though eventually.

@jameshadfield
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We should probably unhardcode authors in export though eventually.

Yes. My memory was that we used "authors" (in metadata TSVs) to represent "Roemer et al" etc, and augur export was designed around that. We've since switched to encoding the entire author list as "authors" without updating augur export.

@genehack
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☝️ created issue in augur repo for removing the hard-coded export.

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4 participants