Allow users to specify a titer attribute prefix #1106
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Codecov ReportBase: 63.38% // Head: 67.97% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #1106 +/- ##
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+ Coverage 63.38% 67.97% +4.58%
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Files 57 57
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+ Hits 4208 4514 +306
+ Misses 2147 1823 -324
- Partials 284 304 +20
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huddlej
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This LGTM by inspection.
One non-blocking comment, which can be resolved later:
Allows users to prefix the node data JSON attributes produced by augur titers subcommands (e.g., cTiter, dTiter, etc.) with a custom string.
I went to look at the augur titers doc to see the full list of output fields, but didn't find it. If we don't have this documented elsewhere, it would be good to add it to the augur titers {tree,sub} --help output. If we do doc it elsewhere, then good to link out to it.
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Separately, it would also be nice to add a JSON schema, e.g. |
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Thank you, @tsibley! In addition to the JSON schema, we also need to expand the content of that titer docs page. |
Allows users to prefix the node data JSON attributes produced by `augur titers` subcommands (e.g., `cTiter`, `dTiter`, etc.) with a custom string. This change allows users to run multiple titer models for a single build and collect their results into an Auspice JSON without collisions in the node data attribute namespace.
Adds test data based on public titer data and sequences from the measurements panel paper [1] and adds functional tests for basic titer model commands and the new commands with attribute prefixes. [1] https://github.com/blab/measurements-panel/tree/main/data
Documents the specific attributes that get the custom prefix in titer model node data JSON outputs and clarifies the use case for the attribute prefix argument.
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Description of proposed changes
Allows users to prefix the node data JSON attributes produced by
augur titerssubcommands (e.g.,cTiter,dTiter, etc.) with a custom string. This change allows users to run multiple titer models for a single build and collect their results into an Auspice JSON without collisions in the node data attribute namespace.Testing
Checklist