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This is useful for ignoring categories in specific builds even if they share the same default ordering TSV. Changes modified from mpox <nextstrain/mpox@b6b793c>
Adding the option to support the force included color orderings in mpox <nextstrain/mpox@f9221c0>
| parser.add_argument('--ordering', type=str, required=True, | ||
| help="""Input TSV file defining the color ordering where the first | ||
| column is the field and the second column is the trait in that field. | ||
| column is the category and the second column is the trait in that category. |
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[sidebar] I always struggle to name these things, especially when they have a value attached. Category / trait / value seems pretty good.
| parser.add_argument('--ignore-categories', type=str, default=[], nargs='*', | ||
| help="""Do not create colors for these categories even if they are | ||
| included in the metadata and ordering TSV. This is useful for ignoring | ||
| categories in specific builds even if they share the same default | ||
| ordering TSV.""") |
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[discussion] An alternative UI would be to have ordering TSVs for different categories and then allow multiple --ordering values. Thoughts? Do we plan on vendoring some big ordering list, or copy-paste across repos?
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I suspect that there will be some overlap in ordering but not always. Even for division/location, the ordering may depend on where the pathogen is circulating? I'd think each pathogen would have it's own ordering TSV to support their own uses.
| parser.add_argument('--force-include-categories', type=str, default=[],nargs='*', | ||
| help="""Force include all color orderings for these categories even if | ||
| there are traits not included in the metadata TSV. This is useful for | ||
| creating colorings for traits not (yet) present in metadata to solve | ||
| bootstrapping issue.""") |
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I have no idea what a "bootstrapping issue" is. I suspect this is a valid use-case, but perhaps adjust the argument help text?
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To be honest, I'm not 100% sure what the bootstrapping issue is either, I was just trying to support the changes added in mpox from nextstrain/mpox@f9221c0.
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Description of proposed changes
Add optional flags to support uses of the similar assign-colors script in mpox
Related issue(s)
Related to nextstrain/mpox#286
Checklist