Gray out early clades by trvrb · Pull Request #1132 · nextstrain/ncov (original) (raw)
1 task
When assigning colors gray out clades that are not in recent samples. Use clade_recency parameter to consider how many months back to consider "recent".
Set up a build-specific override for colors: clade_recency parameter. Make the default to be empty string "" and have this keep all clades colored. Override for the Nextstrain GISAID profile to specify clade_recency of
1month for "1m" build2months for "2m" build6months for "6m" build""(all months) for "all-time" build
Per rationale in issue 1131 (#1131), switch to following a three step look up for setting build-specific parameters of colors:clade_recency.
Rather than previous behavior of setting --clade-recency 6 by building --clade-recency {params.clade_recency}, instead build the entire argument via {params.clade_recency_argument}.
This allows setting colors.global_all-time.clade_recency to "all" in builds.yaml and in this case handing assign-colors.py nothing for clade_recency. This keeps the behavior of assign-colors.py as expected and backwards compatible, while simultaneously allowing for the "all" sensible default in parameters.yaml rather than the previous empty string to accomplish this same behavior.
The colors.clade_recency parameter can be specified in a build-specific fashion. If specifying a default for use, use the pattern of specifying colors.default.clade_recency rather than the previous colors.clade_recency.
Show a meaningful error message if the value is improperly formatted.
Keeps consistent with other existing usage of this format.
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