Improve temporal colors#3
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Without this the `augur ancestral` step in the nextclade pipeline fails: "KeyError: 'GPC'". Augur ancestral's reading of GenBank files is: > for 'CDS' features use the locus_tag or the gene. If neither, then silently ignore [1] [1] https://github.com/nextstrain/augur/blob/4b9397bacea57a2436267c1312c075e925201191/augur/io/sequences.py#L455
The previous (default) date categorical scale didn't define a custom color scale so auspice sorted the values by the number of occurrences on the tree and generated a linear scale from these values. This resulted in a non-chronological ordering and didn't emphasize the new data which is particularly relevant. One improvement is to just use a "temporal" scale type, but here we use a custom approach which projects the observed date range into a our canonical rainbow color scale non-linearly in order to space out the colors of more recent sequences.
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Current situation
collectionDateformats of of (empty string), YYYY, YYYY-MM-DDChanging to scale type "temporal" improves things, but only a little bit:
This PR
We use a script to projects the observed date range into our canonical rainbow color scale non-linearly
in order to space out the colors of more recent sequences.
(Long term we can move this script somewhere else, but I think this is appropriate for now)