Fix RBD level coloring and filter #1094
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victorlin
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Jan 30, 2024
The clade labels were updated in #1065. Update the clade label so that the `assign_rbd_levels` script can find the correct basal clade. I had considered pulling this value out as a parameter in the config YAML, but the original commit message¹ implies that this should _not_ be configurable. ¹ fb5f44e
The JSON output from `augur clades` was updated to separate `nodes` and `branches` in nextstrain/augur#728 so now the `assign_rbd_levels` script needs to parse the `branches` in order to find the basal node.
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Waiting on internal discussion of whether we should update the RBD definitions or just drop them entirely. |
joverlee521
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Jan 31, 2024
Prompted by #1094, which led to internal conversation¹ that determined we should just drop the RBD-levels. ¹ https://bedfordlab.slack.com/archives/CSKMU6YUC/p1706643360558109
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Closing in favor of #1097 |
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Merging to get RBD-levels in a working state so we can easily reinstate the feature in the future. |
joverlee521
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Jan 31, 2024
Prompted by #1094, which led to internal conversation¹ that determined we should just drop the RBD-levels. ¹ https://bedfordlab.slack.com/archives/CSKMU6YUC/p1706643360558109
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Description of proposed changes
Came down this rabbit hole when I was thinking about augur export v2 and the filter footers. I noticed the ncov build had empty filter footers for
levelandrbd_leveland investigated.See commits for details.
Testing
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If this pull request introduces backward incompatible changes, complete the following steps for a new release of the workflow:
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docs/src/reference/change_log.mdin this pull request to document these changes by the date they were added.