Initial efforts to accomplish this goal involved exporting the Nextclade tree using branch lengths in tree.nwk (rather than in branch_lengths.json), under the assumption that these were divergence branch lengths, but actually they are time branch lengths. Therefore we need a different approach to remove time information.
This PR first reverts the changes from the initial approach, and then removes all node attributes except divergence branch lengths (mutation_length attribute) from branch_lengths.json before exporting the Nextclade tree.
Description of proposed changes
The goal of this PR is to remove time information from the Nextclade dataset tree, since Nextclade doesn't use this information. This change was originally recommended in https://github.com/nextstrain/nextclade_data/pull/202#issuecomment-2130148472
Initial efforts to accomplish this goal involved exporting the Nextclade tree using branch lengths in tree.nwk (rather than in branch_lengths.json), under the assumption that these were divergence branch lengths, but actually they are time branch lengths. Therefore we need a different approach to remove time information.
This PR first reverts the changes from the initial approach, and then removes all node attributes except divergence branch lengths (
mutation_lengthattribute) from branch_lengths.json before exporting the Nextclade tree.Related issue(s)
https://github.com/nextstrain/nextclade_data/pull/202#issuecomment-2130148472 https://github.com/nextstrain/measles/pull/33
Checklist