John SJ Anderson
John SJ Anderson
Extracted from [Q4 planning](https://docs.google.com/document/d/1RVt6UFIji8b0BbN0pS2mqpVD9KF48EHBtbPE7oD0gQI/edit); please update and/or redirect to existing issue as appropriate.
Extracted from [Q3 planning meeting](https://docs.google.com/document/d/150k8VU2q5IXYU3a2_g4mLLJGCh-A5AJNguppu9dCU-A/edit) notes. Currently, auspice will log certain warnings and errors to the console. Discoverability of this is obviously pretty poor. To make it these more clear,...
Extracted from [Q3 planning session](https://docs.google.com/document/d/150k8VU2q5IXYU3a2_g4mLLJGCh-A5AJNguppu9dCU-A/edit)
Extracted from [Q3 planning meeting](https://docs.google.com/document/d/150k8VU2q5IXYU3a2_g4mLLJGCh-A5AJNguppu9dCU-A/edit) notes for tracking. @huddlej Maybe draft a plan in here?
### Current Behavior [Slack context](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1723675141029349) Copying the deprecation message from there: ``` DEPRECATION: Legacy editable install of nextstrain-augur[dev]==25.2.0 from file:///home/tom/nextstrain/augur (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour...
These availability statements are great, but it makes me realize we should be using ```rst .. versionadded:: x.y.z ``` directives in our Sphinx/rST docs so those availability statements are also...
The link doesn't make sense for the link text "conda environment" but I think the only way to address this is to update this entire sentence with newer terminology such...
### Current Behavior [slack context](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1721783848746329) Data was being indexed by `strain`, but the node names in the tree were drawn from `accession` -- so when `augur traits` was run, no...
This is a prerequisite for #134, but has expanded beyond that to the point where I think a distinct isuse will be helpful. This should be considered a meta-issue, to...