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First noticed in https://github.com/nextstrain/augur/pull/1550#discussion_r1683425790 our blind use of first row as headers can cause misleading errors.
We should assert that the headers are uniqu…
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When there are no messages associated with an issue or pull request, which is quite rare, we need to keep going, perhaps throw a warning, and continue. Here is an example error response:
```
Traceba…
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### Context
Previously mentioned in https://github.com/nextstrain/augur/pull/1039#issuecomment-1252912107 and https://github.com/nextstrain/augur/issues/1475.
A lot of public health folks use …
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### Context
Originally implemented in `augur curate rename` but dropped due to discussion on UI in https://github.com/nextstrain/augur/pull/1506#discussion_r1669411291.
There are many cases wher…
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Hi All,
I went through the documentation but couldn't find the answer. What is the unit of the branch length of the newick tree from `augur refine` output? I can't find out what is the appropriate …
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### Context
Bioconda has supported linux-aarch64 for a few months now and all augur deps are available now on that aarch.
Making conda-base support linux-aarch64 would have the advantage that we c…
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## Tasks
_@victorlin to fill this out_
## Links
- [2021-08-17 take 1](https://github.com/nextstrain/augur/pull/762)
- [2021-08-23 take 2 (moved to ncov)](https://github.com/nextstrain/ncov/p…
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I've been able to get the augur docker containers up and running using the Docker quick start instructions on windows as described on this page https://oss-augur.readthedocs.io/en/main/docker/quick-…
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Prompted by https://github.com/nextstrain/pathogen-repo-guide/pull/54#issuecomment-2229193810
Taking a closer look at the use of `csvtk` in the nextclade.smk
https://github.com/nextstrain/pathog…
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TL;DR: A call to boltzmann.py within CCL is failing in the derivative calculation, presumably due to O(10^-9) values in A_s.
Explanation: When attempting a 3x2pt forecast, it runs and completes whe…