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Inspired by @kimandrews 's work in https://github.com/nextstrain/rabies/pull/8
Copying [my comment](https://github.com/nextstrain/rabies/pull/8#discussion_r1723756826) as an official proposal for a…
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Getting this error in `dev` for GitLab reviews:
```bash
Traceback (most recent call last):
File "/home/ubuntu/github/virtualenvs/hosted/lib/python3.11/site-packages/celery/app/trace.py", line 451, …
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For different reasons there are sometimes links for messages or events associated with Issues and PRs that do not exist. Sometimes it is because the issue is deleted or issues have been disabled. Some…
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When the GH API Doesn't return data, we are not checking the code, or not handling NULL values:
```bash
Traceback (most recent call last):
File "/home/ubuntu/github/virtualenvs/hosted/lib/python3.…
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## Scope
Any CLI option that uses the `store_false` action, which are these options on version 25.2.0:
- `augur curate format-dates --no-mask-failure`
- `augur filter --no-probabilistic-samplin…
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I've just run into [this error](https://github.com/nextstrain/augur/actions/runs/10530367718/job/29180176987#step:6:731) on an Augur PR which did not change any docs links:
```
(api/developer/augu…
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Current default configs for `strain` requires it to be a non-empty string with `accession` as the backup field.
https://github.com/nextstrain/pathogen-repo-guide/blob/89b3c5dbc9b8f6a009f4a19c3ac561…
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## Context
See [parent issue](https://github.com/nextstrain/augur/issues/1575) for context on how Pandas is used in augur filter and why it is slow.
The alternative way of working with large dat…
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`augur filter` allows `--output`, `--output-sequences`, and `-o` to be used interchangeably:
https://github.com/nextstrain/augur/blob/da1c89d4b3232aa977b69fb8df33d666532c9a56/augur/filter/__init__.…
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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…