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Example: `augur filter --group-by-weights`
Rendered rST docs is formatted nicely:
CLI help text is not great:
```
--group-by-weights FILE
TSV file defining wei…
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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…
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Description:
Create a high-level overview of the Augur project:
- Newcomer resources - how to connect to the community
- Guide to join the project on GitHub
Write Script for Intro to Augur P…
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`augur merge` should support input `--sequences` and `--output-sequences`.
Features:
- Sequences with same id are coalesced right-to-left, as with metadata rows.
- Duplication handling within F…
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Hi @luongnt95 we are trying to fix false positive results in Augur project for
* Assertion Failures
* Re-Entrancy Vulnerability
See
https://github.com/AugurProject/augur-core/issues/689
…
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Currently the formatting of the help messages (defined via the leading docstrings at the start of each script in `augur/*.py`) is not respected by `augur --help`. We should improve this which will en…
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Augur lacks a standard test environment across individual developer machines and CI. This results in some test implementations that must use the "lowest common denominator" of programs expected to be …
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We should pick between either [IANA TSVs](https://www.iana.org/assignments/media-types/text/tab-separated-values) or [RFC 4180 CSV-like TSVs](https://datatracker.ietf.org/doc/html/rfc4180) and then be…
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Projects more and mroe are using the self identified github topics feature:
![Screenshot 2024-04-01 at 10 59 24 AM](https://github.com/chaoss/augur/assets/47504866/3e0971d8-3660-4bb1-9cc7-d26d3408ae…