Victor Lin
Victor Lin
_from https://github.com/nextstrain/docs.nextstrain.org/issues/91#issuecomment-1068585825_ Invalid page links (e.g. https://docs.nextstrain.org/invalid-page) currently serve the same content as https://readthedocs.org/invalid-page. A [custom 404 page](https://docs.readthedocs.io/en/stable/hosting.html#custom-not-found-404-pages) would provide more context to users who end up in the wrong...
## Description of proposed changes This reflects my understanding of how tests are used in Augur (and somewhat shaped by changes that I've pushed over the years). Open to suggestions....
## Description of proposed changes ## Related issue(s) - Prompted by [Slack discussion](https://bedfordlab.slack.com/archives/C7SDVPBLZ/p1715923786459859) ## Checklist - [ ] Address FIXMEs - [ ] Checks pass - [ ] If making...
Currently, Augur is pinned to pandas version 1: https://github.com/nextstrain/augur/blob/1694a3fe1f2e4271849120ee08b29cb8286dc1fa/setup.py#L64 There have been numerous requests with good reason to support pandas version 2: - #1303 - #1316 - #1436 - #1471...
## Description of proposed changes Allow users to use Augur with newer versions of pandas. ## Related issue(s) - #1303 - #1436 ## Checklist - [ ] Checks pass -...
Pyright was added in #1246. The [default Pyright configuration options](https://github.com/microsoft/pyright/blob/-/docs/configuration.md) result in many violations from Augur's code as-is. To allow incremental adoption of Pyright, all default rule violations were [disabled](https://github.com/nextstrain/augur/blob/e5ced1c8b5e1aeb1923bc00219594336e8ceeb34/pyrightconfig.json#L6-L29)....
## Description of proposed changes This new option takes a weights file to determine group sizes. Summarized by the help text: https://github.com/nextstrain/augur/blob/0a321a6e13e9ba0c86eb3b195fab98abc90c92b6/augur/filter/__init__.py#L73-L83 ## Related issue(s) Closes #1318 Based on #1460...
Issue for tracking release progress. - [x] [Check changelog](https://github.com/nextstrain/augur/pull/1464) - [x] [Run release workflow](https://github.com/nextstrain/augur/actions/runs/9103863090) - [x] [Docker image rebuilt](https://github.com/nextstrain/docker-base/actions/runs/9104015859) - [ ] [Bioconda PR](https://github.com/bioconda/bioconda-recipes/pull/47921) - Manually created due to [broken](https://github.com/bioconda/bioconda-recipes/issues/47929)...
### Context Currently, `--lat-longs` overrides the default mappings provided by [augur/data/lat_longs.tsv](https://github.com/nextstrain/augur/blob/-/augur/data/lat_longs.tsv). ### Description Add an option to extend the default mappings in addition to the existing behavior of replacing them....
> [!NOTE] > This isn't an issue with Augur. It's really about the interaction within or between Python package managers, e.g. `conda` and `pip`, but I couldn't find a good...