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innextstrain/augur (press backspace or delete to remove)Context
Currently, the default metadata id column is auto-inferred as strain or name based on whichever is the leftmost column.
This may have worked with earlier datasets when strain was preferred with ...
enhancement
victorlin
- 4
- Opened 5 days ago
- #1780
When using/trying out weighted sampling with a weights file I noticed that the output is extremely verbose, full of
warnings, at least 200 lines, completely overwhelming the snakemake output.
I could ...
corneliusroemer
- 1
- Opened 9 days ago
- #1777
I m trying to increase the weight for a few years, therefore specifying that year and default for the rest. However that
sort of weight file gives me a pandas error:
Sampling with weights defined by resources/lineage-b.1/weights.tsv. ...
bug
- 1
- Opened 9 days ago
- #1776
Part of #936
augur filter when called with --group-by year|month|week has its own logic to parse dates in the form of year - month -
day, year - month, or year (src).
This should use standard date parsing ...
- Opened 11 days ago
- #1774
Context
When augur refine runs with the --clock-filter-iqd argument, refine can prune older strains in the tree that user may
have force-included during subsampling. For example, a recent seasonal-flu ...
enhancement
huddlej
- 3
- Opened on Feb 27
- #1768
- [x] Update changelog
- [x] Run release workflow
- [x] Rebuild Docker image
- [x] Bioconda auto-bump PR
- [x] Rebuild Conda package
joverlee521
- Opened on Feb 26
- #1765
Context
Following up on comments in https://github.com/nextstrain/augur/pull/1762
Currently the CI does a fresh install of the dev dependencies during the check-docs job and flags changes in the API ...
- 1
- Opened on Feb 25
- #1764
Automated CI failed due to check-docs. Similar to failure in
https://github.com/nextstrain/augur/pull/1760#issuecomment-2667966493.
Likely related to release of sphinx-autodoc-typehints v3.1.0.
- 1
- Opened on Feb 20
- #1761
Discovered in ebola workflow
If the NDJSON includes values that are null, they get parsed as None values in the Python dict. However, the command
expects string values as long as the geolocation field ...
bug
- Opened on Feb 14
- #1758
Discovered in ebola workflow
If some requested fields in the --field-map do not exist, then some fields might not be renamed as expected. This is due
to the use of field_map.pop while looping through ...
bug
- Opened on Feb 14
- #1757
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