augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Standardize error handling and console output functions
- Add instructions on adding subcommands
- augur clades should assign clades hierarchically and parsimonously
- curate format-dates : `--expected-date-formats` builtins cannot be overridden
- CI: Add new core pathogens to pathogen-repo-ci
- Rename `master` to `main`
- Remove `authors` hard-coding in `augur export`
- Add internal changes to changelog to improve visibility for developers and give credit
- parse: crash on invalid dates "0", "99999" instead of handling gracefully as intended
- Replace use of internal, non-public pandas API in parse.fix_dates
- Docs
- Python not yet supported