25.3.0

These release notes are automatically extracted from the full changelog.

Features

• A new command, augur merge, now allows for generalized merging of two or more metadata tables. #1563 (@tsibley)
• Two new commands, augur read-file and augur write-file, now allow external programs to do i/o like Augur by piping from/to these new commands. They provide handling of compression formats and newlines consistent with the rest of Augur. #1562 (@tsibley)
• A new debugging mode can be enabled by setting the AUGUR_DEBUG environment variable to 1 (or any non-empty value). Currently the only effect is to print more information about handled (i.e. anticipated) errors. For example, stack traces and parent exceptions in an exception chain are normally omitted for handled errors, but setting this env var includes them. Future debugging and troubleshooting features, like verbose operation logging, will likely also condition on this new debugging mode. #1577 (@tsibley)
• filter: Added the ability to use weights in subsampling. See help text of --group-by-weights and the updated Filtering and Subsampling guide for more information. #1454 (@victorlin)

Bug Fixes

• Embedded newlines in quoted field values of metadata files read/written by many commands, annotation files read by augur curate apply-record-annotations, and index files written by augur index are now properly handled. #1561 #1564 (@tsibley)
• Output written to stderr (e.g. informational messages, warnings, errors, etc.) is now always line-buffered regardless of the Python version in use. This helps with interleaved stderr and stdout. Previously, stderr was block-buffered on Python 3.8 and line-buffered on 3.9 and higher. #1563 (@tsibley)