32.1.0

These release notes are automatically extracted from the full changelog.

Features

• augur.io.read_metadata: Added a new parameter keep_id_as_column to keep the resolved id column as a column in addition to setting it as the DataFrame index. #1917 (@victorlin)
• subsample: Filepaths in the config file can now be relative to the config file's parent directory in addition to the current working directory. Custom directories can also be specified using a new command line option --search-paths or environment variable AUGUR_SEARCH_PATHS. #1897 (@victorlin)
• A helper function – augur.subsample.get_referenced_files – has been added to optimize usage of augur subsample in Snakemake workflows. This is experimental and not yet part of the public API. #1918 (@victorlin)

Bug fixes

• filter: Previously, --query, --exclude-where, and --include-where did not work for the id column (strain, name, or other from --metadata-id-columns). This has been fixed. #1915 (@corneliusroemer, @victorlin)
• export v2: Support export of URLs for non-string values. #1926 (@joverlee521)