31.3.0

These release notes are automatically extracted from the full changelog.

Features

• traits: Added new options --branch-labels and --branch-confidence to export branch labels for nodes which have a corresponding state change. These are useful for creating streamtrees which convey geographic jumps. #1814 (@jameshadfield)
• filter, merge: Added a new option --nthreads to configure parallelism. Right now, it is only passed to SeqKit, but it may be used for other internal optimizations in the future. #1833 (@victorlin)
• filter: Added a new option --skip-checks to bypass checks for duplicates in sequences and whether ids in metadata have a sequence entry. Mainly useful when working with larger files. #1833 (@victorlin)
• Added a new AUGUR_PROFILE environment variable. If set, Augur will run with Python's cProfile profiler and save results to the value which should be a file path. This may result in slightly slower run times, and should only be used for debugging purposes. #1835 (@victorlin)

Bug fixes

• filter, merge: Improved run time of sequence I/O operations, especially in the common use case of having a workflow manager run multiple invocations simultaneously. #1833 (@victorlin)
• filter, merge: Previously, SeqKit was hardcoded to use its default of 4 threads per command, which could have resulted in oversubscription of resources in the common use case of having a workflow manager run multiple invocations simultaneously. The default behavior has been updated to use 1 thread per command to discourage oversubscription of resources. It is configurable with the new --nthreads option described above. #1833 (@victorlin)