18.0.0

Major Changes

• export: The --node-data option may now be given multiple times to provide additional .json files. Previously, subsequent occurrences of the option overrode prior occurrences. This is a breaking change, although we expect few usages to be impacted. Each occurrence of the option may still specify multiple files at a time. #1010 (@tsibley)

Bug Fixes

• refine: 17.1.0 updated TreeTime to version 0.9.2 and introduced the refine flag --use-fft. This makes previously costly marginal date inference cheaper. This update adjusts when refine runs marginal date inference during its iterative optimization. Without the use-fft flag, it will now behave as it did before 17.1.0 (marginal inference only during final iterations). With the --use-fft flag, marginal date inference will be used at every step during the iteration if refine is run with --date-inference marginal #1034. (@rneher)
• tree: When using IQtree as tre builder, --nthreads now sets the maximum number of threads (IQtree argument -ntmax). The actual number of threads to use can be specified by the user through the tree-builder-arg -nt which defaults to -nt AUTO, causing IQtree to automatically chose the best number of threads to use #1042 (@corneliusroemer)
• Make cvxopt as a required dependency, since it is required for titer models to work #1035. (@victorlin)
• filter: Fix compatibility with Pandas 1.5.0 which could cause an unexpected AttributeError with an invalid --query given to augur filter. #1050 (@tsibley)
• refine: Add --verbosity argument that is passed down to TreeTime to facilitate monitoring and debugging. #1033 (@anna-parker)
• Improve handling of errors from TreeTime. #1033 (@anna-parker)