Releases: nextstrain/augur
Releases · nextstrain/augur
19.3.0
Features
- titers: Support parsing of thresholded values (e.g., "<80" or ">2560"). #1118 (@huddlej)
- tree: Support bootstrapped trees generated with RAxML via user-provided
--tree-builder-args
. #1127 (@tsibley)
Bug Fixes
- utils: Serialize common numpy data types in
write_json
. #1119 (@victorlin) - filter: Standardize exit codes from internal error handling. #931 (@victorlin)
- tree: Suppress the
Cannot specify --substitution-model unless using IQTree
warning when--substitution-model
is left at its default. #1127 (@tsibley) - tree: Print the underlying error message when tree building fails. #1127 (@tsibley)
- Previously,
numpy
andscipy
were installed as dependencies of dependencies. Mark them as direct dependencies since they are used directly within Augur. #1120 (@victorlin)
19.2.0
19.1.0
Features
- io: Add
open_file
andwrite_sequences
to the Python Pubic API. #1114 (@joverlee521)
19.0.0
Major Changes
- io: Only
read_metadata
andread_sequences
are available as part of the Python Public API. Other Python API functions of theaugur.io
module are no longer directly available. This is a breaking change, although we suspect few users to be impacted. If you still need to use other imports in your scripts, they can be imported from the Developer API but note that they are no longer part of the Public API. #1087 (@victorlin)
Bug Fixes
- docs: Update the API documentation to reflect the latest state of things in the codebase. #1087 (@victorlin)
- Fix support for Biopython version 1.80 which deprecated
Bio.Seq.Seq.ungap()
. #1102 (@victorlin) - export v2: Fixed a bug where colorings for zero values via
--colors
would not get applied to the exported Auspice JSON. #1100 (@joverlee521) - curate: Fixed a bug where metadata TSVs failed to parse if data within a column included comma separated values #1110 (@joverlee521)
18.2.0
Features
- Add the curate subcommand with two sub-subcommands, passthru and normalize-strings. The curate subcommand is intended to be a suite of commands to help users with data curation prior to running Nextstrain analyses. We will continue to add more subcommands as we identify other common data curation tasks. Please see the usage docs for details. #1039 (@joverlee521)
18.1.2
18.1.1
18.1.0
Features
- filter: Add support to group by ISO week (
--group-by week
) during subsampling. #1067 (@victorlin)
Bug Fixes
- filter: Fixed unintended behavior in which grouping by
day
would "work" when used withmonth
and/oryear
. Updated so it will be ignored. #1070 (@victorlin) - filter: Fixed unintended behavior in which grouping by
month
with ambiguous years would "work". Updated so date ambiguity is checked properly for all generated columns. #1072 (@victorlin)
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 whenrefine
runs marginal date inference during its iterative optimization. Without theuse-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 toaugur 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)
17.1.0
Features
- refine: Upgrade TreeTime from 0.8.6 to >= 0.9.2 which enables a speedup of timetree inference in marginal mode due to the use of Fast Fourier Transforms #1018. (@rneher and @anna-parker)
Bug Fixes
- refine, export v1: Use pandas.DataFrame.at instead of .loc for single values #979. (@victorlin)
- refine: Gracefully handle all exceptions from TreeTime #1023. (@anna-parker)
- refine: Document branch length units
treetime
expects #1024. (@anna-parker) - dates: Raise an error when metadata to
get_numerical_dates()
is not a pandas DataFrame #1026. (@victorlin)