CHANGELOG

NEXT

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)

18.2.0 (15 November 2022)

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 (1 November 2022)

Bug Fixes

• traits: Fix trait inference when tips have missing values. #1081 (@huddlej)

18.1.1 (1 November 2022)

Bug Fixes

• filter: Fixed a bug where --group-by week would fail when all samples in a chunk have been dropped due to ambiguous dates. #1080 (@victorlin)

18.1.0 (26 October 2022)

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 with month and/or year. 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 (21 September 2022)

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)

17.1.0 (19 August 2022)

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). Use the refine flag --use-fft to use this feature.

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)

17.0.0 (9 August 2022)

Major Changes

• Moved the following modules to subpackages #1002. (@joverlee521) These are technically breaking changes for the API, but they do not change the Augur CLI commands.
  • import.py -> import_/__init__.py
  • import_beast.py -> import_/beast.py
  • measurements.py -> measurements/__init__.py + measurements/concat.py + measurements/export.py
• Move the following internal functions/classes #1002. (@joverlee521)
  • augur.add_default_command -> argparse_.add_default_command
  • utils.HideAsFalseAction -> argparse_.HideAsFalseAction
• Subcommands must include a register_parser function to add their own parser instead of a register_arguments function #1002. (@joverlee521)
• utils: Remove internal function utils.read_metadata() #978. (@victorlin)
  • Use io.read_metadata() going forwards.
  • To switch to using metadata as a pandas DataFrame (recommended):
    • Iterate through strains: metadata.items() -> metadata.iterrows()
    • Check strain presence: strain in metadata -> strain in metadata.index
    • Check field presence: field in metadata[strain] -> field in metadata.columns
    • Get metadata for a strain: metadata[strain] -> metadata.loc[strain]
    • Get field for a strain: metadata[strain][field] -> metadata.at[strain, field]
  • To keep using metadata in a dictionary:

      metadata = read_metadata(args.metadata)
      metadata.insert(0, "strain", metadata.index.values)
      columns = metadata.columns
      metadata = metadata.to_dict(orient="index")
    

Features

• export: --skip-validation now also skips version compatibility checks #902. (@corneliusroemer)
• filter: Report names of duplicate strains found during metadata parsing #1008 (@huddlej)
• translate: Add support for Nextclade gene map GFFs #1017 (@huddlej)

Bug Fixes

• filter: Rename internal force inclusion filtering functions #1006 (@victorlin)

16.0.3 (6 July 2022)

Bug Fixes

• filter: Move register_arguments to the top of the module for better readability #995. (@victorlin)
• filter: Fix a regression introduced in 16.0.2 that caused grouping with subsampled max sequences and force-included strains to fail in a data-specific way #1000. (@huddlej)

16.0.2 (30 June 2022)

Bug Fixes

• The entropy panel was unavailable if mutations were not translated #881. This has been fixed by creating an additional annotations block in augur ancestral containing (nucleotide) genome annotations in the node-data #961 (@jameshadfield)
• ancestral: WARNINGs to stdout have been updated to print to stderr #961 (@jameshadfield)
• filter: Explicitly drop date/year/month columns from metadata during grouping. #967 (@victorlin)
  • This fixes a bug #871 where augur filter would crash with a cryptic ValueError if year and/or month is a custom column in the input metadata and also included in --group-by.
• filter: Fix duplicates that may appear in metadata when using --include/--include-where with subsampling #986 (@victorlin)

16.0.1 (21 June 2022)

Bug Fixes

• filter: Handle errors from filter_by_query #942 (@victorlin)
• translate: output nuc annotation when reading from gff3 gene map #976 (@corneliusroemer)
• CI: Remove step for selecting PyPI instance #974 (@victorlin)
• CI: Add token to use GitHub CLI #958 (@victorlin)

16.0.0 (16 June 2022)

Major Changes

• filter: Error when any group-by column is not found #933 (@victorlin)
  • Check your workflows for any new errors that may arise from this.
• parse: Error on duplicates instead of silently passing #918 (@victorlin)
  • Check your workflows for any new errors that may arise from this.
• utils: Remove utils.myopen() #926 (@victorlin)
  • Use io.open_file() going forwards.
• Moved the following internal functions #929, #923 (@victorlin):
  • utils.read_vcf -> io.read_vcf
  • utils.run_shell_command -> io.run_shell_command
  • utils.shquote -> io.shquote
  • utils.ambiguous_date_to_date_range -> dates.ambiguous_date_to_date_range
  • utils.is_date_ambiguous -> dates.is_date_ambiguous
  • utils.get_numerical_date_from_value -> dates.get_numerical_date_from_value
  • utils.get_numerical_dates -> dates.get_numerical_dates
    • Drop support for dict type as the first parameter #934
  • filter.write_vcf -> io.write_vcf

Features

• Add the measurements subcommand with two sub-subcommands, export and concat #879 (@joverlee521)
• filter: Report min and max date separately #930 (@victorlin)
• export v2: Allow the color scale type to be temporal #969 (@jameshadfield)
• Handle FileNotFoundError and unexpected exceptions gracefully #914 (@victorlin)

Bug Fixes

• filter: Properly handle error on duplicates #918 (@victorlin)
• filter: Reorganize Cram test files #943 (@victorlin)
• filter: Reword comment on vcftools #924 (@victorlin)
• io: Split io.py into smaller files under new io/ #949 (@victorlin)
• io: Add tests for io.open_file() #926 (@victorlin)
• Move AugurError to new errors.py, replace RuntimeError #921 (@victorlin)
• Remove internal usage of utils.read_metadata() #934, #972 (@victorlin)
• schemas: Add missing display_default properties for Auspice config v2 #916 (@tsibley)
• CI: Split codecov into separate job, combine coverage of all matrix jobs #968 (@tsibley)
• CI: Temporarily disable failing test #962 (@victorlin)
• CI: pip install without editable mode #956 (@victorlin)
• CI: Include functional tests in code coverage #899 (@huddlej)
• CI: Move –quiet flag to accommodate snakemake=7.7.0 behavior #927 (@victorlin)
• CI: Move docker rebuild step to release workflow #912 (@victorlin)
• Update release process #913 (@victorlin)

15.0.2 (5 May 2022)

Bug Fixes

• docs: Fix API documentation rendering and add page for io module #896 (@joverlee521)
• CI: Use GitHub Actions for release process #904 (@victorlin)
• utils: Fix branch length annotations in json_to_tree function #908 (@huddlej)
• export v2: Use io.read_metadata during export, fixing a bug caused when the user’s input metadata does not have any valid strain id columns #909 (@huddlej)
• CI: Call new GitHub Actions workflow to rebuild images #910 (@victorlin)

15.0.1 (25 April 2022)

Bug Fixes

• traits: Fix crash when inferring traits with a single value. #891 (@huddlej)
• index: Properly handle missing inputs. #900 (@huddlej)
• index: Use standard UNIX-style line endings for output. #900 (@huddlej)

15.0.0 (15 April 2022)

Major Changes

• export: Move extensions block to meta #888 (@corneliusroemer)

  Note: this is technically a breaking change, but the misplaced extensions block was added in version 14.1.0 and intended for internal use by Nextclade. We don’t expect any users to be impacted by this.

Features

• filter: Support relative dates for --min-date and --max-date #740 (@benjaminotter, @victorlin)
• frequencies: Support relative dates for --min-date and --max-date #890 (@victorlin, @huddlej)
• docs: Add page describing how to use your own tree builder #884 (@jameshadfield, @joverlee521)

Bug Fixes

• parse: Fix --fix-dates #878 (@huddlej)
• tree: Fix internal comment on excluded sites #880 (@jameshadfield)

14.1.0 (31 March 2022)

Features

• schemas: Extend export v2 schema to support an array of trees #851 (@tsibley)
• schemas: Add JSON schemas for our root-sequence and tip-frequencies sidecars #852 (@tsibley)
• schemas: Add JSON schema for measurements sidecar #859 (@joverlee521)
• filter: Send warnings to stderr to be consistent with other warnings #862 (@victorlin)
• export: Allow an extensions block in auspice config & dataset JSONs #865 (@jameshadfield)
• export: Allow skipping of input/output schema validation #865 (@jameshadfield)
• export: Order keys in dataset for easier reading #868 (@jameshadfield)

Bug Fixes

• parse: Fix typo in internal variable name #850 (@emmahodcroft)

14.0.0 (8 February 2022)

Major Changes

• Drop support for Python 3.6, add support for 3.9 and 3.10 #822 (@victorlin)

Features

• refine: Enable bootstrap support by passing confidence values through to Auspice JSONs from augur refine node data JSONs #839 (@huddlej)
• tree: Allow users to override default tree builder arguments with a new --override-default-args flag #839 (@huddlej)
• clades: Allow descendant clades to be defined by explicitly inheriting from ancestral clade names #846 (@corneliusroemer)

Bug Fixes

• tree: Fix segmentation fault that can occur when user-provided tree builder args conflict hardcoded defaults for IQ-TREE’s. The new --override-default-args flag allows users to override the defaults that conflict with their values. #839 (@huddlej)
• filter/utils: fix year-only and numeric date handling #841 (@victorlin)
• CI: test earliest supported Biopython versions in matrix, remove redundant installs #843 (@victorlin)

13.1.2 (28 January 2022)

Features

Bug Fixes

• filter: Set default filter priority to negative infinity instead of 0. #835 (@huddlej)
• filter: Cast strains to list when subsetting metadata to prevent pandas FutureWarning. #833 (@victorlin)
• export v2: Allow periods (.) in accession numbers. #832 (@tsibley)

13.1.1 (21 January 2022)

Bug Fixes

• dependencies: Relax upper bounds on development dependencies. #821 and #830 (@victorlin, @huddlej)
• refine: Inform users when their requested root sequence is not present in the alignment. #816 (@corneliusroemer)
• utils: Fix crash with read_metadata when numexpr is installed. #826 (@victorlin)

13.1.0 (10 December 2021)

Features

• schemas: Add “$id” key to Auspice config schemas so we have a way of referring to these. #806 (@tsibley)

Bug Fixes

• filter: Fix groupby with incomplete dates. #808 (@victorlin)

13.0.4 (8 December 2021)

Bug Fixes

• dependencies: Replace deprecated mutable sequence interface for BioPython. #788 (@Carlosbogo)
• dependencies: Fix backward compatibility with BioPython. #801 (@huddlej)
• data: Add latitude and longitude details for “Reunion”. #791 (@corneliusroemer)
• filter: Use pandas functions to determine subsample groups. #794 and #797 (@victorlin)
• filter: Add clarity to help message and output of probabilistic sampling. #792 (@victorlin)

13.0.3 (19 November 2021)

Bug Fixes

• tree: Handle compressed alignment when excluding sites. #786 (@huddlej)
• docs: Fix typos (ce0834c) and clarify exclude sites inputs (5ad1574). (@corneliusroemer)

13.0.2 (12 October 2021)

Bug Fixes

• dependencies: Support latest versions of BioPython. #777 (@huddlej)
• tree: Allow users to specify arbitrary IQ-TREE models. #776 (@huddlej)

13.0.1 (1 October 2021)

Bug Fixes

• docs: Fix broken link to latitude/longitude documentation. #766 (@victorlin)
• filter: Fix reproducibility of subsampling by using the user-defined random seed in all random function calls and by ordering strain sets as lists prior to adding strains to group-by priority queues. #772 (@huddlej)

13.0.0 (17 August 2021)

Major Changes

• filter: Skip metadata records with ambiguous month information in the date column when grouping by month instead of randomly generating month values for those records. This change alters the behavior of the filter command for metadata with ambiguous month values. For these data, consider using --group-by year instead of --group-by year month. #761 (@huddlej)

Features

• filter: When grouping by year or month, report the number of strains skipped due to ambiguous year and month both in the summary report at the end of filtering and in the --output-log contents #761 (@huddlej)

12.1.1 (13 August 2021)

Bug Fixes

• filter: Fix parsing of missing data in metadata #758 (@huddlej)
• filter: Fix probabilistic sampling with small values #759 (@huddlej)

12.1.0 (12 August 2021)

Features

• export: Add support for custom legend and color scale specifications in Auspice config files #727 (@jameshadfield)
• utils: Add support for compressed strain name files (e.g., “include.txt.gz”) #730 (@benjaminotter)
• filter: Rewrite internal logic to use pandas DataFrames (#743), define filters and subsampling logic as individual functions (#745 and #746), and iterate through chunks of metadata instead of loading all records into memory at once (#750) (@tsibley, @huddlej)

Bug Fixes

• distance: Change numeric type of distance output to float #729 (@benjaminotter)
• filter: Disable probabilistic sampling when users provide --sequences-per-group #737 (@benjaminotter)
• export: Provide correct missing file error messages for metadata and node data JSON inputs #752 (@benjaminotter)

12.0.0 (13 April 2021)

Major Changes

• filter: Date bounds (--min-date and --max-date) are now inclusive instead of exclusive such that records matching the given dates will pass date filters #708 (@benjaminotter)

Bug Fixes

• refine: Recommend an alternate action when skyline optimization fails #712 (@huddlej)

Features

• distance: Count insertion/deletion events once in pairwise distances #698 (@huddlej, @benjaminotter)
• distance: Optionally ignore specific list of characters defined in a distance map’s top-level ignored_characters list #707 (@benjaminotter)
• filter: Allow --subsample-max-sequences without --group-by #710 (@benjaminotter)
• tree: Prefer iqtree2 binary over iqtree when possible #711 (@benjaminotter)

11.3.0 (19 March 2021)

Bug Fixes

• filter: Clarify how the --priority input affects subsampling in the command line help documentation #695
• tests: Clean up outputs created by tests #703, ignore log files #701, and remove unnecessary Conda environment file #702

Features

• io: Add new io module with open_file, read_sequences, and write_sequences functions that support compressed inputs and outputs #652
• parse, index, filter, mask: Add support for compressed inputs/outputs #652
• export v2: Add optional data_provenance field to auspice JSON output for better provenance reporting in Auspice #705

11.2.0 (8 March 2021)

Bug Fixes

• ancestral: Mask positions that are ambiguous in all tip sequences before inferring ancestral sequence states, to avoid assigning arbitrary ancestral values based on rounding errors #682
• titers: Add missing kwargs attribute to TiterCollection class #690

Documentation

• Update API documentation to include newer Python modules and the index subcommand #687
• Remove Zika and TB tutorials in favor of copies in docs.nextstrain.org #689

Features

• filter: Enable filtering by metadata only such that sequence inputs/outputs are optional and metadata/strain list outputs are now possible #679
• filter: Enable extraction of sequences from multiple lists of strains with a new --exclude-all flag and support for multiple inputs to the --include argument #679

11.1.2 (16 February 2021)

Bug Fixes

• index: Remove call to deprecated BioPython SeqIO.close method #684

11.1.1 (16 February 2021)

Bug Fixes

• filter: Retry probabilistic subsampling when it doesn’t select any samples #676
• titers: Skip infinite log titer values caused by zero-valued raw titers #677
• setup: Include license file with distribution artifacts instead of Python installation root #678

11.1.0 (12 February 2021)

Bug Fixes

• align/utils: Improve external command errors #638
• filter: Fix parsing of priorities files to allow spaces in sequence IDs #668
• utils: Ensure columns strain and name in metadata get parsed as strings #669

Features

• index/filter: Add new index subcommand and optional --sequence-index argument for filter command to enable filtering without inspecting sequences #651
• titers: Bump supported cvxopt version to latest 1.* release #671

11.0.0 (22 January 2021)

Major Changes

• filter: Use probabilistic sampling by default when requesting a maximum number of sequences to subsample with --subsample-max-sequences. Adds --no-probabilistic-sampling flag to disable this default behavior and prevent users from requesting fewer maximum sequences than there are subsampling groups. #659

10.3.0 (14 January 2021)

Bug Fixes

• scripts: Fix typo in verify_meta_json.py #656 (@felixonmars)
• CI: Use the expected Python version in conda environments #658
• CI: Minimize codecov feedback #661

Features

• frequencies: Add --pivot-interval-units argument with support for weekly pivots #660
• frequencies: Add support for ISO dates for --min-date and --max-date arguments #660

10.2.0 (1 January 2021)

Features

• filter: Add --probablistic-sampling flag to allow subsampling with --subsample-max-sequences when the number of groups exceeds the requested number of samples #629
• scripts: Add script to identify emerging clades from existing Nextstrain build JSONs #653
• docs: Add instructions to update conda installations prior to installing Augur #655

10.1.1 (16 November 2020)

Bug Fixes

• dependencies: Require the most recent minor versions of TreeTime (0.8.X) to fix numpy matrix errors #633

10.1.0 (13 November 2020)

Features

• docs: Migrate non-reference documentation to docs.nextstrain.org #620
• filter: Add --exclude-ambiguous-dates-by flag to enable exclusion of samples with ambiguous dates #623 and #631

10.0.4 (6 November 2020)

Bug Fixes

• tree: Use a more generic approach to escape special characters from alignment sequence names prior to running IQ-TREE #625
• filter: Reduce memory usage by not reading sequences into memory #627

10.0.3 (23 October 2020)

Bug Fixes

• refine: Report divergence by number of mutations as an integer instead of a floating point value #618
• validate: Allow internal nodes with a single child and do not allow duplicate node names #621

10.0.2 (8 September 2020)

Bug Fixes

• align: Remove references to BioPython’s deprecated Alphabet attributes #615
• Pin BioPython dependency to a max supported version to prevent breaking changes to augur in the future #615

10.0.1 (8 September 2020)

Bug Fixes

• ancestral: Clarify default values for inference of ambiguous bases #613

10.0.0 (17 August 2020)

Major Changes

• Remove Snakemake as a dependency of the augur Python package #557
  • Updated documentation to reflect external Snakemake dependency #600 and Snakemake’s required --cores argument #599
• utils: read_colors refactor #588
  • raises an exception when the requested color file is missing instead of printing a warning to stdout
  • splits out logic to parse colors file into separate classes (util_support/color_parser.py and util_support/color_parser_line.py) with unit tests
• utils: read_metadata interface improvements
  • raises exceptions when 1) input file is missing or unreadable or 2) required columns (strain or name) are missing instead of failing silently #584
  • automatically detects delimiter in metadata file instead of assuming delimiter based on filename extension #587
• utils: read_node_data interface improvements #595, #605
  • exits with a nonzero code when node data node names don’t match tree nodes and when the input tree cannot be loaded
  • refactors logic to read node data into separate classes with unit tests

Bug Fixes

• ancestral: Fix docstring for collect_mutations_and_sequences 4c474a9
• parse: Fix date parsing bug caused by a change in the API for parse_time_string in pandas 1.1.0 #601
• refine: Enable divergence unit scaling without timetree e9b3eec
• tree: Use IQ-TREE’s -nt AUTO mode when users request more threads than there are input sequences, avoiding an IQ-TREE error #598

Features

• docs: Document support for installation from Bioconda #604
• filter: Add --subsample-max-sequences argument to limit the maximum number of sequences to be included in subsampled output #593
• mask: Add --mask-invalid flag to mask invalid nucleotides from FASTA files #592

9.0.0 (29 June 2020)

Major Changes

• align: The API to the read_sequences function now returns a list of sequences instead of a dictionary #536

Bug Fixes

• align: Prevent duplicate strains warning when using --reference-name #536
• docs: Sync and deduplicate installation documentation from README to main docs #578
• export: Flexibly disambiguate multiple publications by the same author #581
• frequencies: Avoid interpolation of a single data point during frequency estimation with sparse data #569
• parse: Actually remove commas during prettify when this behavior is requested #573
• tests: Always use the local helper script (bin/augur) to run tests instead of any globally installed augur executables #527
• tree: Keep log files after trees are built #572
• utils: Do not attempt to parse dates with only ambiguous months (e.g., 2020-XX-01) #532
• utils: Parse name column of metadata as a data field instead of a pandas DataFrame attribute #564

Features

• docs: Updates description of how missing data are handled by augur traits
• filter: Add support for ISO 8601 dates (YYYY-MM-DD) for --min-date and --max-date #568
• tests: Add tests for utilities (ambiguous date parsing #532 and run_shell_command #577), parse #573, and translate #546
• tree: Allow VCF input without an --exclude-sites argument #565

8.0.0 (8 June 2020)

Major Changes

• utils: Add a consolidated generic load_mask_sites function and specific read_mask_file and read_bed_file functions for reading masking sites from files. Changes the Python API by moving mask-loading functionality out of augur mask and tree into utils #514 and #550
• mask: Parse BED files as zero-indexed, half-open intervals #512

Bug Fixes

• traits: Export mugration models to the same output directory as traits JSON #544
• Explicitly open files with UTF-8 file encoding #499, #503, and #560
• refine: Only request confidence intervals from TreeTime when no clock rate is provided #548
• refine: Catch failed skyline optimization #556

Features

• align: Report insertions stripped during alignment #449
• Require minimum pandas version of 1.0.0 #488
• parse: Reduce memory use and clarify code with standard Python idioms #496
• mask: Allow masking of specific sites passed by the user with --mask-sites and masking of a fixed number of sites from the beginning or end of each sequence with --mask-from-beginning and --mask-from-end #512
• clades, import: Use defaultdict to simplify code #533
• tests: Add initial functional tests of the augur command line interface using Cram #542
• refine: Add a --seed argument to set the random seed for more reproducible outputs across runs #542
• ancestral, refine, and traits: Print the version of TreeTime being used for these commands #552
• filter: Add support for flexible pandas-style queries with new --query argument #555
• export: Allow display defaults for transmission lines #561

7.0.2 (7 April 2020)

Bug Fixes

• filter: Fix regression introduced in 7.0.0 which caused an error to be raised if a priorities file didn’t include every sequence. Sequences which are not explicitly listed will once again default to a priority of 0. #530

7.0.1 (7 April 2020)

Bug Fixes

• Fix typo with Python classifiers in setup.py

7.0.0 (7 April 2020)

Major Changes

• Drop support for Python 3.4 and 3.5 #482
• Drop support for --output flag in augur ancestral, clades, sequence-traits, traits, and translate in favor of --output-node-data flag #529

Features

• improve testing by
  • adding a simple shell script to run tests and improving pytest configuration and output #463
  • adding code coverage reports (#486, #491) and integration with codecov.io #508
  • adding unit tests for align (#477), filter (#478, #479, #487), utils (#501)
• align: reverse complement sequences when necessary using mafft’s autodirection flag #467
• align: speed up replacement of gaps with “ambiguous” bases #474
• mask: add support for FASTA input files #493
• traits: bump TreeTime version to 0.7.4 and increase maximum number of unique traits allowed from 180 to 300 #495

Bug Fixes

• align: enable filling gaps in input sequences even if no reference is provided instead of throwing an exception #466
• align: detect duplicate sequences by comparing sequence objects instead of (often truncated) string representations of those objects #468
• import_beast: use raw strings for regular expressions to avoid syntax errors in future versions of Python #469
• scripts: update exception syntax to new style #484
• filter: fail loudly when a given priority file is invalid and exit instead of just printing an error #487

Documentation

• README: document need for brew tap prior to brew install #471
• DEV_DOCS: add a proper section on how to write and run tests #481
• README: improve discoverability of core documentation with RTD badge #490

6.4.3 (25 March 2020)

Bug Fixes

• align: Remove reference sequence from alignments even when no gaps exist in input sequences relative to the reference. Thank you @danielsoneg! #456

Documentation

• Reorganize README, improve findability of documentation, and add separate dev docs. #461

6.4.2 (17 March 2020)

Bug Fixes

• Require Snakemake less than 5.11 to avoid a breaking change. The --cores argument is now required by 5.11, which will affect many existing augur-based workflows. Reported upstream as snakemake/snakemake#283.

• align: Run mafft with the --nomemsave option. This makes alignments of sequences over 10k in length run much, much faster in the general case and shouldn’t cause issues for most modern hardware. We may end up needing to add an off-switch for this mode if it causes issues for other users of augur, but the hope is that it will make things just magically run faster for most folks! There is likely more tuning that could be done with mafft, but this is a huge improvement in our testing. #458

• align: Ignore blank lines in --include files. Thanks @CameronDevine! #451

• align: Properly quote filenames when invoking mafft. Thanks @CameronDevine! #452

6.4.1 (4 March 2020)

Bug Fixes

• export: AA labels are now exported for branches where a clade is also labeled See PR 447

• export / validation: a dataset title is no longer required

• release script now works on MacOS & code-signing is optional See PR 448

• traits: Missing data is correctly handled

6.4.0 (26 February 2020)

Features

• align: New sequences can now be added to an existing alignment. #422

• align: Multiple sequence files can be provided as input. #422

• align: Extra debugging files such as *.pre_aligner.fasta and *.post_aligner.fasta are no longer produced by default. To request them, pass the --debug flag. #422

• align: De-duplicate input sequences, with a warning. #422

• export v2: Add support for the branch_label property in display_defaults, which was recently added to Auspice. #445

Bug fixes

• align: Exits with an error earlier if arguments are invalid instead of only printing a warning. #422

• align: Performs more error checking and clarifies the help and error messages. #422

• export v2: Traits which are filters but not colorings are now exported as well, instead of being left out. #442

• export v2: Exits non-zero when validation fails, instead of masking errors. #441

• validate: In order to improve clarity, messages now include the filenames involved and distinguish between schema validation and internal consistency checks. #441

6.3.0 (13 February 2020)

Features

• Augur refine, ancestral and traits now use the upgraded TreeTime v0.7 This should have a number of under-the-hood improvements. See PR 431
• ancestral: New options to either --keep-ambiguous or --infer-ambiguous. If using --infer-ambiguous the previous behavior will be maintained in which tips with N will have their nucleotide state inferred. If using --keep-ambiguous, these tips will be left as N. With this upgrade, we are still defaulting to --infer-ambiguous, however, we plan to swap default to --keep-ambiguous in the future. If this distintion matters to you, we would suggest that you explicitly record --keep-ambiguous / --infer-ambiguous in your build process. Also part of PR 431
• traits: Allow input of --weights which references a .tsv file in the following format:

  division	Hubei	10.0
  division	Jiangxi	1.0
  division	Chongqing	1.0
  

  where these weights represent equilibrium frequencies in the CTMC transition model. We imagine the primary use of user-specified weights to correct for strong sampling biases in available data. See PR 443

Bug fixes

• Improvements to make shell scripts run more easily on Windows. See PR 437

6.2.0 (25 January 2020)

Features

• refine: Include --divergence-units option to distinguish between mutations and mutations-per-site. Keep mutations-per-site as default behavior. See PR 435

Bug fixes

• utils: Support v2 auspice JSONs in json_to_tree utility function. See PR 432

6.1.1 (17 December 2019)

Bug fixes

• frequencies: Fix bug in string matching for weighted frequencies introduced in v6.1.0. See PR 426.

6.1.0 (13 December 2019)

Features

• export: Include --description option to pass in a Markdown file with dataset description. This is displays in Auspice in the footer. For rationale, see Auspice issue 707 and for Augur changes see PR 423.

Bug fixes

• frequencies: Fix weighted frequencies when weight keys are unrepresented. See PR 420.

6.0.0 (10 December 2019)

Overview

Version 6 is a major release of augur affecting many augur commands. The format of the exported JSON (v2) has changed and now merges the previously separate files containing tree and meta information. To maintain backward compatibility, the export command was split into export v1 (old) and export v2 (new). Detailed release notes are provided in the augur documentation on read-the-docs. For a migration guide, consult migrating-v5-v6.

Major features / changes

• export: Swap from a separate _tree.json and _meta.json to a single “unified” dataset.json output file
• export: Include additional command line options to alleviate need for Auspice config
• export: Include option for reference sequence output
• export: Move to GFF-style annotations
• export: Validate exported JSONs against schema
• ancestral: Allow output of FASTA and JSON files
• import: Include import beast command to import labeled BEAST MCC tree
• parse: Include --prettify-fields option to cleanup metadata fields
• Documentation improvements

Minor features / changes

• colors.tsv: Allow whitespace, but insist on tab delimiting
• lat_longs.tsv: Allow whitespace, but insist on tab delimiting
• Remove code for old “non-modular” augur, old “non-modular” builds and Python tests
• Improve test builds
• filter: More interpretable output of how many sequences have been filtered
• filter: Additional flag --subsample-seed to seed the random number generator and thereby make subsampling reproducible
• sequence-traits: Numerical output as originally intended, but required an Auspice bugfix
• traits: Explanation of what is considered missing data & how it is interpreted
• traits: GTR models are exported in the output JSON for better accountability & reproducibility

5.4.1 (12 November 2019)

Bug fixes

• export v1: Include --minify-json option that was mistakenly not included in PR 398. See PR 409

5.4.0 (7 November 2019)

Features

• frequencies: Include --minimal-clade-size-to-estimate command line option. See PR 383
• lbi: Include --no-normalization command line option. See PR 380

Compatibility fixes

• export: Include v1 subcommand to allow forwards compatibiliy with Augur v6 builds. See PR 398

Bug fixes

• export: Include warning if using a mismatched v6 translate file. See PR 392
• frequencies: Fix determination of interval for clipping of non-informative pivots

5.3.0 (9 September 2019)

Features

• export: Improve printing of error messages with missing or conflicting author data. See issue 274
• filter: Improve printing of dropped strains to include reasons why strains were dropped. See PR 367
• refine: Add support for command line flag --keep-polytomies to not resolve polytomies when producing a time tree. See PR 345

Bug fixes

• Catch and throw error when there are duplicate strain names. See PR 356
• Fix missing annotation of “parent” attribute for the root node
• Run shell commands with more robust error checking. See PR 350
• Better handling of rerooting options for trees without temporal information. See issue 348

Data

• Small fixes in geographic coordinate file

5.2.1 (4 August 2019)

Bug fixes

• Print more useful error message if Python recursion limit is reached. See issue 328
• Print more useful error message if vcftools if missing. See PR 312

Development

• Significantly relax version requirements specified in setup.py for biopython, pandas, etc… Additionally, move lesser used packages (cvxopt, matplotlib, seaborn) into an “extras_require” field. This should reduce conflicts with other pip installed packages. See PR 323

Data

• Include additional country lat/longs in base data

5.2.0 (23 July 2019)

Features

• ancestral: Adds a new flag --output-sequences and logic to support saving ancestral sequences and leaves from the given tree to a FASTA file. Also adds a redundant, more specific flag --output-node-data that will replace the current --output flag in the next major version release of augur. For now, we issue a deprecation warning when the --output flag is used. Note that FASTA output is only allowed for FASTA inputs and not for VCFs. We don’t allow FASTA output for VCFs anywhere else and, if we did here, the output files would be very large. See PR 293

• frequencies: Allow --method kde flag to compute frequencies via KDE kernels. This complements existing method of --method diffusion. Generally, KDE frequencies should be more robust and faster to run, but will not project as well when forecasting frequencies into the future. See PR 271

Bug fixes

• ancestral, traits, translate: Print warning if supplied tree is missing internal node names (normally provided by running augur refine). See PR 283

• Include pip in Conda enviroment file. See PR 309

Documentation

• Document environment variables respected by Augur

Development

• Remove matplotlib and seaborn from setup.py install. These are still called a few places in augur (like titers.validate()), but it was deemed rare enough that remove this from setup.py would ease general install for most users. Additionally, the ipdb debugger has been moved to dev dependencies. See PR 291

• Refactor logic to read trees from multiple formats into a function. Adds a new function read_tree to the utils module that tries to safely handle reading trees in multiple input formats. See PR 310

5.1.1 (1 July 2019)

Features

• tree: Add support for the GTR+R10 substitution model.
• tree: Support parentheses in node names when using IQ-TREE.

Bug fixes

• Use the center of the UK for its coordinates instead of London.
• filter: Mark --output required, which it always was but wasn’t marked.
• filter: Avoid error when no excluded strains file is provided.
• export: Fix for preliminary version 2 schema support.
• refine: Correct error handling when the tree file is missing or empty.

Documentation

• Add examples of Augur usage in the wild.
• Rename and reorganize CLI and Python API pages a little bit to make “where do I start learning to use Augur?” clearer to non-devs.

Development

• Relax version requirements of pandas and seaborn. The hope is this will make installation smoother (particularly alongside other packages which require newer pandas versions) while not encountering breaking changes in newer versions ourselves.

5.1.0 (29 May 2019)

Documentation

• Documentation is now available online for the augur CLI and Python API via Read The Docs: https://nextstrain-augur.readthedocs.io. The latest version on RTD points to the git master branch, and the stable version to the most recent tagged release. Instructions for building the docs locally are in the README.

5.0.0 (26 May 2019)

Features

• ancestral: New option to --keep-ambiguous, which will not infer nucleotides at ambiguous (N) sites on tip sequences and instead leave as ‘N’ See PR 280.
• ancestral: New option to --keep-overhangs, which will not infer nucleotides for gaps on either side of the alignment and instead leave as ‘-‘. See PR 286.
• clades: This module has been reconfigured to identify clade defining mutations on top of a reference rather than identifying mutations along the tree. The command line arguments are the same except for the addition of --reference, which explicitly passes in a reference sequence. If --reference is not defined, then reference will be drawn from the root node of the phylogeny by looking for sequence attribute attached to root node of --tree. See PR 288.
• refine: Revise rooting behavior. Previously --root took ‘best’, ‘residual’, ‘rsq’ and ‘min_dev’ as options. In this update --root takes ‘best’, least-squares’, ‘min_dev’ and ‘oldest’ as rooting options. This eliminates ‘residual’ and ‘rsq’ as options. This is a backwards-incompatible change. This requires updating TreeTime to version 0.5.4 or above. See PR 263.
• refine: Add --keep-root option that overrides --root specification to preserve tree rooting. See PR 263.
• refine: Add --covariance and --no-covariance options that specify TreeTime behavior. See PR 263.
• titers: This command now throws an InsufficientDataException if there are not sufficient titers to infer a model. This is paired with a new --allow-empty-model flag that proceeds past the InsufficientDataException and writes out a model JSON corresponding to an ‘empty’ model. See PR 281.
• By default JSONs are written with index=1 to give a pretty-printed JSON. However, this adds significant file size to large tree JSONs. If the environment variable AUGUR_MINIFY_JSON is set then minified JSONs are printed instead. This mirror the explicit --minify-json argument available to augur export. See PR 278.

Bug fixes

• export: Cast numeric values to strings for export. See issue 287.
• export: Legend order preserves ordering passed in by user for traits that have default colorings (‘country’ and ‘region’). See PR 284.
• refine: Previously, the --root argument was silently ignored when no timetree was inferred. Re-rooting with an outgroup is sensible even without a timetree. See PR 282.

4.0.0 (24 April 2019)

Features

• distance: New interface for specifying distances between sequences. This is a backwards-incompatible change. Refer to augur distance --help for all the details.

• export: Add a --minify-json flag to omit indentation in Auspice JSONs.

Bug fixes

• frequencies: Emit one-based coordinates (instead of zero-based) for KDE-based mutation frequencies

Data

• Include additional country lat/longs in base data

3.1.8 (13 February 2019)

Bug fixes

• titers: fix calculation of mean_potentency for model export

3.1.7 (5 February 2019)

Bug fixes

• Update to TreeTime 0.5.3
• tree: Fix bug in printing causing errors in Python versions <3.6
• tree: Alter site masking to not be so memory intensive

3.1.6 (29 January 2019)

Features

• filter: Allow negative matches to --exclude-where. For example, --exclude-where country!=usa would exclude all samples where metadata country does not equal usa.
• tree: Allow --exclude-sites to work with FASTA input. Ensure that indexing of input sites is one-based.

Bug fixes

• fix loading of strains when loading titers from file, previously strains had not been filtered to match the tree appropriately

3.1.5 (13 January 2019)

Features

• frequencies: Add --ignore-char and --minimal-clade-size as options.
• frequencies: Include --stiffness and --inertia as options.
• titers: Allow multiple titer date files in --titers import.

Bug fixes

• filter: Fix --non-nucleotide call to include ? as allowed character.
• tree: Fix --method raxml to properly delimit interim RAxML output so that simultaneous builds don’t conflict.

Data

• Include additional country lat/longs in base data

3.1.4 (1 January 2019)

Bug fixes

• frequencies: Include counts in augur frequencies output JSON to support downstream plotting.

Data

• Include additional country lat/longs in base data

3.1.3 (29 December 2018)

Features

• filter: Add --non-nucleotide option to remove sequences with non-conforming nucleotide characters.

Bug fixes

• Revise treatment of -, ` ` in augur parse to leave - as is and remove white space. Also delimit [ and ] to _.
• Fix bug in naming of temp IQTREE fixes to prevent conflicts from simultaneous builds.

Data

• Include additional country lat/longs in base data

Development

• Remove non-modular measles build in favor of nextstrain/measles repo.

3.1.2 (21 December 2018)

Bug fixes

• Update dependencies

3.1.1 (21 December 2018)

Bug fixes

• filter: Fix --include-where. Adds an all_seq variable needed by the logic to include records by value. This was previously working for VCF but threw an exception for sequences in FASTA format.
• Update flu reference viruses and lat longs.
• Update dependencies

3.1.0 (18 December 2018)

Features

• reconstruct-sequences: Include augur reconstruct-sequences module that reconstructs alignments from mutations inferred on the tree
• distance: Include augur distance module that calculates the distance between amino acid sequences across entire genes or at a predefined subset of sites
• lbi: Include augur lbi module that calculates local branching index (LBI) for a given tree and one or more sets of parameters.
• frequencies: Include --method kde as option to augur frequencies, separate from the existing --method diffusion logic. KDE frequencies are faster and better for smaller clades but don’t extrapolate as well as diffusion frequencies.
• titers: Enable annotation of nodes in a tree from the substitution model

3.0.5.dev1 (26 November 2018)

Bug fixes

• translate: Nucleotide (“nuc”) annotation for non-bacterial builds starts at 0 again, not 1, fixing a regression.

Documentation

• Schemas: Correct coordinate system description for genome start/end annotations.

3.0.4.dev1 (26 November 2018)

Bug fixes

• validate: Fix regression for gene names containing an asterisk.

Development

• Fix Travis CI tests which were silently not running.

3.0.3.dev1 (26 November 2018)

Features

• refine: Add a --clock-std-dev option

• traits: Add a --sampling-bias-correction option for mugration model

• validate: Gene names in tree annotations may now contain hyphens. Compatible with Auspice version 1.33.0 and later.

• All JSON is now emitted with sorted keys, making it easier to diff and run other textual comparisons against output.

Bug fixes

• filter: Only consider A, T, C, and G when calculating sequence length for the --min-length option.

• filter: Allow comments in files passed to --exclude.

• filter: Ignore case when matching trait values against excluded values.

• Normalize custom geographic names to lower case for consistent matching.

Data

• Fix typo in geographic entry for netherlands.

• Schemas: Reconcile naming patterns used in gene definitions and tree annotations.

Development

• Upgrade TreeTime dependency to 0.5.x and at least 0.5.1.

• Add an environment.yml file for use with conda env create.

• Stop testing under Python 2.7 on Travis CI.

3.0.2.dev1 (27 September 2018)

Bug fixes

• translate: Fix broken --help message

3.0.1.dev1 (27 September 2018)

Features

• align and tree: The –nthreads option now accepts the special value “auto” to automatically set the number of threads to the number of CPU cores available.

• Alias augur --version to augur version

Bug fixes

• tree: The –nthreads option is now respected. Previously all tree builders were ignoring the value and using either 2 threads (RAxML, IQ-TREE) or as many threads as cores (FastTree, if the OpenMP version).

• translate: Check for and, if necessary pad, nucleotide sequences which aren’t a multiple of 3 earlier to avoid errors later.

• export: Optionally write inferred nucleotide and amino acid sequences (or mutations) to a separate file.

• export: Omit genes with no amino acid mutations.

• validate: Allow underscores in gene names.

• refine: Remove unused –nthreads argument.

• ancestral, filter, tree, refine: Exit 1 instead of -1 on error.

• Print the help message, instead of throwing an exception, when augur is run without arguments.

Documentation

• Briefly describe each command in its --help output and in the global augur --help output.

• Revamp README to emphasize new, modular augur and make it suitable for inclusion on PyPi.

• Reconciled conflicting license declarations; augur is AGPLv3 (not MIT) licensed like the rest of Nextstrain.

• Include URLs for bug reports, the change log, and the source on PyPi.

Data

• Geographic coordinates added for the Netherlands and the Philippines.

Development

• Reset the release branch when rewinding a failed local release process.

• Refactor the augur program and command architecture for improved maintainability.

3.0.0.dev3 (4 September 2018)

Development

• Use an allowed Topic classifier so we can upload to PyPi

• Ignore distribution egg-info build files

3.0.0.dev2 (4 September 2018)

Features

• Export: Add safety checks for optional annotations and geo data

• Include more lat/longs in the default geo data

Development

• Add release tooling

• Document the release process and a few development practices

• Travis CI: Switch to rebuilding the Docker image only for new releases

• Remove ebola, lassa, tb, WNV, and zika builds now in their own repos. These builds are now available at URLs like https://github.com/nextstrain/ebola, for example.

3.0.0.dev1 (unreleased)

Development

• Start versioning augur beginning with 3.0.0. A new augur version command reports the running version.