Nextstrain-augur

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][]

[557]: https://github.com/nextstrain/augur/pull/557
[584]: https://github.com/nextstrain/augur/pull/584
[587]: https://github.com/nextstrain/augur/pull/587
[588]: https://github.com/nextstrain/augur/pull/588
[592]: https://github.com/nextstrain/augur/pull/592
[593]: https://github.com/nextstrain/augur/pull/593
[595]: https://github.com/nextstrain/augur/pull/595
[598]: https://github.com/nextstrain/augur/pull/598
[599]: https://github.com/nextstrain/augur/pull/599
[600]: https://github.com/nextstrain/augur/pull/600
[601]: https://github.com/nextstrain/augur/pull/601
[604]: https://github.com/nextstrain/augur/pull/604
[605]: https://github.com/nextstrain/augur/pull/605
[e9b3eec]: https://github.com/nextstrain/augur/commit/e9b3eec670b9603874e195cc1ccd4f3c1aeef5dd
[4c474a9]: https://github.com/nextstrain/augur/commit/4c474a96232e9cc333e3fc4c0971336a090b703c

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][]

[527]: https://github.com/nextstrain/augur/pull/527
[532]: https://github.com/nextstrain/augur/pull/532
[536]: https://github.com/nextstrain/augur/pull/536
[546]: https://github.com/nextstrain/augur/pull/546
[564]: https://github.com/nextstrain/augur/pull/564
[565]: https://github.com/nextstrain/augur/pull/565
[568]: https://github.com/nextstrain/augur/pull/568
[569]: https://github.com/nextstrain/augur/pull/569
[572]: https://github.com/nextstrain/augur/pull/572
[573]: https://github.com/nextstrain/augur/pull/573
[577]: https://github.com/nextstrain/augur/pull/577
[578]: https://github.com/nextstrain/augur/pull/578
[581]: https://github.com/nextstrain/augur/pull/581

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][]

[449]: https://github.com/nextstrain/augur/pull/449
[488]: https://github.com/nextstrain/augur/pull/488
[496]: https://github.com/nextstrain/augur/pull/496
[499]: https://github.com/nextstrain/augur/pull/499
[503]: https://github.com/nextstrain/augur/pull/503
[512]: https://github.com/nextstrain/augur/pull/512
[514]: https://github.com/nextstrain/augur/pull/514
[533]: https://github.com/nextstrain/augur/pull/533
[542]: https://github.com/nextstrain/augur/pull/542
[544]: https://github.com/nextstrain/augur/pull/544
[548]: https://github.com/nextstrain/augur/pull/548
[550]: https://github.com/nextstrain/augur/pull/550
[552]: https://github.com/nextstrain/augur/pull/552
[555]: https://github.com/nextstrain/augur/pull/555
[556]: https://github.com/nextstrain/augur/pull/556
[560]: https://github.com/nextstrain/augur/pull/560
[561]: https://github.com/nextstrain/augur/pull/561

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][]

[530]: https://github.com/nextstrain/augur/pull/530

Bug Fixes

* Fix typo with Python classifiers in setup.py

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][]

[463]: https://github.com/nextstrain/augur/pull/463/
[466]: https://github.com/nextstrain/augur/pull/466
[467]: https://github.com/nextstrain/augur/pull/467
[468]: https://github.com/nextstrain/augur/pull/468
[469]: https://github.com/nextstrain/augur/pull/469
[471]: https://github.com/nextstrain/augur/pull/471
[474]: https://github.com/nextstrain/augur/pull/474
[477]: https://github.com/nextstrain/augur/pull/477
[478]: https://github.com/nextstrain/augur/pull/478
[479]: https://github.com/nextstrain/augur/pull/479
[481]: https://github.com/nextstrain/augur/pull/481
[482]: https://github.com/nextstrain/augur/pull/482
[484]: https://github.com/nextstrain/augur/pull/484
[486]: https://github.com/nextstrain/augur/pull/486
[487]: https://github.com/nextstrain/augur/pull/487
[490]: https://github.com/nextstrain/augur/pull/490
[491]: https://github.com/nextstrain/augur/pull/491
[493]: https://github.com/nextstrain/augur/pull/493
[495]: https://github.com/nextstrain/augur/pull/495
[501]: https://github.com/nextstrain/augur/pull/501
[508]: https://github.com/nextstrain/augur/pull/508
[529]: https://github.com/nextstrain/augur/pull/529