Nextstrain-augur

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][]

[620]: https://github.com/nextstrain/augur/pull/620
[623]: https://github.com/nextstrain/augur/pull/623
[631]: https://github.com/nextstrain/augur/pull/631

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][]

[625]: https://github.com/nextstrain/augur/pull/625
[627]: https://github.com/nextstrain/augur/pull/627

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][]

[618]: https://github.com/nextstrain/augur/pull/618
[621]: https://github.com/nextstrain/augur/pull/621

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][]

[615]: https://github.com/nextstrain/augur/pull/615

Bug Fixes

* ancestral: Clarify default values for inference of ambiguous bases [613][]

[613]: https://github.com/nextstrain/augur/pull/613

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