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v3.4.0

@luizirber luizirber released this
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Major new features:

  • enable seamless loading of signatures from indexed databases (#1059, #1083, #1090)
  • add signature cat and signature split commands to combine/split signature files (#1044, #1074)
  • add compute-optimized MinHash (for small scaled or large cardinalities) in Rust (#1045)
  • optionally weight lca summarize output by hashval abundance. (#1022)
  • enable moltypes other than DNA in LCA databases (#1013)

Minor improvements:

  • add --num-results/-n to gather (#1047)
  • improve lca index error message when inserting num signature (#1076)
  • autodetect FASTA/FASTQ files if given as signatures (#1078)
  • add is_lineage_match, pop_to_rank, make_lineage to lca_utils (#1081)
  • use stricter niffler versions and add new gz feature to it (#1070)
  • added MinHash.clear() and MinHash.add_hash_with_abundance to Python API (#1046)

Bugs fixed:

  • investigations and fixes around new gather behavior. (#1001)

Refactoring:

  • move tests from test_lca into test_lca_functions (#1035)
  • remove unused run_shell_cmd function (#1032)
  • refactor some tests in test_sourmash.py to use @utils.in_tempdir decorators (#1020)
  • use install scripts from py-ipfs-http-client (#1068)

Documentation:

  • Improve documentation around abundance projection (#1073)
  • Replace recommonmark with myst (docs) (#1021)
  • Fix doctest filename error (#1040)

Thanks to @luizirber @ctb @bluegenes @erikyoung85 for their contributions!