v3.2.0: 3.2.0

Features:

• Move functionality to Rust for signature computation and downsampling code in sbtmh.py (#845) (#856)
• add --labeltext to plot (#854)

Improvements:

• Improve sketching performance with lookup tables for complement and DNA validation (#861) (#865)
• refactor argparse.FileType out of sourmash argument handling. (#853)

Bugs:

• Fix 'gather' threshold reporting to report threshold, not match. (#850)
• Fix counting of species during lca index (#841)

Build, CI and docs:

• Fix travis conditions and pip usage (#873)
• Use Python dev mode on 3.7, and build PRs that merge against any branch (#864)
• Use tarpaulin instead of grcov (#862)
• only run rust checks if it changes rust code (#852)
• Release process update for 3.1.0 (#847)
• Ignore .sig and .sbt files for repo language stats (#846)

v3.1.0: 3.1.0

Features:

• Implement improved & consistent argument parsing (#785)
• Moving loading and save sigs to rust (#532)
• Update gather implementations for LCA and SBT to use thresholding (#843)

Improvements:

• Do add_many in Rust, use it in LCA _signatures (#826) (#840)
• Expose an unload method for SBT nodes (#784)

Build, CI and docs:

• Trigger new Software Heritage archival snapshot on new tags (#839)
• Fix netlify build (#842)
• Document code structure in dev guide (#832)
• use python 3.7 in RTD build (#825)

v3.0.1: 3.0.1

Improvements:

- Add a 'display_lineage' function to lca_utils.py (#813)

Build, CI and docs:

- Fix read the docs build (#820)

3.0.0

Features:

• Replacing C++ with Rust (#424)
• Create an Index abstract base class (#556)

Improvements:

• improve error handling etc. in sourmash lca index. (#798)
• Move similarity with abundance computation into Rust (#808)

Bugs:

• fix mem leak in get_mins (#807)
• Fix LCA search error if query has abundance (#804)

Build, CI and docs:

• Set up MSRV, minimum supported rust version (#806)
• update docs and add recommonmark as a test dependency (#805)
• Release process updates and sourmash 3.0 release notes (#776)

v2.3.1: 2.3.1

Bugs:

• fix some bugs in rankinfo (#797)
• Better molecule type checks (#782)

v2.3.0: 2.3.0

Features:

• Add hp encoding for proteins (#758)
• Add sourmash signature filter to do abundance filtering. (#748)
• add a --abundances-from flag to sourmash signature intersect, to preserve abundances (#747)

Improvements:

• Include more base deps: numpy, scipy and matplotlib (#770)
• bam2fasta package to simplify sourmash compute (#768)
• Optimize KmerMinHash add_sequence (#744)

Bugs:

• Force signature order in test_sig_filter_1 to fix heisenbug (#761)
• save_signatures with a file opened in binary mode fails (#746)
• saved fasta files incorrectly (#740)
• Bug: segfault with set_abundances (#745)

Build, CI and docs:

• update cibuildwheel (#774)
• Fix asv benchmarks (#509) (#759)
• add the f1000 paper (#739)
• release docs update (#554)

Rust changes:

• Experimental SBT with MQF internal nodes in Rust (#772)
• Fixes for WASI compilation (#771)
• changes to rust code from core/rust branch (#760)

v2.2.0

• Parallelized compare function with multiprocessing (#709)
• add compute signatures for 10x bam file (#713)
• Experimental v5 SBT format (#694)
• initial refactor of compute command (and associated test module) (#734)
• Fix --output-unassigned to output abundances if available. (#726)
• Update docstring for --traverse-directory on sourmash index (#727)

v2.1.0: 2.1.0

- New feature: Dayhoff encoding of amino acids (#689) @olgabot
- Compare outputs can be saved to an output dir (#715) @ctb
- Fix `MinHash.merge` on scaled signatures with abundance tracking (#718) @ctb
- Documentation fixes #719 #717 @ctb

v2.0.1: 2.0.1

- Fix memory leaf in MinHash.intersection (#687)
- Update README with correct install instructions (#677) (#592)
- Travis build fixes (#681) (#676)
- Remove pre-release note from docs (#675)

v2.0.0

[MRG] release notes for v2.0 (#630)
[MRG] update documentation & add notebooks to docs (#631)
Smaller 10x test case (#569)
fix path issue with numpy and 2.7; fix travis badge (#640)
update lca link (#633)
[MRG] update `sourmash sig rename` to work on multiple signatures (#620)
remove lingering uses of sourmash_lib (#626)
try mocking the broken _minhash import for autodoc (#621)
shrink the size of the test data directory by downscaling a sig and removing an unnecessary file (#627)
add citation output (#617)
[MRG] gather optimizations (#615)
[MRG] output unassigned hashes when there are no gather matches (#613)
[MRG] add 'sourmash signature' signature manipulation utilities.  (#587)
Make sure either scaled or num is set on `MinHash(...)` construction (#605)
update documentation version (#598)