Sourmash

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)

None

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)

Bugs:

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

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)

- 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)