Releases: sourmash-bio/sourmash
Releases · sourmash-bio/sourmash
3.0.0
v2.3.1: 2.3.1
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:
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
onsourmash 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)
v1.0
version 0.9.6
Fix package import problem.
version 0.9.5
Update of minor release-related issues.