Sourmash

Bugs:

- re-add 'signature' as alias for 'sig' (881)

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)

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)