Sourmash

Improvements:

- Deal with duplicated MD5 in storages (994)
- Hide internal representation in core, and update FFI and cbindgen (986)

Build, CI and docs:

- upgrade sourmash index usage docs on CLI (975)
- Fix two temp files output locations in tests (989)

Improvements:

* add `ZipStorage`, support loading SBT databases from storage; `.sbt.zip` extensions. (648)
* Replace `khmer.Nodegraph` with rust nodegraph; ~5x speedup of SBT search & gather. (799)

Bugs:

* Document and (lightly) fix the `LCA_Database` API. (966)
* Fix bug when using Python 3.5 and before; refactor `LCA_Database` tests (962)

Documentation:

* Document gather abund tests a bit better; minor refactoring (886)
* Improve lca index error (963)

Incompatibilities with previous versions due to bugs:
* `sourmash gather` on SBT databases was setting `--threshold-bp=0` in all cases. This was fixed in 942, and output may change. Specify `--threshold-bp=0` to recover old behavior.

Improvements:

* refactor LCA_Database class to support programmatic creation. (946)
* add --singleton option to lca summarize (922)
* update gather to calculate fraction of match that was in original query (938)
* add compare --containment (937)
* add --outdir argument to `sourmash compute` (935)
* improvements to sourmash argparse output for compute. (931)

Bugs:
* fix `lca classify` bug with -o (902)
* set_abundances now works with large signatures (911)
* test & fix LinearIndex, SBT, and LCA `gather` thresholding. (942)

Build, CI and docs:
* create .sonarcloud.properties
* pin virtualenv version for asv, and also run GH actions on rust version tags (903)
* add make clean & rustup update to dev docs (927)

Improvements:

- more refactoring of MinHash API (889)
- add_hash_with_abundance method in core library (892)
- Replace mins_push and abunds_push with set_abundances (887)
- More refactoring of MinHash comparison code (882)
- better sourmash compare error handling (876)

Bugs:

- add_hash with num doesn't set abundances properly (891)
- name signatures based on md5sum, not on name() (884)

Build, CI and docs:

- update docs for how to run Rust tests (888)

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)