Sourmash

Major new features:
* Document `sourmash.fig` usage and behavior; enable output of `compare` clustering with labels (859)
* Adds --majority option to `lca classify` using majority vote algorithm (1113)

Minor improvements:
* MinHash compatibility check to sourmash sig intersect (1116)

Bugs fixed:
* add ksize selectors back into sourmash sig functions (1105)

Documentation updates:
* Minor updates to release procedure (1102)
* Update DB links in docs (1084)

Major new features:
* enable seamless loading of signatures from indexed databases (1059, 1083, 1090)
* add `signature cat` and `signature split` commands to combine/split signature files (1044, 1074)
* add compute-optimized MinHash (for small scaled or large cardinalities) in Rust (1045)
* optionally weight lca summarize output by hashval abundance. (1022)
* enable moltypes other than DNA in LCA databases (1013)

Minor improvements:
* add --num-results/-n to gather (1047)
* improve lca index error message when inserting num signature (1076)
* autodetect FASTA/FASTQ files if given as signatures (1078)
* add is_lineage_match, pop_to_rank, make_lineage to lca_utils (1081)
* use stricter niffler versions and add new gz feature to it (1070)
* added `MinHash.clear()` and `MinHash.add_hash_with_abundance` to Python API (1046)

Bugs fixed:
* investigations and fixes around new gather behavior. (1001)

Refactoring:
* move tests from `test_lca` into `test_lca_functions` (1035)
* remove unused run_shell_cmd function (1032)
* refactor some tests in test_sourmash.py to use utils.in_tempdir decorators (1020)
* use install scripts from py-ipfs-http-client (1068)

Documentation:
* Improve documentation around abundance projection (1073)
* Replace recommonmark with myst (docs) (1021)
* Fix doctest filename error (1040)

Thanks to luizirber ctb bluegenes erikyoung85 for their contributions!

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)