dib-lab/sourmash: v4.0.0rc1

This is a pre-release version of sourmash v4.0.0. Draft release notes are below; comments appreciated! Major changes for 4.0 4.0 is a major new version of sourmash, and it contains a number of new and breaking features. Please see our migration guide for more information on how to migrate from v3.x to version 4.0! New or changed behavior default SBT storage is now .sbt.zip (#1174, #1170) add sourmash sketch command for creating signatures (#1159) protein ksizes in MinHash are now divided by 3, except in sourmash compute (#1277) refactor MinHash API and implementation: add, iadd, merge, hashes, and max_hash (#1282, #1154, #1139, #1301) add HyperLogLog implementation (#1223) SourmashSignature.name is now a property (not a method): use str(sig) instead of name() (#1179, #1232) lca summarize no longer merges all signatures, and uses hash abundance by default (#1175) indexand lca index (#1186, #1222) now support --from-file and no longer require signature files on command line --traverse-directory is now on by default for signature loading behavior (#1178) Feature removal remove Python 2.7 support (& end Python 2 compatibility) (#1145, #1144) remove lca gather (#1307) remove 10x support from sourmash compute (#1229) remove 'dump' command (#1157) Feature/function deprecations deprecate sourmash compute (#1159) deprecate load_signatures, sourmash.load_one_signature, create_sbt_index, and load_sbt_index (#1279, #1304) deprecate import_csv in favor of new sourmash sig import --csv (#1281) Refactoring, improvements, and minor bug fixes: accept file list in sourmash sig cat (#1236) add unique_intersect_bp and gather_result_rank to gather CSV output (#1219) remove deprecated minhash functions (#1149) fix Rust panic error in signature creation (#1172) cache nodes in SBT during search (#1161) fix two bugs in gather --output-unassigned (#1156) Refactor the gather code so that it uses 'hashes' instead of 'mins' (#1329) Update output from gather w/o abundances, so that abund output is empty instead of 0(#1328) Documentation updates substantial revisions and updates to the documentation (#1283) add information about versioning, migrations, etc to the docs (#1153) Infrastructure and CI changes: update finch requirement from 0.3.0 to 0.4.1 (#1290) update rand for test, and activate "js" feature for getrandom (#1275) dev updates (configs and doc) (#1298) move wheel building from Travis to GitHub Actions (#1295) fix new clippy warnings from Rust 1.49 (#1267) use tox for running tests locally (#696) CI: small build fixes (#1252) CI: Fix releases in GitHub Actions (#1250) update build_wheel action paths CI: moving python tests from travis to GH actions (#1249) CI: move wheel building to GitHub actions (#1244) remove last .rst file from docs (#1185) update CI for latest branch name change (#1150