Draft release notes for v4.0

[ctb]

release notes sourmash 4.0

created from git log --oneline v3.5.0..3bfd0fa1cf48 followed by hand editing.

hackmd here: https://hackmd.io/ZA14lQDfTgqh6l0gaW2BxQ

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!

Numerical output and search results are unchanged

There are no changes to numerical output or search results in this release; you should get the same results with v4 as you get with v3, except where command-line parameters need to be adjusted as noted below (see: protein ksize #1277, lca summarize changes #1175, sourmash gather on signatures without abundance #1328). Please file an issue if your results change!

New or changed behavior

• default SBT storage is now .sbt.zip ([MRG] switch sbt.zip over to default SBT storage #1174, [MRG] Remove TarStorage and replace usage with ZipStorage #1170)
• add sourmash sketch command for creating signatures ([MRG] Explore addition of a sketch command. #1159)
• protein ksizes in MinHash are now divided by 3, except in sourmash compute ([MRG] Divide non-DNA MinHash ksize by 3 for external consumption. #1277)
• refactor MinHash API and implementation: add, iadd, merge, hashes, and max_hash ([MRG] Refactor/expand MinHash add, iadd, and merge functionality. #1282, [MRG] define get_mins in terms of .hashes, not the other way around #1154, Replace mx by scaled #1139, [MRG] Fix max hash deprecation warnings #1301)
• add HyperLogLog implementation ([MRG] Add a HLL implementation #1223)
• SourmashSignature.name is now a property (not a method): use str(sig) instead of name() ([MRG] rationalize SourmashSignature.name and str(sig) #1179, [MRG] use str(best_match), not best_match.name, in gather #1232)
• lca summarize no longer merges all signatures, and uses hash abundance by default ([MRG] change default behavior in lca summarize #1175)
• index and lca index (make cmdline sigs optional for index #1186, make cmdline sigs optional for lca index #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 ([MRG] Remove --traverse-directory from commands & make default #1178)
• sourmash sketch and sourmash compute no longer create empty signatures from empty files and stdin ([MRG] fix issue with identifiers in the LCA code #1347);
• sourmash sketch and sourmash compute set sig.filename to empty string when filename is - ([MRG] fix issue with identifiers in the LCA code #1347);

Feature removal

• remove Python 2.7 support (& end Python 2 compatibility) ([MRG] Remove Python 2.7 support (& end Python 2 compatibility) #1145, [MRG] remove __reduce__ from MinHash class #1144)
• remove lca gather ([MRG] Remove lca gather #1307)
• remove 10x support from sourmash compute ([MRG] remove 10x support #1229)
• remove 'dump' command ([MRG] remove 'dump' command #1157)

Feature/function deprecations

• deprecate sourmash compute ([MRG] Explore addition of a sketch command. #1159)
• deprecate load_signatures, sourmash.load_one_signature, create_sbt_index, and load_sbt_index ([MRG] Deprecate sourmash.load_signatures as public API; refactor a bit. #1279, [MRG] Switch use of load_signatures over to load_file_as_signatures throughout. #1304)
• deprecate import_csv in favor of new sourmash sig import --csv ([MRG] deprecate import_csv for 4.0 (to be removed in 5.0) #1281)

Refactoring, improvements, and minor bug fixes:

• accept file list in sourmash sig cat ([MRG] Accept file list in sourmash sig cat #1236)
• add unique_intersect_bp and gather_result_rank to gather CSV output ([MRG] add unique_intersect_bp and gather_result_rank to gather CSV output #1219)
• remove deprecated minhash functions ([MRG] Remove deprecated minhash functions #1149)
• fix Rust panic error in signature creation ([MRG] fix Rust panic error in signature creation #1172)
• cache nodes in SBT during search ([MRG] cache nodes in SBT during search #1161)
• fix two bugs in gather --output-unassigned ([MRG] fix two bugs in gather --output-unassigned #1156)
• Refactor the gather code so that it uses 'hashes' instead of 'mins' ([MRG] 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([MRG] update output from gather w/o abundances, so that abund output is empty #1328)

Documentation updates

• substantial revisions and updates to the documentation ([MRG] Documentation updates for 4.0 release #1283)
• add information about versioning, migrations, etc to the docs ([MRG] 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 (Update finch requirement from 0.3.0 to 0.4.1 #1290)
• update rand for test, and activate "js" feature for getrandom ([CI] update rand for test, and activate "js" feature for getrandom #1275)
• dev updates (configs and doc) ([MRG] Dev updates (configs and doc) #1298)
• move wheel building from Travis to GitHub Actions (Move wheel building from Travis to GitHub Actions #1295)
• fix new clippy warnings from Rust 1.49 ([MRG] Fix new clippy warnings from Rust 1.49 #1267)
• use tox for running tests locally ([MRG] use tox for running tests locally #696)
• CI: small build fixes (CI: small build fixes #1252)
• CI: Fix releases in GitHub Actions (CI: Fix releases in GitHub Actions #1250)
• update build_wheel action paths
• CI: moving python tests from travis to GH actions ([MRG] CI: moving python tests from travis to GH actions #1249)
• CI: move wheel building to GitHub actions ([MRG] add cibuildwheel to GitHub actions #1244)
• remove last .rst file from docs ([MRG] Replace last .rst file from docs #1185)
• update CI for latest branch name change ([MRG] update CI for latest branch name change #1150)

[ctb]

this is now part of #1283

[ctb]

(and when we do the release, we should copy them from doc/release-notes/sourmash-4.0.md over to the github release notes, and also link to the migration notes there)

[ctb]

is released!