draft release notes for v4.5.0

[ctb]

git log --oneline v4.4.3..latest shows:

(edit here: https://hackmd.io/QUqiZHbTSYyoDYOaVy7vfg)

release notes sourmash v4.5.0

sourmash v4.5.0 provides several minor bug fixes, as well as a number of new features.

This release also includes two minor Python API breaking changes - by default, SourmashSignature objects loaded from files are "frozen", and we force explicit keyword arguments on MinHash object construction.

Finally, this release updates the sourmash documentation with several new tutorials, including one on using sourmash tax to classify metagenomes with MAGs + GTDB.

Bug fixes

• Fix sourmash tax argument parsing for multiple -g and -t arguments (#2218)
• Prevent loading multiple independent gather results files in sourmash tax (#2244)
• Fix query_abundance column when --ignore-abundance is set in gather (#2251)
• fix pickle protocol to properly adjust ksize in __getstate__ (#2265)
• clean up zip error handling for bad zip files (#2270)

Minor new features

• Use the bias factor for containment when estimating ANI (#2057)
• add human output format to sourmash tax; provide tutorials (#2158)
• add kreport output format to tax metagenome (#2239, #2249)
• add --distance-matrix option to sourmash compare (#2225)
• update database load UX for gather etc. (#2204)
• add generic support for gzipped and zipfile CSVs (#2195)
• implement tax grep to produce identifier picklists from taxonomies (#2178)

Cleanup and documentation fixes

• add sourmash tax tutorial (#2158)
• revise command-line docs for sourmash sig subcommands (#1714, #1717)
• Clarify containment direction for matrix output (#2215)
• Add ANGUS tutorial to docs (#1114)
• update links to static rmd (#1177)
• update search documentation, help, and output. (#2222)
• Fix signature filter command (#2159)
• fix notification message about query scaled (#2183)
• adjust gather output width on terminal (#2176)

Developer updates

• Add FrozenSourmashSignature (#1610)
• force explicit kwargs on MinHash constructor (#2174)
• fix ReadTheDocs by using a more recent conda version (#2231)
• refactor and add tests for containment direction for ANI calculation (#2215)
• fix test_storage_convert to allow success of sourmash convert (#2232)
• Updating tests/test_sourmash.py::test_storage_convert to use runtmp fixture instead of utils.TempDirectory() (#1739)
• Bump pypa/cibuildwheel from 2.8.1 to 2.9.0 (#2207)
• use stderr for test output printing (#2217)
• fix for sphinx 5.10 (#2147)

[bluegenes]

git log --oneline v4.4.2..latest shows:

From 4.4.3 instead? Mostly bc the -F human went into that release, right?

[ctb]

git log --oneline v4.4.2..latest shows:

From 4.4.3 instead? Mostly bc the -F human went into that release, right?

good catch! thanks :)

[ctb]

interestingly... no?

https://github.com/sourmash-bio/sourmash/releases/tag/v4.4.3

or if it did, I didn't put it in the descriptions. and the correct git log --oneline doesn't report it.

I'll have to dig.

[ctb]

indeed, -F human was not in v4.4.3. So I ran the right command 😓 , despite putting the wrong one in this issue 😆

[ctb]

sourmash v4.5.0 available on pypi! https://pypi.org/project/sourmash/

[ctb]

• [x] PyPI page updated
• [x] Zenodo DOI successfully minted upon new github release - see search results
• [x] pip install sourmash installs the correct version
• [x] mamba create -n smash-release -y sourmash installs the correct version

[ctb]

on zenodo! https://zenodo.org/record/7058348

[ctb]

conda-forge build of sourmash-minimal going on here: https://github.com/conda-forge/sourmash-minimal-feedstock/pull/34

[ctb]

bioconda build here: https://github.com/bioconda/bioconda-recipes/pull/36859

[ctb]

huh. does bioconda automatically merge now?? ok.

[ctb]

no... closed w/o merge. new bioconda build here: https://github.com/bioconda/bioconda-recipes/pull/36868

[ctb]

done! 🎉