MRG: adjust how ANI is calculated in the revindex code. #3218
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3218 +/- ##
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- Coverage 86.70% 86.70% -0.01%
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Files 136 136
Lines 15829 15830 +1
Branches 2716 2716
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Hits 13725 13725
- Misses 1794 1795 +1
Partials 310 310
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ctb
changed the title
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Ready for review @bluegenes ! |
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(Once this is merged, I will release a new sourmash core, 0.14.1, and then complete the PR here: sourmash-bio/sourmash_plugin_branchwater#361) |
ctb
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Jun 19, 2024
## [0.14.1] - 2024-06-19 MSRV: 1.65 Changes/additions: * adjust how ANI is calculated in the revindex code. (#3218) Updates: * Bump histogram from 0.10.2 to 0.11.0 (#3216) * Bump histogram from 0.10.1 to 0.10.2 (#3207) * Bump statrs from 0.16.1 to 0.17.1 (#3205) * Bump roaring from 0.10.4 to 0.10.5 (#3206) * Bump primal-check from 0.3.3 to 0.3.4 (#3208) * Bump niffler from 2.5.0 to 2.6.0 (#3204)
luizirber
reviewed
Jun 19, 2024
| @@ -44,7 +44,7 @@ md5 = "0.7.0" | |||
| memmap2 = "0.9.4" | |||
| murmurhash3 = "0.0.5" | |||
| needletail = { version = "0.5.1", default-features = false } | |||
| niffler = { version = "2.6.0", default-features = false, features = [ "gz" ] } | |||
| niffler = { version = "2.4.0", default-features = false, features = [ "gz" ] } | |||
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did you need to revert this for the plugin?
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(I figured no harm done since it will just come up again with dependabot ;))
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but I will document next time I stumble across the error.
ctb
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Jun 29, 2024
Release candidate testing: - [ ] Command line tests pass for a release candidate - [ ] All eight release candidate wheels are built Releasing to PyPI: - [ ] RC tag(s)s deleted on github - [ ] Release tag cut - [ ] Release notes written - [ ] All eight release wheels built - [ ] Release wheels uploaded to pypi - [ ] tar.gz distribution uploaded to pypi After release to PyPI and conda-forge/bioconda packages built: - [ ] [PyPI page](https://pypi.org/project/sourmash/) updated - [ ] Zenodo DOI successfully minted upon new github release - [see search results](https://zenodo.org/search?page=1&size=20&q=sourmash&sort=mostrecent) - [ ] `pip install sourmash` installs the correct version - [ ] [conda-forge sourmash-minimal-feedstock](https://github.com/conda-forge/sourmash-minimal-feedstock) has updated `sourmash-minimal` to the correct version - [ ] `mamba create -n smash-release -y sourmash` installs the correct version Optional but recommended: - [ ] PR submitted to update pyodide version - [ ] PR submitted to update spack version --- ## Release notes Minor new features: * check `select` parameters; enforce types when building manifests (#3212) * patch-fix `sig extract` to no longer create empty zips (#3214) Bug fixes: * adjust how ANI is calculated in the revindex code. (#3218) Cleanup and documentation updates: * final updates for 2024 JOSS publication (#3225) * Improve JOSS paper affiliations (#3224) * fix DOI for Rahman Hera paper in JOSS pub. (#3221) * upd citations, minor text (#3220) Developer updates: * bump sourmash core version to 0.14.1 (#3219) * bump version to 4.8.10-dev (#3211) Dependabot updates: - Bump proptest from 1.4.0 to 1.5.0 (#3222) - [pre-commit.ci] pre-commit autoupdate (#3223) - [pre-commit.ci] pre-commit autoupdate (#3003) - Bump histogram from 0.10.2 to 0.11.0 (#3216) - Bump pypa/cibuildwheel from 2.19.0 to 2.19.1 (#3217) - Bump histogram from 0.10.1 to 0.10.2 (#3207) - Bump statrs from 0.16.1 to 0.17.1 (#3205) - Bump roaring from 0.10.4 to 0.10.5 (#3206) - Bump primal-check from 0.3.3 to 0.3.4 (#3208) - Bump niffler from 2.5.0 to 2.6.0 (#3204) - Bump pypa/cibuildwheel from 2.18.1 to 2.19.0 (#3202)
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Calculate ANI of matches against original query with
f_orig_queryandf_match_orig, instead of againstf_unique_to_queryandf_match.This fixes the ANI differences between
sourmash gatherand RocksDB branchwater gather for the columnsquery_containment_ani,match_containment_ani,max_containment_ani, andaverage_containment_ani.Refs:
sourmash gathersourmash_plugin_branchwater#331