MRG: check select parameters; enforce types when building manifests
#3212
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## latest #3212 +/- ##
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+ Coverage 86.69% 86.74% +0.05%
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Files 136 136
Lines 15830 15871 +41
Branches 2716 2728 +12
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+ Hits 13724 13768 +44
+ Misses 1796 1794 -2
+ Partials 310 309 -1
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select parametersselect parameters; enforce types when building manifests
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ready for review @sourmash-bio/devs ! |
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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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This PR checks the types and values of parameters to
Index.select. Specifically, it makes sure that:Also adds manifest column type enforcement in general, & explicit manifest content checking to
sig manifestandsig summarize.Related issues:
sourmash sig extractwill create empty zip file from directsketch databases #3191 - invalid manifest rows will be revealed bysig manifestandsig summarizeIndex.selectallows ksizes that aren't an integer. #3107