MRG: patch-fix sig extract to no longer create empty zips
#3214
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This was referenced Jun 16, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3214 +/- ##
==========================================
- Coverage 86.71% 86.70% -0.02%
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Files 136 136
Lines 15849 15829 -20
Branches 2716 2716
==========================================
- Hits 13744 13724 -20
Misses 1795 1795
Partials 310 310
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
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Ready for review @sourmash-bio/devs ! @ccbaumler might be yours to review :) Note, the failed tests do not seem important (looks like rounding error on the coverage one, in particular?) |
ccbaumler
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Jun 16, 2024
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LGTM. Love the simple solution.
$ sourmash sig extract --dna ~/database-releases/genbank-20240614/temp/genbank-20240614-viral.zip -o test.zip
== This is sourmash version 4.8.10.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==
loaded 0 total that matched ksize & molecule type
no matching signatures to save!
$ sourmash sig summarize test.zip
== This is sourmash version 4.8.10.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==
** loading from 'test.zip'
path filetype: ZipFileLinearIndex
location: /home/baumlerc/sourmash/test.zip
is database? yes
has manifest? no
num signatures: 0
** examining manifest...
total hashes: 0
summary of sketches:
$ sourmash sig describe test.zip
== This is sourmash version 4.8.10.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==
loaded 0 signatures total, from 1 files
$ sourmash sig cat -k 21 test.zip
== This is sourmash version 4.8.10.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==
loaded 0 signatures total, from 1 files
loaded 0 signatures total.
output 0 signatures
$ unzip -v test.zip
Archive: test.zip
Length Method Size Cmpr Date Time CRC-32 Name
-------- ------ ------- ---- ---------- ----- -------- ----
128 Stored 128 0% 2024-06-16 14:21 7c2b036b SOURMASH-MANIFEST.csv
-------- ------- --- -------
128 128 0% 1 file
ctb
added a commit
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this pull request
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 fixes
sourmash sig extractto properly close thesourmash_args.SaveSignaturesToLocationupon error exit.The proper thing to do is really to use the context manager tho 😭 . But I want to fix this problem first.
Fixes #3191