MRG: propagate zipfile errors #3431
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3431 +/- ##
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- Coverage 86.43% 86.42% -0.02%
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Files 137 137
Lines 16103 16103
Branches 2219 2219
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- Hits 13919 13917 -2
- Misses 1877 1879 +2
Partials 307 307
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@luizirber ready for review! Will need to bump the sourmash version b/c of header change, I'll deal with that too. |
luizirber
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Dec 15, 2024
ctb
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Dec 20, 2024
## [0.18.0] - 2024-12-20 MSRV: 1.66 Changes/additions: * add skipmer capacity to sourmash python layer via ffi (#3446) * add skipmers; switch to reading frame approach for translation, skipmers (#3395) * Refactor: Use to_writer/from_reader across the codebase (#3443) * adjust `Signature::name()` to return `Option<String>` instead of `filename()` and `md5sum()` (#3434) * propagate zipfile errors (#3431) Updates: * Bump proptest from 1.5.0 to 1.6.0 (#3437) * Bump roaring from 0.10.8 to 0.10.9 (#3438) * Bump serde from 1.0.215 to 1.0.216 (#3436) * Bump statrs from 0.17.1 to 0.18.0 (#3426) * Bump roaring from 0.10.7 to 0.10.8 (#3423) * Bump needletail from 0.6.0 to 0.6.1 (#3427) * Bump web-sys from 0.3.72 to 0.3.74 (#3411) * Bump js-sys from 0.3.72 to 0.3.74 (#3412) * Bump roaring from 0.10.6 to 0.10.7 (#3413) * Bump serde_json from 1.0.132 to 1.0.133 (#3402) * Bump serde from 1.0.214 to 1.0.215 (#3403)
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bluegenes
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Dec 27, 2024
This PR integrates the changes to `BuildUtils` (`MultiSelection` details, minor changes to `BuildCollection` filtering + writing) that arose from integration into branchwater. It also makes the number of simultaneous downloads tunable, since I was having trouble when using the 3 default permits with large eukaryotic genomes. It also handles changes associated with zipfile handling from sourmash-bio/sourmash#3431 arising from updating sourmash core to 0.18.0 ref #134
ctb
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Jan 11, 2025
Release issue: #3481 ---- NOTE: This release adds basic support for skipmers, but they are not yet fully supported. Minor new features: * add genbank plant db to docs (#3429) * add skipmer capacity to sourmash python layer via ffi (#3446) * add skipmers; switch to reading frame approach for translation, skipmers (#3395) * additional moltype specification needed for `sig downsample` with skipmers (#3457) * update with misc animal genomes (#3422) Cleanup and documentation updates: * add comment about semver and column headings (#3433) Developer updates: * Deps: update to rocksdb 0.23 (#3456) * Refactor: Use to_writer/from_reader across the codebase (#3443) * adjust `Signature::name()` to return `Option<String>` instead of `filename()` and `md5sum()` (#3434) * bump version to 4.8.13-dev (#3474) * fix comment in _set_num_scaled (#3451) * propagate zipfile errors (#3431) * update rust CHANGELOG in preparation for r0.18.0 (#3450) * CI: github actions updates (#3476) Dependabot updates: * Bump itertools from 0.13.0 to 0.14.0 (#3471) * Bump needletail from 0.6.0 to 0.6.1 (#3427) * Bump proptest from 1.5.0 to 1.6.0 (#3437) * Bump roaring from 0.10.7 to 0.10.8 (#3423) * Bump roaring from 0.10.8 to 0.10.9 (#3438) * Bump serde from 1.0.215 to 1.0.216 (#3436) * Bump serde from 1.0.216 to 1.0.217 (#3464) * Bump serde_json from 1.0.133 to 1.0.134 (#3453) * Bump statrs from 0.17.1 to 0.18.0 (#3426) * Bump tempfile from 3.14.0 to 3.15.0 (#3472) * Bump thiserror from 2.0.3 to 2.0.6 (#3425) * Bump thiserror from 2.0.6 to 2.0.7 (#3435) * Bump thiserror from 2.0.7 to 2.0.8 (#3448) * Bump thiserror from 2.0.8 to 2.0.9 (#3452) * Update maturin requirement from <1.8.0,>=1 to >=1,<1.9.0 (#3465) * [pre-commit.ci] pre-commit autoupdate (#3428) * [pre-commit.ci] pre-commit autoupdate (#3439) * [pre-commit.ci] pre-commit autoupdate (#3454) * [pre-commit.ci] pre-commit autoupdate (#3473)
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This PR switches from
ZipStorageBuildertoZipStorageTryBuilderin order to propagate errors from bad zip files.Fixes #3430