MRG: additional moltype specification needed for sig downsample with skipmers
#3457
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## latest #3457 +/- ##
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- Coverage 88.02% 88.01% -0.02%
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Files 137 137
Lines 22317 22317
Branches 2225 2225
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- Hits 19645 19642 -3
- Misses 2359 2362 +3
Partials 313 313
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bluegenes
changed the title
sig downsample with skipmers
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@ctb ready for review |
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A few comments:
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CI isn't passing b/c of coverage -- which is true of the other skipmer additions as well. There are no skipmer tests in the sourmash python codebase yet. I think we decided it was ok for now b/c there is actually no way to make skipmer sigs through the python codebase, either, and these additions don't break our existing tests. But we should not call attention to skipmers in here until we add tests and docs, #3449. The changes I've thus far added enable the following There are tests in branchwater and directsketch that cover the array of skipmer sketch building and uses there. |
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fantastic - I'd go ahead and merge :) |
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)
needed to enable skipmers with
sig downsampleAdding moltypes would be easier with some unified functions for handling + testing...