MRG: transition internal signature loading functions #3161
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## latest #3161 +/- ##
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Coverage 86.66% 86.66%
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Files 136 136
Lines 15821 15830 +9
Branches 2713 2716 +3
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+ Hits 13711 13719 +8
- Misses 1800 1801 +1
Partials 310 310
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ctb
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This feels done! It changes a lot of code in dumb ways, and cleans up the warnings emitted by the test, too; probably shouldn't be combined with any more changes 😅 Ready for review, @sourmash-bio/devs |
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**Note:** PR into #3161 This PR cleans up and regularizes naming output on `sig` subcommands. Specifically, it: - [x] adds `--set-name` to `sig intersect` and `sig subtract` to set names on output signatures. - [x] confirms and tests default names for output from `sig inflate`, `sig filter`, `sig downsample`, and `sig flatten` - [x] updates documentation appropriately - [x] aliases `--name` to `--set-name` on `sig merge`, and nominates `--name` for deprecation and removal on v5 - [x] nominates `--name` on `sig extract`, `sig filter`, and `sig flatten` for deprecation and removal on v5 - [x] highlights `--name` on `sketch dna`, `sketch protein`, and `sketch translate` - ref #3152 Fixes #1801 Fixes #3152 Related issues: * #3173 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Note: PR into #3153
Tackles some signature loading and saving cleanup throughout the codebase. Most changes are in the tests, and this is a significant cleanup of the test code!
Fixes #1062.
Goals:
sourmash.signatureload/save functions, because they are JSON-specific and inflexible.In brief,
sourmash.signature.load_signaturestoload_signatures_from_json;sourmash.signature.load_one_signaturetoload_one_signature_from_json;sourmash.signature.save_signaturestosave_signatures_to_json;sourmash.save_signaturesandsourmash.load_one_signaturefor 5.0 (joiningload_signatures, which was already deprecated);sourmash.signatureinstead of from the top-level sourmash import.Done:
load_signaturestoload_signatures_from_json,load_one_signaturetoload_one_signatures_from_json, andsave_signaturestosave_signatures_to_json; make tests pass.sourmash.load_one_signatureandsourmash.save_signatures.TODO: