MRG: upgrade sig overlap and sig subtract to load more than JSON signatures
#3153
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3153 +/- ##
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+ Coverage 86.64% 86.65% +0.01%
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Files 136 136
Lines 15807 15821 +14
Branches 2713 2713
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+ Hits 13696 13710 +14
Misses 1801 1801
Partials 310 310
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ctb
changed the title
sig overlap and sig subtractsig overlap and sig subtract
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Ready for review @sourmash-bio/devs |
5 tasks
ctb
changed the title
sig overlap and sig subtractsig overlap and sig subtract to load more than JSON signatures
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@ccbaumler @AnneliektH would either of you be able to look at this and (potentially) approve it? lmk if you don't have review privileges. |
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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: * deprecate external use of `sourmash.signature` load/save functions, because they are JSON-specific and inflexible. * simplify and standardize signature load/save function usage during tests; * get rid of deprecation messages during tests; In brief, * rename `sourmash.signature.load_signatures` to `load_signatures_from_json`; * rename `sourmash.signature.load_one_signature` to `load_one_signature_from_json`; * rename `sourmash.signature.save_signatures` to `save_signatures_to_json`; * deprecate `sourmash.save_signatures` and `sourmash.load_one_signature` for 5.0 (joining `load_signatures`, which was already deprecated); * reduce/eliminate deprecations by transitioning internal test code to use these three functions directly from `sourmash.signature` instead of from the top-level sourmash import. * **bonus**: eliminate zipfile UserWarning around overwriting files, which causes lots of warnings when running tests. --- Done: - [x] in sourmash.signature submodule, rename `load_signatures` to `load_signatures_from_json`, `load_one_signature` to `load_one_signatures_from_json`, and `save_signatures` to `save_signatures_to_json`; make tests pass. - [x] deprecate `sourmash.load_one_signature` and `sourmash.save_signatures`. - [x] catch zipfile UserWarning for duplicate filenames in ZipStorage.save TODO: - [x] transition internal sourmash code+tests away from deprecated functions - [ ] create issue around changing API documentation prior to 5.0; --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fix
sig overlapandsig subtractto take more than just JSON signatures.Also, adds a function
sourmash_args.load_one_signaturethat I think should (eventually) replace the now-deprecatedsourmash.signature.load_one_signature. This will be the topic of a new PR - for now, I think it's a nice quick fix!Fixes #3136
Related issues:
load_one_signatureuseload_file_as_signaturesAPI #1062 - will do another PR to close this issueload_*sig/db functions insourmash_args.py#1877TODO: