EXP: try setting up --v4 and --v5 behavior differences for sig check
#3072
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## latest #3072 +/- ##
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Coverage 86.55% 86.55%
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Files 136 136
Lines 15809 15819 +10
Branches 2713 2717 +4
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+ Hits 13683 13692 +9
Misses 1816 1816
- Partials 310 311 +1
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hi @sourmash-bio/devs any thoughts on this approach? It feels not-wrong to me... but curious about possible fine tuning! |
This was referenced Mar 11, 2024
ctb
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Apr 12, 2024
This PR refactors code to eliminate any internal dependencies on the `compute` command or codebase, in preparation for removing `sourmash compute` in v5.0, per #1286. Specifically, this PR: * shifts common sketching code from `src/sourmash/command_compute.py` to `src/sourmash/command_sketch.py`; * refactors three tests that were still using `sourmash compute` to use `sourmash sketch` instead. No functionality is altered or adjusted in this PR; it's all just code refactoring. The next step for #1286 would maybe be adjust the code and the tests to respect the `--v4` and `--v5` flags (as used in #3072 / #3074). The actual compute code and command wouldn't be removed until after a 5.0 release, I think.
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This PR adds
--v5functionality tosig collectandsig check, switching the default behavior (when--v5is specified) over to the new--relpathfunctionality per #3071.This PR is a proposed step along the road to support a sourmash v5 release 🎉.
As part of this, the PR adds support for
--v4and--v5command-line arguments tosig checkandsig collect, along with test fixtures and aversion=...argument toruntmp.sourmash.--v4would retain the current default v4 behavior, while--v5would switch the behavior over to the new, exciting (proposed) sourmash v5 behavior.sig checkandsig collectbehavior to use--relpathfor v5 #3071