MRG: prepare to remove sourmash compute for sourmash v5.0
#3103
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## latest #3103 +/- ##
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- Coverage 86.90% 86.55% -0.36%
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Files 136 136
Lines 15554 15809 +255
Branches 2640 2713 +73
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+ Hits 13517 13683 +166
- Misses 1735 1816 +81
- Partials 302 310 +8
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sourmash compute for sourmash v5.0sourmash compute for sourmash v5.0
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sourmash compute for sourmash v5.0sourmash compute for sourmash v5.0
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Minor new features: * add `--set-name` to `sig intersect` and `sig subtract` (#3162) * upgrade `sig overlap` and `sig subtract` to load more than JSON signatures (#3153) * force continue past `tax genome` classification errors (#3100) Bug fixes: * fix `remaining_bp` output from sourmash gather (#3195) * fix RocksDB-based gather & other rust-based infelicities revealed by plugins (#3193, #3197) * use correct denominator in f_unique_to_query (#3138) Cleanup and documentation updates: * update JOSS for sourmash v4 (#3114, #3203, #3209) * fix links to taxonomy spreadsheets (#3119) * fix description of `f_unique_weighted` (#3164) Developer updates: * transition internal signature loading functions (#3161) * allow get/set record.filename (#3121) * round a number that is losing precision in 15th place in `test_distance_utpy` (#3126) * disable ppc64le wheel building (#3127) * prepare to remove `sourmash compute` for sourmash v5.0 (#3103) * add rustup target x86_64-apple-darwin (#3148) * mv `.cargo/config` to `config.toml` (#3147) * fix clippy warnings about max_value (#3146) * bump to v4.8.9-dev (#3135) * update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0 (#3199) Dependabot updates: * Bump DeterminateSystems/nix-installer-action from 11 to 12 (#3184) * Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (#3185) * Bump statrs from 0.16.0 to 0.16.1 (#3186) * Bump serde from 1.0.202 to 1.0.203 (#3175) * Bump ouroboros from 0.18.3 to 0.18.4 (#3176) * Bump itertools from 0.12.1 to 0.13.0 (#3166) * Bump camino from 1.1.6 to 1.1.7 (#3169) * Bump serde from 1.0.201 to 1.0.202 (#3168) * Bump thiserror from 1.0.60 to 1.0.61 (#3167) * Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (#3165) * Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (#3157) * Bump DeterminateSystems/nix-installer-action from 10 to 11 (#3156) * Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (#3155) * Bump serde_json from 1.0.116 to 1.0.117 (#3159) * Bump thiserror from 1.0.59 to 1.0.60 (#3158) * Bump serde from 1.0.200 to 1.0.201 (#3160) * Bump roaring from 0.10.3 to 0.10.4 (#3142) * Bump histogram from 0.10.0 to 0.10.1 (#3141) * Bump getrandom from 0.2.14 to 0.2.15 (#3143) * Bump num-iter from 0.1.44 to 0.1.45 (#3140) * Bump jinja2 from 3.1.3 to 3.1.4 (#3145) * Bump serde from 1.0.199 to 1.0.200 (#3144) * Bump serde from 1.0.198 to 1.0.199 (#3130) * Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#3131) * Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0 (#3132) * Bump myst-parser from 2.0.0 to 3.0.1 (#3133) * Bump thiserror from 1.0.58 to 1.0.59 (#3123) * Bump serde_json from 1.0.115 to 1.0.116 (#3124) * Bump serde from 1.0.197 to 1.0.198 (#3122) * Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22 (#3116)
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This PR refactors code to eliminate any internal dependencies on the
computecommand or codebase, in preparation for removingsourmash computein v5.0, per #1286.Specifically, this PR:
src/sourmash/command_compute.pytosrc/sourmash/command_sketch.py;sourmash computeto usesourmash sketchinstead.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
--v4and--v5flags (as used in #3072 / #3074). The actual compute code and command wouldn't be removed until after a 5.0 release, I think.