MRG: allow get/set record.filename #3121
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3121 +/- ##
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Coverage 86.55% 86.55%
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Files 136 136
Lines 15809 15809
Branches 2713 2713
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Hits 13683 13683
Misses 1816 1816
Partials 310 310
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bluegenes
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luizirber
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Apr 20, 2024
bluegenes
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May 10, 2024
…multigather` (#298) This PR adds utilities for building full gather results file for `fastgather` and non-rocksdb `fastmultigather`, and makes full output default. - Fixes #287 - Fixes #187 - Fixes #254 - includes a local fix for #318, which means that the `fastgather` and **non-rocksdb** `fastmultigather` full output here matches sourmash gather. Issues with rocksdb gather are being handled elsewhere. ## Benchmarking | software/version | command | details | time | max RAM | | -------- | -------- | -------- | -- | -- | | branchwater v0.9.3 | `fastgather` | minimal result | <span style="color:green">**1m 47s**</span> | <span style="color:black">**14 GB**</span> | | branchwater v0.9.3-dev | `fastgather` | full result | <span style="color:green">**1m 57s**</span> | <span style="color:black">**14 GB**</span> | | branchwater v0.9.3 | `fastmultigather` | minimal result | <span style="color:red">**8m 3s**</span> | <span style="color:black">**25 GB**</span> | | branchwater v0.9.3-dev | `fastmultigather` | full result | <span style="color:red">**8m 9s**</span> | <span style="color:black">**25 GB**</span> | | branchwater v0.9.3 | `fastmultigather` | rocksdb full result | <span style="color:green">**24s**</span> | <span style="color:green">**600 MB**</span> | progress/separate PRs: - [x] Fill out `match_filename` in full results (#303; requires new sourmash core release with sourmash-bio/sourmash#3121) - [x] switch to using `KmerMinHashBTree` for hash subtraction +benchmark. Per luiz, `KmerMinHashBTree` are better for any situation where we'll be subtracting/adding hashes to a sketch #310 - [x] sourmash: make getting `Record`.filename public in order to keep match_filename and write it to full results. (sourmash-bio/sourmash#3121) - [x] remove --full-results and make full results default #327 --------- Co-authored-by: C. Titus Brown <[email protected]>
ctb
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Jun 10, 2024
#3199) ## [0.14.0] - 2024-06-10 MSRV: 1.65 Changes/additions: * fix cargo fmt for updated `disk_revindex.rs` code (#3197) * fix RocksDB-based gather & other rust-based infelicities revealed by plugins (#3193) * use correct denominator in f_unique_to_query (#3138) * fix clippy warnings about max_value (#3146) * allow get/set record.filename (#3121) Updates: * 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 serde_json from 1.0.116 to 1.0.117 (#3159) * 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 num-iter from 0.1.44 to 0.1.45 (#3140) * Bump serde from 1.0.199 to 1.0.200 (#3144) * Bump serde from 1.0.198 to 1.0.199 (#3130) * Bump serde_json from 1.0.115 to 1.0.116 (#3124) * Bump serde from 1.0.197 to 1.0.198 (#3122) * Bump histogram from 0.9.1 to 0.10.0 (#3109) * Bump enum_dispatch from 0.3.12 to 0.3.13 (#3102) * Bump serde_json from 1.0.114 to 1.0.115 (#3101) * Bump rayon from 1.9.0 to 1.10.0 (#3098)
ctb
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Jun 11, 2024
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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I need to be able to access a record's
filenamefrom branchwater to reproduce full gather results. I think this should allow that.any thoughts/objections, @luizirber? Should I make it
getonly?