MRG: misc Rust updates to core #3297

ctb · 2024-08-18T13:54:18Z

A few useful things from the branchwater plugin perspective:

add getters to num, scaled, and n_hashes in Record
add misc documentation, based in part on descriptions in Feat: on-disk RevIndex based on RocksDB #2230
add #[derive Clone] to Collection and CollectionSet
add Collection::from_rocksdb(...)

codecov · 2024-08-18T14:04:11Z

Codecov Report

Attention: Patch coverage is 90.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 86.68%. Comparing base (c621bd5) to head (b6640c2).
Report is 66 commits behind head on latest.

Files with missing lines	Patch %	Lines
src/core/src/collection.rs	80.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           latest    #3297   +/-   ##
=======================================
  Coverage   86.67%   86.68%           
=======================================
  Files         137      137           
  Lines       15998    16003    +5     
  Branches     2728     2728           
=======================================
+ Hits        13867    13872    +5     
  Misses       1822     1822           
  Partials      309      309

Flag	Coverage Δ
hypothesis-py	`25.40% <ø> (ø)`
python	`92.37% <ø> (ø)`
rust	`62.92% <90.00%> (+0.06%)`	⬆️

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ctb · 2024-08-18T20:14:31Z

for your delectation @luizirber

…s_updates

src/core/src/collection.rs

luizirber

👍 overall, but I think the load_sig change should be reverted or better contextualized =]

src/core/src/collection.rs

src/core/src/storage/mod.rs

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

ctb · 2024-08-18T21:23:49Z

ready once tests pass! thx

Developer updates: * build: move ORCID to metadata in pyproject.toml, fix pixi (#3416) * build: simplify Rust release (#3392) * fix: Avoid re-calculating md5sum on clone and conversion to KmerMinHashBTree (#3385) * r0.15.1 release (#3304) * update sourmash core to r0.17.0 (#3381) * Added union method to HLL (#3293) * Build: upgrade to newer maturin (#3366) * CI: use supported ubuntu for codspeed (#3350) * Fix clippy lints from 1.83 beta (#3357) * Implement resumability for revindex (#3275) * add `Manifest::intersect_manifest` to Rust core (#3305) * bump sourmash core to r0.17.2 (#3399) * change `sig_from_record` to use scaled from `Record` to downsample (#3387) * derive Hash for `HashFunctions` (#3344) * enforce a single scaled on a `CollectionSet` (#3397) * fix formatting from #3306 (#3307) * have ruff ignore ipynb so as to avoid triggering an error during CI (#3325) * improve downsampling behavior on `KmerMinHash`; fix `RevIndex::gather` bug around `scaled`. (#3342) * panic when `FSStorage::load_sig` encounters more than one `Signature` in a JSON record (#3333) * propagate error from `RocksDB::open` on bad directory (#3306) * refactor `calculate_gather_stats` to disallow repeated downsampling (#3352) * release core r0.17.1 (#3388) * release sourmash rust core r0.16.0 (#3356) * standardize on u32 for scaled, and introduce `ScaledType` (#3364) * update plugin documentation for users (#3286) * update sourmash core to r0.15.2 (#3338) * when lingroups are provided, use them for `csv_summary` (#3311) * Misc Rust updates to core (#3297) * Resolve issue for high precision MLE estimation (#3296) Dependabot and pre-commit CI updates: * Bump DeterminateSystems/magic-nix-cache-action from 7 to 8 (#3319) * Bump DeterminateSystems/nix-installer-action from 13 to 14 (#3320) * Bump DeterminateSystems/nix-installer-action from 14 to 15 (#3374) * Bump DeterminateSystems/nix-installer-action from 15 to 16 (#3401) * Bump camino from 1.1.7 to 1.1.9 (#3301) * Bump codspeed-criterion-compat from 2.6.0 to 2.7.2 (#3324) * Bump conda-incubator/setup-miniconda from 3.0.4 to 3.1.0 (#3373) * Bump csv from 1.3.0 to 1.3.1 (#3390) * Bump getset from 0.1.2 to 0.1.3 (#3328) * Bump histogram from 0.11.0 to 0.11.1 (#3377) * Bump js-sys from 0.3.72 to 0.3.74 (#3412) * Bump memmap2 from 0.9.4 to 0.9.5 (#3326) * Bump myst-parser from 3.0.1 to 4.0.0 (#3277) * Bump needletail from 0.5.1 to 0.6.0 (#3376) * Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 (#3278) * Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 (#3332) * Bump pypa/cibuildwheel from 2.21.1 to 2.21.2 (#3345) * Bump pypa/cibuildwheel from 2.21.2 to 2.21.3 (#3353) * Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 (#3408) * Bump roaring from 0.10.6 to 0.10.7 (#3413) * Bump serde from 1.0.204 to 1.0.207 (#3289) * Bump serde from 1.0.207 to 1.0.208 (#3298) * Bump serde from 1.0.208 to 1.0.209 (#3310) * Bump serde from 1.0.209 to 1.0.210 (#3318) * Bump serde from 1.0.210 to 1.0.214 (#3368) * Bump serde from 1.0.214 to 1.0.215 (#3403) * Bump serde_json from 1.0.120 to 1.0.121 (#3267) * Bump serde_json from 1.0.121 to 1.0.122 (#3280) * Bump serde_json from 1.0.122 to 1.0.124 (#3288) * Bump serde_json from 1.0.124 to 1.0.125 (#3302) * Bump serde_json from 1.0.125 to 1.0.127 (#3309) * Bump serde_json from 1.0.127 to 1.0.128 (#3316) * Bump serde_json from 1.0.128 to 1.0.132 (#3358) * Bump serde_json from 1.0.132 to 1.0.133 (#3402) * Bump sphinx-design from 0.5.0 to 0.6.0 (#3268) * Bump sphinx-design from 0.6.0 to 0.6.1 (#3276) * Bump tempfile from 3.10.1 to 3.11.0 (#3279) * Bump tempfile from 3.11.0 to 3.12.0 (#3287) * Bump tempfile from 3.12.0 to 3.13.0 (#3340) * Bump tempfile from 3.13.0 to 3.14.0 (#3391) * Bump thiserror from 1.0.63 to 1.0.64 (#3335) * Bump thiserror from 1.0.64 to 1.0.65 (#3367) * Bump thiserror from 1.0.65 to 1.0.68 (#3379) * Bump thiserror from 1.0.68 to 2.0.3 (#3389) * Bump web-sys from 0.3.69 to 0.3.70 (#3299) * Bump web-sys from 0.3.70 to 0.3.72 (#3354) * Bump web-sys from 0.3.72 to 0.3.74 (#3411) * Update pytest-cov requirement from <6.0,>=4 to >=4,<7.0 (#3375) * Update sphinx requirement from <8,>=6 to >=6,<9 (#3269) * Upgrade rocksdb to 0.22.0, bump MSRV to 1.66 (#3383) * [pre-commit.ci] pre-commit autoupdate (#3281) * [pre-commit.ci] pre-commit autoupdate (#3290) * [pre-commit.ci] pre-commit autoupdate (#3312) * [pre-commit.ci] pre-commit autoupdate (#3330) * [pre-commit.ci] pre-commit autoupdate (#3336) * [pre-commit.ci] pre-commit autoupdate (#3341) * [pre-commit.ci] pre-commit autoupdate (#3346) * [pre-commit.ci] pre-commit autoupdate (#3360) * [pre-commit.ci] pre-commit autoupdate (#3369) * [pre-commit.ci] pre-commit autoupdate (#3380) * [pre-commit.ci] pre-commit autoupdate (#3393) * [pre-commit.ci] pre-commit autoupdate (#3404) * [pre-commit.ci] pre-commit autoupdate (#3409) * [pre-commit.ci] pre-commit autoupdate (#3414)

ctb added 3 commits August 18, 2024 06:50

provide getters for num, scaled, n_hashes

eb8816d

add some minimal docs (based on #2230)

cc8dbc6

docs

1ee2f34

ctb added 13 commits August 18, 2024 07:09

more

d23ef6b

upd

952ccf6

debugging

cc2aea4

debug

4227ddc

add more dbg

51b9d7f

add more dbg

dccf0e3

add more dbg

6bc2c51

cleanup

38013af

cleanup 2

08459a8

bork bork

644ffe2

remove

3df7c9e

compile?

e67415c

remove println

ea637a7

ctb changed the title ~~WIP: misc Rust updates to core~~ MRG: misc Rust updates to core Aug 18, 2024

Merge branch 'latest' of github.com:sourmash-bio/sourmash into misc_r…

e9fc1c2

…s_updates

luizirber reviewed Aug 18, 2024

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luizirber requested changes Aug 18, 2024

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ctb and others added 3 commits August 18, 2024 14:21

revert change to load_sig

603fa0b

Update src/core/src/collection.rs

b6b547b

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

Update src/core/src/collection.rs

e560e32

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

luizirber and others added 4 commits August 18, 2024 14:56

fmt

5c66e33

Merge branch 'latest' into misc_rs_updates

f0c7ad6

add test

fbe851c

clippy fixes

eeeee67

fmt

b6640c2

luizirber self-requested a review August 19, 2024 04:46

luizirber approved these changes Aug 19, 2024

View reviewed changes

luizirber merged commit d90c507 into latest Aug 19, 2024
44 checks passed

luizirber deleted the misc_rs_updates branch August 19, 2024 04:46

ctb mentioned this pull request Dec 5, 2024

MRG: 4.8.12 release branch #3417

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MRG: misc Rust updates to core #3297

MRG: misc Rust updates to core #3297

ctb commented Aug 18, 2024 •

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ctb commented Aug 18, 2024

MRG: misc Rust updates to core #3297

MRG: misc Rust updates to core #3297

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