Resolved issue for high precision MLE estimation #3296
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@luizirber do check out also this PR please, being an actual bug I believe it is more important |
luizirber
approved these changes
Aug 18, 2024
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## latest #3296 +/- ##
==========================================
- Coverage 86.74% 86.66% -0.09%
==========================================
Files 137 137
Lines 15923 15962 +39
Branches 2728 2728
==========================================
+ Hits 13813 13834 +21
- Misses 1801 1819 +18
Partials 309 309
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
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Dec 5, 2024
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)
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MultiplicityIntegerto handle cleanly without code duplication and the dispatching of different data types given the requested precision at runtime, without introducing marker structs or other distinctive struct attributes. Since the MLE estimation is rather slow, adding an if chain before calling the optimal variant does not add any significant time overhead.