From 7e744e77e6e4a43a394320cbbb7fd665466a79c9 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 8 Dec 2024 08:55:47 -0800 Subject: [PATCH 1/6] MRG: update with misc animal genomes (#3422) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds common hosts and also hg38. Tackles https://github.com/sourmash-bio/sourmash/issues/2717 Screenshot 2024-12-07 at 9 17 40 AM ## Rendered preview: --- doc/databases.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/doc/databases.md b/doc/databases.md index 781d2a6f66..3d607bdb9f 100644 --- a/doc/databases.md +++ b/doc/databases.md @@ -30,6 +30,25 @@ The databases do not need to be unpacked or prepared in any way after download. You can verify that they've been successfully downloaded (and view database properties such as `ksize` and `scaled`) with `sourmash sig summarize `. +## Sketches for human and animal genomes + +These sketches are of the latest releases of a number of animal +genomes. Among other uses, they can be used to detect host +contamination in microbial metagenomes. + +Each file includes sketches at k=21, k=31, and k=51, at a scaled of +1000, and is about 110 MB. + +* Human (hg38) - [hg38.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/hg38.sig.zip) +* Cow (bosTau9) - [bosTau9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/bosTau9.sig.zip) +* Dog (canFam6) - [canFam6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/canFam6.sig.zip) +* Horse (equCab3) - [equCab3.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/equCab3.sig.zip) +* Cat (felCat9) - [felCat9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/felCat9.sig.zip) +* Chicken (galGAl6) - [galGal6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/galGal6.sig.zip) +* Mouse (mm39) - [mm39.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/mm39.sig.zip) +* Goat (oviAri4) - [oviAri4.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/oviAri4.sig.zip) +* Pig (susCr11) - [susScr11.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/susScr11.sig.zip) + ## GTDB R08-RS214 - DNA databases [GTDB R08-RS214](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r08-rs214/456) consists of 402,709 genomes organized into 85,205 species clusters. From 585e2e7394199e37e8e0fdea6a1a3dc2ee701718 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 04:21:32 -0800 Subject: [PATCH 2/6] [pre-commit.ci] pre-commit autoupdate (#3428) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.8.1 → v0.8.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.1...v0.8.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 029426105d..c50d4e6266 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: - id: check-toml - id: debug-statements - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.1 + rev: v0.8.2 hooks: - id: ruff-format - id: ruff From 7cfc15f0e5922b7065ad0f37f8a0113758499ec6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 05:29:36 -0800 Subject: [PATCH 3/6] Bump needletail from 0.6.0 to 0.6.1 (#3427) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [needletail](https://github.com/onecodex/needletail) from 0.6.0 to 0.6.1.
Release notes

Sourced from needletail's releases.

v0.6.1

  • Add position method to return current line number and byte offset of parser (thanks @​olliecheng)
Commits
  • 5a96081 Run cargo fmt
  • f48ad5e Add basic tests for start_line_number and position
  • 5d73e1f Add position method to Record to make &Position accessible
  • 7186377 Fix Clippy error: elide lifetime
  • 0901123 Fix Clippy error: elide lifetime
  • a4c203e feat: add zstd support (#86)
  • See full diff in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- Cargo.lock | 6 +++--- src/core/Cargo.toml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 7c1d93d734..f1fd38c7f2 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1034,9 +1034,9 @@ dependencies = [ [[package]] name = "needletail" -version = "0.6.0" +version = "0.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f29a3c5015d6985f33318d154fa0c41315eb2e7df29432c844c74a83434bfe21" +checksum = "de3de09e373770238e3d30eb1a9f09f4754134d0ef354d0570bc1203d2517257" dependencies = [ "buffer-redux", "bytecount", @@ -1664,7 +1664,7 @@ dependencies = [ "md5", "memmap2", "murmurhash3", - "needletail 0.6.0", + "needletail 0.6.1", "niffler", "nohash-hasher", "num-iter", diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index fcf6bccd23..e815084507 100644 --- a/src/core/Cargo.toml +++ b/src/core/Cargo.toml @@ -43,7 +43,7 @@ log = "0.4.22" md5 = "0.7.0" memmap2 = "0.9.5" murmurhash3 = "0.0.5" -needletail = { version = "0.6.0", default-features = false } +needletail = { version = "0.6.1", default-features = false } niffler = { version = "2.4.0", default-features = false, features = [ "gz" ] } nohash-hasher = "0.2.0" num-iter = "0.1.45" From 63713bd8ac683e5a74e12f00841244553732ea8a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:48:25 +0000 Subject: [PATCH 4/6] Bump roaring from 0.10.7 to 0.10.8 (#3423) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [roaring](https://github.com/RoaringBitmap/roaring-rs) from 0.10.7 to 0.10.8.
Release notes

Sourced from roaring's releases.

v0.10.8

What's Changed

New Contributors

Full Changelog: https://github.com/RoaringBitmap/roaring-rs/compare/v0.10.7...v0.10.8

Commits
  • 00992ee Merge pull request #303 from RoaringBitmap/bump-to-v1-10-8
  • 9b0cb8f Bump roaring to v1.10.8
  • 56ba1ff Merge pull request #288 from lemolatoon/from-bitmap-bytes
  • a10a29c Add naive fallback for non-multiple 8 offset of from_lsb0_bytes
  • a44cc0b Fix cargo clippy warning
  • 94f1734 Fix CI error
  • f45cf7f Rename from_bitmap_bytes to from_lsb0_bytes
  • 1b42145 Apply cargo fmt
  • 2f8d368 add special case for creating a full bitmap container
  • 120e9aa Speed up from_bitmap_bytes, and use less unsafe
  • Additional commits viewable in compare view

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=roaring&package-manager=cargo&previous-version=0.10.7&new-version=0.10.8)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- Cargo.lock | 4 ++-- src/core/Cargo.toml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index f1fd38c7f2..a8d5907470 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1459,9 +1459,9 @@ dependencies = [ [[package]] name = "roaring" -version = "0.10.7" +version = "0.10.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f81dc953b2244ddd5e7860cb0bb2a790494b898ef321d4aff8e260efab60cc88" +checksum = "395b0c39c00f9296f3937624c1fa4e0ee44f8c0e4b2c49408179ef381c6c2e6e" dependencies = [ "bytemuck", "byteorder", diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index e815084507..3d5e6ec7e4 100644 --- a/src/core/Cargo.toml +++ b/src/core/Cargo.toml @@ -53,7 +53,7 @@ piz = "0.5.0" primal-check = "0.3.4" rayon = { version = "1.10.0", optional = true } rkyv = { version = "0.7.44", optional = true } -roaring = "0.10.7" +roaring = "0.10.8" roots = "0.0.8" serde = { version = "1.0.215", features = ["derive"] } serde_json = "1.0.133" From 80799970b57cb6a03ed6da6aedae5ca5fb5a90ea Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 14:47:10 +0000 Subject: [PATCH 5/6] Bump thiserror from 2.0.3 to 2.0.6 (#3425) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [thiserror](https://github.com/dtolnay/thiserror) from 2.0.3 to 2.0.6.
Release notes

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2.0.6

  • Suppress deprecation warning on generated From impls (#396)

2.0.5

  • Prevent deprecation warning on generated impl for deprecated type (#394)

2.0.4

  • Eliminate needless_lifetimes clippy lint in generated From impls (#391, thanks @​matt-phylum)
Commits
  • 2075e87 Release 2.0.6
  • e9a9085 Merge pull request #396 from dtolnay/deprecatedfrom
  • 6e8c724 Suppress deprecation warning on generated From impls
  • caf585c Add test of deprecated type in From impl
  • f1f159d Release 2.0.5
  • 366a7b2 Merge pull request #395 from dtolnay/fallback
  • 88a4603 Move fallback expansion to separate module
  • 6712f8c Merge pull request #394 from dtolnay/deprecated
  • 07e7d99 Add "in this derive macro expansion" to missing Display errors
  • 714229d Work around deprecation warning on generated impl for deprecated type
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- Cargo.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index a8d5907470..ee19304d6a 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1684,7 +1684,7 @@ dependencies = [ "statrs", "streaming-stats", "tempfile", - "thiserror 2.0.3", + "thiserror 2.0.6", "twox-hash", "typed-builder", "vec-collections", @@ -1781,11 +1781,11 @@ dependencies = [ [[package]] name = "thiserror" -version = "2.0.3" +version = "2.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c006c85c7651b3cf2ada4584faa36773bd07bac24acfb39f3c431b36d7e667aa" +checksum = "8fec2a1820ebd077e2b90c4df007bebf344cd394098a13c563957d0afc83ea47" dependencies = [ - "thiserror-impl 2.0.3", + "thiserror-impl 2.0.6", ] [[package]] @@ -1801,9 +1801,9 @@ dependencies = [ [[package]] name = "thiserror-impl" -version = "2.0.3" +version = "2.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f077553d607adc1caf65430528a576c757a71ed73944b66ebb58ef2bbd243568" +checksum = "d65750cab40f4ff1929fb1ba509e9914eb756131cef4210da8d5d700d26f6312" dependencies = [ "proc-macro2", "quote", From 7362b4355f2c5f3d3e3053ee2467f9ea37a0a30f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 15:23:45 +0000 Subject: [PATCH 6/6] Bump statrs from 0.17.1 to 0.18.0 (#3426) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [statrs](https://github.com/statrs-dev/statrs) from 0.17.1 to 0.18.0.
Changelog

Sourced from statrs's changelog.

[0.18.0] - 2024-12-02

✨ Added

  • Added more inverse cumulative distribution functions.
  • Introduced feature flags: rand and nalgebra.
  • Added the std_dev method to the Distribution trait explicitly.
  • Supported sampling integers from discrete distributions.
  • Added support for the Gumbel distribution.

⚠️ Breaking Changes

  • Migrated multivariate distributions to generic dimensions.
  • Replaced StatsError with module-level error types in distribution and its children.
  • Changed checked_logit, checked_multinomial, and similar methods to return Option to handle invalid inputs.
  • Changed Chi distribution to use u64 for degrees of freedom.

🛠️ Changed

  • Upgraded nalgebra to version 0.33.
    • Upgrades MSRV to 1.65+
  • Improved documentation and added examples (e.g., for Hypergeometric distribution).
  • Added MSRV (Minimum Supported Rust Version) metadata to Cargo.toml and documentation.
  • Introduced coverage reporting with llvm-cov.
  • Updated CI to check all feature combinations and ensure MSRV compliance.
  • Added an MSRV badge to crates.io.

✅ Fixed

  • Corrected formatting issues in documentation.
  • Fixed several rustdoc warnings.
  • Expanded test coverage for Dirichlet and Multinomial distributions.
  • Improved ergonomics at cli for tests and ensured compatibility with updated NIST data.

❌ Removed

  • Replaced StatsError with module-level error types.
  • Deprecated the error module and preformatted NIST data.
  • Removed rustfmt.toml as part of CI clean-up.

🎉 New Contributors

Commits
  • 2f40250 ci: update lockfile to use statrs@0.18.0
  • 5bfd9c2 chore: update changelog and version in manifest for release
  • 650fe7d refactor: impl MeanN over generic dimension
  • ab55c61 Fixed typo in MultivariateNormal PDF equation
  • 748aa55 refactor!: Empirical::new -> Result<_, Infallible>
  • b73f189 refactor: Empirical::add: Use and_modify
  • 6ad4291 refactor: Empirical::remove: Try to modify inplace
  • af648be refactor: Rewrite Empirical::cdf and ::sf
  • 7456947 refactor: Separate Empirical::mean_and_var
  • f685851 refactor: Use u64 to store Empirical::sum
  • Additional commits viewable in compare view

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=statrs&package-manager=cargo&previous-version=0.17.1&new-version=0.18.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- Cargo.lock | 24 ++++++------------------ src/core/Cargo.toml | 2 +- 2 files changed, 7 insertions(+), 19 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index ee19304d6a..9c45cfc7c8 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -991,13 +991,12 @@ checksum = "a2983372caf4480544083767bf2d27defafe32af49ab4df3a0b7fc90793a3664" [[package]] name = "nalgebra" -version = "0.32.5" +version = "0.33.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3ea4908d4f23254adda3daa60ffef0f1ac7b8c3e9a864cf3cc154b251908a2ef" +checksum = "26aecdf64b707efd1310e3544d709c5c0ac61c13756046aaaba41be5c4f66a3b" dependencies = [ "approx", "matrixmultiply", - "nalgebra-macros", "num-complex", "num-rational", "num-traits", @@ -1007,17 +1006,6 @@ dependencies = [ "typenum", ] -[[package]] -name = "nalgebra-macros" -version = "0.2.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91761aed67d03ad966ef783ae962ef9bbaca728d2dd7ceb7939ec110fffad998" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.104", -] - [[package]] name = "needletail" version = "0.5.1" @@ -1610,9 +1598,9 @@ checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64" [[package]] name = "simba" -version = "0.8.1" +version = "0.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "061507c94fc6ab4ba1c9a0305018408e312e17c041eb63bef8aa726fa33aceae" +checksum = "b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa" dependencies = [ "approx", "num-complex", @@ -1701,9 +1689,9 @@ checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" [[package]] name = "statrs" -version = "0.17.1" +version = "0.18.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f697a07e4606a0a25c044de247e583a330dbb1731d11bc7350b81f48ad567255" +checksum = "2a3fe7c28c6512e766b0874335db33c94ad7b8f9054228ae1c2abd47ce7d335e" dependencies = [ "approx", "nalgebra", diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index 3d5e6ec7e4..41cf944fac 100644 --- a/src/core/Cargo.toml +++ b/src/core/Cargo.toml @@ -57,7 +57,7 @@ roaring = "0.10.8" roots = "0.0.8" serde = { version = "1.0.215", features = ["derive"] } serde_json = "1.0.133" -statrs = "0.17.1" +statrs = "0.18.0" streaming-stats = "0.2.3" thiserror = "2.0" twox-hash = "1.6.0"