From 9c2d5c73dc68e1801c8679f5551780d4e22ba972 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Sep 2025 18:47:20 +0000 Subject: [PATCH] chore(deps): bump rustyms from 0.8.3 to 0.11.0 Bumps [rustyms](https://github.com/snijderlab/rustyms) from 0.8.3 to 0.11.0. - [Release notes](https://github.com/snijderlab/rustyms/releases) - [Commits](https://github.com/snijderlab/rustyms/compare/v0.8.3...v0.11.0) --- updated-dependencies: - dependency-name: rustyms dependency-version: 0.11.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Cargo.lock | 378 ++++++++++++++++++++++++++++++++++++--- rust/timsseek/Cargo.toml | 2 +- 2 files changed, 354 insertions(+), 26 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index a878b4d..6c76a96 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -16,7 +16,7 @@ checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011" dependencies = [ "cfg-if", "const-random", - "getrandom", + "getrandom 0.2.15", "once_cell", "version_check", "zerocopy", @@ -323,13 +323,34 @@ version = "0.22.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6" +[[package]] +name = "base64-simd" +version = "0.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "339abbe78e73178762e23bea9dfd08e697eb3f3301cd4be981c0f78ba5859195" +dependencies = [ + "outref", + "vsimd", +] + [[package]] name = "bincode" -version = "1.3.3" +version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad" +checksum = "36eaf5d7b090263e8150820482d5d93cd964a81e4019913c972f4edcc6edb740" dependencies = [ + "bincode_derive", "serde", + "unty", +] + +[[package]] +name = "bincode_derive" +version = "2.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf95709a440f45e986983918d0e8a1f30a9b1df04918fc828670606804ac3c09" +dependencies = [ + "virtue", ] [[package]] @@ -403,6 +424,20 @@ name = "bytemuck" version = "1.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef657dfab802224e671f5818e9a4935f9b1957ed18e58292690cc39e7a4092a3" +dependencies = [ + "bytemuck_derive", +] + +[[package]] +name = "bytemuck_derive" +version = "1.10.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4f154e572231cb6ba2bd1176980827e3d5dc04cc183a75dea38109fbdd672d29" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.96", +] [[package]] name = "byteorder" @@ -441,7 +476,9 @@ checksum = "1a7964611d71df112cb1730f2ee67324fcf4d0fc6606acbbe9bfe06df124637c" dependencies = [ "android-tzdata", "iana-time-zone", + "js-sys", "num-traits", + "wasm-bindgen", "windows-link", ] @@ -519,11 +556,20 @@ version = "0.1.16" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f9d839f2a20b0aee515dc581a6172f2321f96cab76c1a38a4c584a194955390e" dependencies = [ - "getrandom", + "getrandom 0.2.15", "once_cell", "tiny-keccak", ] +[[package]] +name = "context_error" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "da7e1b8dc6f4cdc4f6b897d6aa1b7eaec6d95331bdb765d2a51cdd948e157ee0" +dependencies = [ + "serde", +] + [[package]] name = "core-foundation-sys" version = "0.8.7" @@ -623,6 +669,12 @@ version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "34aa73646ffb006b8f5147f3dc182bd4bcb190227ce861fc4a4844bf8e3cb2c0" +[[package]] +name = "equivalent" +version = "1.0.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f" + [[package]] name = "fallible-iterator" version = "0.3.0" @@ -672,6 +724,15 @@ version = "1.0.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1" +[[package]] +name = "font-types" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "02a596f5713680923a2080d86de50fe472fb290693cf0f701187a1c8b36996b7" +dependencies = [ + "bytemuck", +] + [[package]] name = "gethostname" version = "0.2.3" @@ -690,7 +751,19 @@ checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7" dependencies = [ "cfg-if", "libc", - "wasi", + "wasi 0.11.0+wasi-snapshot-preview1", +] + +[[package]] +name = "getrandom" +version = "0.3.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "26145e563e54f2cadc477553f1ec5ee650b00862f0a58bcd12cbdc5f0ea2d2f4" +dependencies = [ + "cfg-if", + "libc", + "r-efi", + "wasi 0.14.7+wasi-0.2.4", ] [[package]] @@ -763,6 +836,23 @@ dependencies = [ "cc", ] +[[package]] +name = "identity-hash" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dfdd7caa900436d8f13b2346fe10257e0c05c1f1f9e351f4f5d57c03bd5f45da" + +[[package]] +name = "indexmap" +version = "2.11.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "206a8042aec68fa4a62e8d3f7aa4ceb508177d9324faf261e1959e495b7a1921" +dependencies = [ + "equivalent", + "hashbrown 0.15.2", + "serde", +] + [[package]] name = "indicatif" version = "0.18.0" @@ -791,9 +881,9 @@ checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf" [[package]] name = "itertools" -version = "0.12.1" +version = "0.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569" +checksum = "2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285" dependencies = [ "either", ] @@ -969,6 +1059,16 @@ dependencies = [ "regex-automata 0.1.10", ] +[[package]] +name = "matrixmultiply" +version = "0.3.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a06de3016e9fae57a36fd14dba131fccf49f74b40b7fbdb472f96e361ec71a08" +dependencies = [ + "autocfg", + "rawpointer", +] + [[package]] name = "memchr" version = "2.7.4" @@ -1002,6 +1102,50 @@ dependencies = [ "adler2", ] +[[package]] +name = "mzdata" +version = "0.59.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7e6c319f4111abe43bbcc33433b727968e30163f0a90e440386978656df8685c" +dependencies = [ + "base64-simd", + "bitflags 2.8.0", + "bytemuck", + "chrono", + "flate2", + "identity-hash", + "indexmap", + "log", + "mzpeaks", + "num-traits", + "regex", + "thiserror 2.0.17", +] + +[[package]] +name = "mzpeaks" +version = "1.0.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "543be9eac70437bfc915b3339e6ae4f23dc034922f13eb2535dcc19e7e9e9481" +dependencies = [ + "num-traits", +] + +[[package]] +name = "ndarray" +version = "0.16.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "882ed72dce9365842bf196bdeedf5055305f11fc8c03dee7bb0194a6cad34841" +dependencies = [ + "matrixmultiply", + "num-complex", + "num-integer", + "num-traits", + "portable-atomic", + "portable-atomic-util", + "rawpointer", +] + [[package]] name = "nohash-hasher" version = "0.2.0" @@ -1040,6 +1184,7 @@ checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9" dependencies = [ "num-integer", "num-traits", + "serde", ] [[package]] @@ -1049,6 +1194,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495" dependencies = [ "num-traits", + "serde", ] [[package]] @@ -1086,6 +1232,7 @@ dependencies = [ "num-bigint", "num-integer", "num-traits", + "serde", ] [[package]] @@ -1115,15 +1262,21 @@ dependencies = [ [[package]] name = "ordered-float" -version = "4.6.0" +version = "5.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7bb71e1b3fa6ca1c61f383464aaf2bb0e2f8e772a1f01d486832464de363b951" +checksum = "e2c1f9f56e534ac6a9b8a4600bdf0f530fb393b5f393e7b4d03489c3cf0c3f01" dependencies = [ "num-traits", - "rand", + "rand 0.8.5", "serde", ] +[[package]] +name = "outref" +version = "0.5.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a80800c0488c3a21695ea981a54918fbb37abf04f4d0720c453632255e2ff0e" + [[package]] name = "overload" version = "0.1.1" @@ -1243,6 +1396,15 @@ version = "1.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "280dc24453071f1b63954171985a0b0d30058d287960968b9b2aca264c8d4ee6" +[[package]] +name = "portable-atomic-util" +version = "0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507" +dependencies = [ + "portable-atomic", +] + [[package]] name = "powerfmt" version = "0.2.0" @@ -1308,6 +1470,12 @@ dependencies = [ "proc-macro2", ] +[[package]] +name = "r-efi" +version = "5.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "69cdb34c158ceb288df11e18b4bd39de994f6657d83847bdffdbd7f346754b0f" + [[package]] name = "rand" version = "0.8.5" @@ -1315,11 +1483,21 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404" dependencies = [ "libc", - "rand_chacha", - "rand_core", + "rand_chacha 0.3.1", + "rand_core 0.6.4", "serde", ] +[[package]] +name = "rand" +version = "0.9.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6db2770f06117d490610c7488547d543617b21bfa07796d7a12f6f1bd53850d1" +dependencies = [ + "rand_chacha 0.9.0", + "rand_core 0.9.3", +] + [[package]] name = "rand_chacha" version = "0.3.1" @@ -1327,7 +1505,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" dependencies = [ "ppv-lite86", - "rand_core", + "rand_core 0.6.4", +] + +[[package]] +name = "rand_chacha" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb" +dependencies = [ + "ppv-lite86", + "rand_core 0.9.3", ] [[package]] @@ -1336,16 +1524,31 @@ version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c" dependencies = [ - "getrandom", + "getrandom 0.2.15", "serde", ] +[[package]] +name = "rand_core" +version = "0.9.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "99d9a13982dcf210057a8a78572b2217b667c3beacbf3a0d8b454f6f82837d38" +dependencies = [ + "getrandom 0.3.3", +] + [[package]] name = "random" version = "0.13.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "474c42c904f04dfe2a595a02f71e1a0e5e92ffb5761cc9a4c02140b93b8dd504" +[[package]] +name = "rawpointer" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3" + [[package]] name = "rayon" version = "1.10.0" @@ -1366,6 +1569,16 @@ dependencies = [ "crossbeam-utils", ] +[[package]] +name = "read-fonts" +version = "0.29.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "04ca636dac446b5664bd16c069c00a9621806895b8bb02c2dc68542b23b8f25d" +dependencies = [ + "bytemuck", + "font-types", +] + [[package]] name = "regex" version = "1.11.1" @@ -1463,20 +1676,29 @@ checksum = "f7c45b9784283f1b2e7fb61b42047c2fd678ef0960d4f6f1eba131594cc369d4" [[package]] name = "rustyms" -version = "0.8.3" +version = "0.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4831e9fe077e1d905b993838753820e0d70f81a20bf86f8837374c0823523353" +checksum = "011d3d672ae44d5e07db0488d855f2b5ed178e3d6bb7ef5b18c6415c20bbd61e" dependencies = [ "bincode", + "context_error", "flate2", "itertools", - "ordered-float 4.6.0", + "mzdata", + "ndarray", + "ordered-float 5.0.0", + "paste", "probability", + "rand 0.9.2", "rayon", "regex", "serde", + "serde_json", "similar", + "swash", + "thin-vec", "uom", + "zeno", ] [[package]] @@ -1552,9 +1774,19 @@ checksum = "e3a9fe34e3e7a50316060351f37187a3f546bce95496156754b601a5fa71b76e" [[package]] name = "similar" -version = "2.6.0" +version = "2.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1de1d4f81173b03af4c0cbed3c898f6bff5b870e4a7f5d6f4057d62a7a4b686e" +checksum = "bbbb5d9659141646ae647b42fe094daf6c6192d1620870b449d9557f748b2daa" + +[[package]] +name = "skrifa" +version = "0.31.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dbeb4ca4399663735553a09dd17ce7e49a0a0203f03b706b39628c4d913a8607" +dependencies = [ + "bytemuck", + "read-fonts", +] [[package]] name = "smallvec" @@ -1589,6 +1821,17 @@ version = "0.11.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f" +[[package]] +name = "swash" +version = "0.2.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f745de914febc7c9ab4388dfaf94bbc87e69f57bb41133a9b0c84d4be49856f3" +dependencies = [ + "skrifa", + "yazi", + "zeno", +] + [[package]] name = "syn" version = "1.0.109" @@ -1634,13 +1877,31 @@ dependencies = [ "syn 1.0.109", ] +[[package]] +name = "thin-vec" +version = "0.2.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "144f754d318415ac792f9d69fc87abbbfc043ce2ef041c60f16ad828f638717d" +dependencies = [ + "serde", +] + [[package]] name = "thiserror" version = "1.0.69" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52" dependencies = [ - "thiserror-impl", + "thiserror-impl 1.0.69", +] + +[[package]] +name = "thiserror" +version = "2.0.17" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f63587ca0f12b72a0600bcba1d40081f830876000bb46dd2337a3051618f4fc8" +dependencies = [ + "thiserror-impl 2.0.17", ] [[package]] @@ -1654,6 +1915,17 @@ dependencies = [ "syn 2.0.96", ] +[[package]] +name = "thiserror-impl" +version = "2.0.17" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3ff15c8ecd7de3849db632e14d18d2571fa09dfc5ed93479bc4485c7a517c913" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.96", +] + [[package]] name = "thread_local" version = "1.1.8" @@ -1714,8 +1986,8 @@ dependencies = [ "indicatif", "mimalloc", "nohash-hasher", - "rand", - "rand_chacha", + "rand 0.8.5", + "rand_chacha 0.3.1", "rayon", "serde", "serde_json", @@ -1741,7 +2013,7 @@ dependencies = [ "rusqlite", "serde", "serde_json", - "thiserror", + "thiserror 1.0.69", "zstd", ] @@ -1955,12 +2227,20 @@ version = "0.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "323402cff2dd658f39ca17c789b502021b3f18707c91cdf22e3838e1b4023817" +[[package]] +name = "unty" +version = "0.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6d49784317cd0d1ee7ec5c716dd598ec5b4483ea832a2dced265471cc0f690ae" + [[package]] name = "uom" -version = "0.35.0" +version = "0.37.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8362194c7a9845a7a7f3562173d6e1da3f24f7132018cb78fe77a5b4474187b2" +checksum = "cd5cfe7d84f6774726717f358a37f5bca8fca273bed4de40604ad129d1107b49" dependencies = [ + "num-bigint", + "num-complex", "num-rational", "num-traits", "serde", @@ -1991,12 +2271,42 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a" +[[package]] +name = "virtue" +version = "0.0.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "051eb1abcf10076295e815102942cc58f9d5e3b4560e46e53c21e8ff6f3af7b1" + +[[package]] +name = "vsimd" +version = "0.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5c3082ca00d5a5ef149bb8b555a72ae84c9c59f7250f013ac822ac2e49b19c64" + [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" +[[package]] +name = "wasi" +version = "0.14.7+wasi-0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "883478de20367e224c0090af9cf5f9fa85bed63a95c1abf3afc5c083ebc06e8c" +dependencies = [ + "wasip2", +] + +[[package]] +name = "wasip2" +version = "1.0.1+wasi-0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0562428422c63773dad2c345a1882263bbf4d65cf3f42e90921f787ef5ad58e7" +dependencies = [ + "wit-bindgen", +] + [[package]] name = "wasm-bindgen" version = "0.2.100" @@ -2248,6 +2558,24 @@ version = "0.53.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "271414315aff87387382ec3d271b52d7ae78726f5d44ac98b4f4030c91880486" +[[package]] +name = "wit-bindgen" +version = "0.46.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f17a85883d4e6d00e8a97c586de764dabcc06133f7f1d55dce5cdc070ad7fe59" + +[[package]] +name = "yazi" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e01738255b5a16e78bbb83e7fbba0a1e7dd506905cfc53f4622d89015a03fbb5" + +[[package]] +name = "zeno" +version = "0.3.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6df3dc4292935e51816d896edcd52aa30bc297907c26167fec31e2b0c6a32524" + [[package]] name = "zerocopy" version = "0.7.35" diff --git a/rust/timsseek/Cargo.toml b/rust/timsseek/Cargo.toml index debacef..b3ee67a 100644 --- a/rust/timsseek/Cargo.toml +++ b/rust/timsseek/Cargo.toml @@ -5,7 +5,7 @@ edition = "2021" license = "Apache-2.0" [dependencies] -rustyms = "0.8.3" +rustyms = "0.11.0" timsquery = { path = "../timsquery" } regex = "1.10.6" csv = "1.3.0"