diff --git a/Cargo.lock b/Cargo.lock index f584a7a..c96eae7 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -19,17 +19,6 @@ dependencies = [ "cpufeatures 0.2.17", ] -[[package]] -name = "ahash" -version = "0.7.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9" -dependencies = [ - "getrandom 0.2.16", - "once_cell", - "version_check", -] - [[package]] name = "ahash" version = "0.8.12" @@ -168,12 +157,6 @@ version = "1.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "03918c3dbd7701a85c6b9887732e2921175f26c350b4563841d0958c21d57e6d" -[[package]] -name = "arrayvec" -version = "0.7.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7c02d123df017efcdfbd739ef81735b36c5ba83ec3c59c80a9d7ecc718f92e50" - [[package]] name = "astral-pubgrub" version = "0.3.3" @@ -413,7 +396,7 @@ checksum = "3b43422f69d8ff38f95f1b2bb76517c91589a924d1559a0e935d7c8ce0274c11" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -442,28 +425,6 @@ dependencies = [ "wasm-bindgen-futures", ] -[[package]] -name = "async-stream" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0b5a71a6f37880a80d1d7f19efd781e4b5de42c88f0722cc13bcb6cc2cfe8476" -dependencies = [ - "async-stream-impl", - "futures-core", - "pin-project-lite", -] - -[[package]] -name = "async-stream-impl" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c7c24de15d275a1ecfd47a380fb4d5ec9bfe0933f309ed5e705b775596a3574d" -dependencies = [ - "proc-macro2", - "quote", - "syn 2.0.108", -] - [[package]] name = "async-task" version = "4.7.1" @@ -478,7 +439,7 @@ checksum = "9035ad2d096bed7955a320ee7e2230574d28fd3c3a0f186cbea1ff3c7eed5dbb" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -578,18 +539,6 @@ version = "2.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "812e12b5285cc515a9c72a5c1d3b6d46a19dac5acfef5265968c166106e31dd3" -[[package]] -name = "bitvec" -version = "1.0.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1bc2832c24239b0141d5674bb9174f9d68a8b5b3f2753311927c172ca46f7e9c" -dependencies = [ - "funty", - "radium", - "tap", - "wyz", -] - [[package]] name = "blake2" version = "0.10.6" @@ -630,29 +579,6 @@ dependencies = [ "piper", ] -[[package]] -name = "borsh" -version = "1.5.7" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ad8646f98db542e39fc66e68a20b2144f6a732636df7c2354e74645faaa433ce" -dependencies = [ - "borsh-derive", - "cfg_aliases", -] - -[[package]] -name = "borsh-derive" -version = "1.5.7" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fdd1d3c0c2f5833f22386f252fe8ed005c7f59fdcddeef025c01b4c3b9fd9ac3" -dependencies = [ - "once_cell", - "proc-macro-crate", - "proc-macro2", - "quote", - "syn 2.0.108", -] - [[package]] name = "boxcar" version = "0.2.14" @@ -718,40 +644,18 @@ version = "3.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "46c5e41b57b8bba42a04676d81cb89e9ee8e859a1a66f80a5a72e1cb76b34d43" -[[package]] -name = "bytecheck" -version = "0.6.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "23cdc57ce23ac53c931e88a43d06d070a6fd142f2617be5855eb75efc9beb1c2" -dependencies = [ - "bytecheck_derive 0.6.12", - "ptr_meta 0.1.4", - "simdutf8", -] - [[package]] name = "bytecheck" version = "0.8.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0caa33a2c0edca0419d15ac723dff03f1956f7978329b1e3b5fdaaaed9d3ca8b" dependencies = [ - "bytecheck_derive 0.8.2", - "ptr_meta 0.3.1", + "bytecheck_derive", + "ptr_meta", "rancor", "simdutf8", ] -[[package]] -name = "bytecheck_derive" -version = "0.6.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3db406d29fbcd95542e92559bed4d8ad92636d1ca8b3b72ede10b4bcc010e659" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.109", -] - [[package]] name = "bytecheck_derive" version = "0.8.2" @@ -760,7 +664,7 @@ checksum = "89385e82b5d1821d2219e0b095efa2cc1f246cbf99080f3be46a1a85c0d392d9" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -934,7 +838,7 @@ dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1180,7 +1084,7 @@ checksum = "c50341f21df64b412b4f917e34b7aa786c092d64f3f905f478cb76950c7e980c" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1214,7 +1118,7 @@ dependencies = [ "proc-macro2", "quote", "strsim", - "syn 2.0.108", + "syn", ] [[package]] @@ -1228,7 +1132,7 @@ dependencies = [ "proc-macro2", "quote", "strsim", - "syn 2.0.108", + "syn", ] [[package]] @@ -1239,7 +1143,7 @@ checksum = "fc34b93ccb385b40dc71c6fceac4b2ad23662c7eeb248cf10d529b7e055b6ead" dependencies = [ "darling_core 0.20.11", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1250,7 +1154,7 @@ checksum = "d38308df82d1080de0afee5d069fa14b0326a88c14f15c5ccda35b4a6c414c81" dependencies = [ "darling_core 0.21.3", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1350,7 +1254,7 @@ checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1424,7 +1328,6 @@ dependencies = [ "phf", "resource", "serde", - "tokio", "url", "utile", ] @@ -1447,7 +1350,7 @@ checksum = "67c78a4d8fdf9953a5c9d458f9efe940fd97a0cab0941c075a813ac594733827" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1645,12 +1548,6 @@ dependencies = [ "tokio", ] -[[package]] -name = "funty" -version = "2.0.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e6d5a32815ae3f33302d95fdcb2ce17862f8c65363dcfd29360480ba1001fc9c" - [[package]] name = "futures" version = "0.3.31" @@ -1720,7 +1617,7 @@ checksum = "162ee34ebcb7c64a8abebc059ce0fee27c2262618d7b60ed8faf72fef13c3650" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -1771,12 +1668,10 @@ dependencies = [ "csv", "either", "env_logger", - "flate2", "futures", "jiff", "log", "noodles", - "pgs_catalog", "phf", "resource", "serde", @@ -1922,16 +1817,12 @@ name = "hail" version = "0.1.0" dependencies = [ "biocore", - "either", "env_logger", - "futures", "log", "noodles", - "pgs_catalog", "phf", "resource", "serde", - "tokio", "url", "utile", ] @@ -1941,9 +1832,6 @@ name = "hashbrown" version = "0.12.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888" -dependencies = [ - "ahash 0.7.8", -] [[package]] name = "hashbrown" @@ -2435,7 +2323,7 @@ checksum = "03343451ff899767262ec32146f6d559dd759fdadf42ff0e227c7c48f72594b4" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -2527,7 +2415,7 @@ dependencies = [ "proc-macro2", "quote", "regex", - "syn 2.0.108", + "syn", ] [[package]] @@ -2768,7 +2656,7 @@ checksum = "4568f25ccbd45ab5d5603dc34318c1ec56b117531781260002151b8530a9f931" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3069,7 +2957,7 @@ checksum = "a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3157,17 +3045,12 @@ version = "0.1.0" dependencies = [ "biocore", "csv", - "flate2", "hail", - "ids", - "log", "ordered-float 5.1.0", "resource", - "rust_decimal", "serde", "serde_json", "tokio", - "tokio-test", "url", "utile", ] @@ -3314,7 +3197,7 @@ dependencies = [ "phf_shared", "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3343,7 +3226,7 @@ checksum = "6e918e4ff8c4549eb882f14b3a4bc8c8bc93de829416eacf579f1207a8fbf861" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3446,7 +3329,7 @@ dependencies = [ "darling 0.20.11", "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3510,7 +3393,6 @@ dependencies = [ "diff", "log", "proptest", - "rand 0.9.2", "regex", "serde", "utile", @@ -3586,33 +3468,13 @@ dependencies = [ "unarray", ] -[[package]] -name = "ptr_meta" -version = "0.1.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0738ccf7ea06b608c10564b31debd4f5bc5e197fc8bfe088f68ae5ce81e7a4f1" -dependencies = [ - "ptr_meta_derive 0.1.4", -] - [[package]] name = "ptr_meta" version = "0.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b9a0cf95a1196af61d4f1cbdab967179516d9a4a4312af1f31948f8f6224a79" dependencies = [ - "ptr_meta_derive 0.3.1", -] - -[[package]] -name = "ptr_meta_derive" -version = "0.1.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "16b845dbfca988fa33db069c0e230574d15a3088f147a87b64c7589eb662c9ac" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.109", + "ptr_meta_derive", ] [[package]] @@ -3623,7 +3485,7 @@ checksum = "7347867d0a7e1208d93b46767be83e2b8f978c3dad35f775ac8d8847551d6fe1" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3755,19 +3617,13 @@ version = "6.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f8dcc9c7d52a811697d2151c701e0d08956f92b0e24136cf4cf27b57a6a0d9bf" -[[package]] -name = "radium" -version = "0.7.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dc33ff2d4973d518d823d61aa239014831e521c75da58e3df4840d3f47749d09" - [[package]] name = "rancor" version = "0.1.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a063ea72381527c2a0561da9c80000ef822bdd7c3241b1cc1b12100e3df081ee" dependencies = [ - "ptr_meta 0.3.1", + "ptr_meta", ] [[package]] @@ -3914,7 +3770,7 @@ checksum = "b7186006dcb21920990093f30e3dea63b7d6e977bf1256be20c3563a5db070da" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -3958,22 +3814,13 @@ version = "0.8.8" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7a2d987857b319362043e95f5353c0535c1f58eec5336fdfcf626430af7def58" -[[package]] -name = "rend" -version = "0.4.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "71fe3824f5629716b1589be05dacd749f6aa084c87e00e016714a8cdfccc997c" -dependencies = [ - "bytecheck 0.6.12", -] - [[package]] name = "rend" version = "0.5.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "cadadef317c2f20755a64d7fdc48f9e7178ee6b0e1f7fce33fa60f1d68a276e6" dependencies = [ - "bytecheck 0.8.2", + "bytecheck", ] [[package]] @@ -4149,38 +3996,24 @@ dependencies = [ name = "resource" version = "0.1.0" dependencies = [ - "ahash 0.8.12", "async-compression", "brotli 8.0.2", "bytes", "directories", "flate2", "futures", - "getrandom 0.2.16", - "getrandom 0.3.4", - "gloo-timers", "indicatif", "log", - "nohash-hasher", "pin-project", - "plotly", - "rand 0.9.2", - "regex", "reqwest", - "rmp-serde", "serde", "serde_json", - "serde_with", "suppaftp", "tempfile", - "thiserror 2.0.17", "tokio", "tokio-util", - "tracing", "url", "utile", - "wasm-bindgen-futures", - "web-time", ] [[package]] @@ -4235,7 +4068,7 @@ dependencies = [ "rinja_parser", "rustc-hash", "serde", - "syn 2.0.108", + "syn", ] [[package]] @@ -4249,55 +4082,26 @@ dependencies = [ "serde", ] -[[package]] -name = "rkyv" -version = "0.7.45" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9008cd6385b9e161d8229e1f6549dd23c3d022f132a2ea37ac3a10ac4935779b" -dependencies = [ - "bitvec", - "bytecheck 0.6.12", - "bytes", - "hashbrown 0.12.3", - "ptr_meta 0.1.4", - "rend 0.4.2", - "rkyv_derive 0.7.45", - "seahash", - "tinyvec", - "uuid", -] - [[package]] name = "rkyv" version = "0.8.15" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1a30e631b7f4a03dee9056b8ef6982e8ba371dd5bedb74d3ec86df4499132c70" dependencies = [ - "bytecheck 0.8.2", + "bytecheck", "bytes", "hashbrown 0.16.0", "indexmap 2.12.0", "munge", - "ptr_meta 0.3.1", + "ptr_meta", "rancor", - "rend 0.5.3", - "rkyv_derive 0.8.15", + "rend", + "rkyv_derive", "smallvec", "tinyvec", "uuid", ] -[[package]] -name = "rkyv_derive" -version = "0.7.45" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "503d1d27590a2b0a3a4ca4c94755aa2875657196ecbf401a42eff41d7de532c0" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.109", -] - [[package]] name = "rkyv_derive" version = "0.8.15" @@ -4306,7 +4110,7 @@ checksum = "8100bb34c0a1d0f907143db3149e6b4eea3c33b9ee8b189720168e818303986f" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4372,22 +4176,6 @@ dependencies = [ "thiserror 1.0.69", ] -[[package]] -name = "rust_decimal" -version = "1.39.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "35affe401787a9bd846712274d97654355d21b2a2c092a3139aabe31e9022282" -dependencies = [ - "arrayvec", - "borsh", - "bytes", - "num-traits", - "rand 0.8.5", - "rkyv 0.7.45", - "serde", - "serde_json", -] - [[package]] name = "rustc-hash" version = "2.1.1" @@ -4540,7 +4328,7 @@ dependencies = [ "proc-macro2", "quote", "serde_derive_internals", - "syn 2.0.108", + "syn", ] [[package]] @@ -4566,7 +4354,7 @@ checksum = "ed76efe62313ab6610570951494bdaa81568026e0318eaa55f167de70eeea67d" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4691,7 +4479,7 @@ checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4702,7 +4490,7 @@ checksum = "18d26a20a969b9e3fdf2fc2d9f21eda6c40e2de84c9408bb5d3b05d499aae711" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4726,7 +4514,7 @@ checksum = "175ee3e80ae9982737ca543e96133087cbd9a485eecc3bc4de9c1a37b47ea59c" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4778,7 +4566,7 @@ dependencies = [ "darling 0.21.3", "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -4974,7 +4762,7 @@ dependencies = [ "proc-macro2", "quote", "rustversion", - "syn 2.0.108", + "syn", ] [[package]] @@ -4999,17 +4787,6 @@ dependencies = [ "thiserror 2.0.17", ] -[[package]] -name = "syn" -version = "1.0.109" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237" -dependencies = [ - "proc-macro2", - "quote", - "unicode-ident", -] - [[package]] name = "syn" version = "2.0.108" @@ -5038,7 +4815,7 @@ checksum = "728a70f3dbaf5bab7f0c4b1ac8d7ae5ea60a4b5549c8a5914361c99147a709d2" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -5062,12 +4839,6 @@ dependencies = [ "libc", ] -[[package]] -name = "tap" -version = "1.0.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369" - [[package]] name = "tar" version = "0.4.44" @@ -5145,7 +4916,7 @@ checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -5156,7 +4927,7 @@ checksum = "3ff15c8ecd7de3849db632e14d18d2571fa09dfc5ed93479bc4485c7a517c913" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -5250,7 +5021,7 @@ checksum = "af407857209536a95c8e56f8231ef2c2e2aff839b22e07a1ffcbc617e9db9fa5" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -5285,19 +5056,6 @@ dependencies = [ "tokio-util", ] -[[package]] -name = "tokio-test" -version = "0.4.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2468baabc3311435b55dd935f702f42cd1b8abb7e754fb7dfb16bd36aa88f9f7" -dependencies = [ - "async-stream", - "bytes", - "futures-core", - "tokio", - "tokio-stream", -] - [[package]] name = "tokio-util" version = "0.7.17" @@ -5443,7 +5201,7 @@ checksum = "81383ab64e72a7a8b8e13130c49e3dab29def6d0c7d76a03087b3cf71c5c6903" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -5566,8 +5324,7 @@ checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821" name = "utile" version = "0.1.1" dependencies = [ - "ahash 0.8.12", - "bytes", + "ahash", "content_disposition", "futures", "getrandom 0.2.16", @@ -5587,8 +5344,6 @@ dependencies = [ "serde_with", "thiserror 2.0.17", "tokio", - "tokio-util", - "tracing", "url", "wasm-bindgen-futures", "web-time", @@ -5753,7 +5508,7 @@ dependencies = [ "astral_async_http_range_reader", "astral_async_zip", "async-trait", - "bytecheck 0.8.2", + "bytecheck", "fs-err", "futures", "h2", @@ -5763,7 +5518,7 @@ dependencies = [ "jiff", "percent-encoding", "reqwest", - "rkyv 0.8.15", + "rkyv", "rmp-serde", "rustc-hash", "serde", @@ -5901,7 +5656,7 @@ version = "0.0.29" source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192cead613c68#988952519528988cf9185ea867b192cead613c68" dependencies = [ "memchr", - "rkyv 0.8.15", + "rkyv", "serde", "smallvec", "thiserror 2.0.17", @@ -5927,7 +5682,7 @@ dependencies = [ "owo-colors", "percent-encoding", "petgraph", - "rkyv 0.8.15", + "rkyv", "rustc-hash", "schemars 1.0.5", "serde", @@ -6132,7 +5887,7 @@ source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192 dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", "textwrap", ] @@ -6159,7 +5914,7 @@ name = "uv-normalize" version = "0.0.29" source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192cead613c68#988952519528988cf9185ea867b192cead613c68" dependencies = [ - "rkyv 0.8.15", + "rkyv", "schemars 1.0.5", "serde", "uv-small-str", @@ -6189,7 +5944,7 @@ version = "0.0.29" source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192cead613c68#988952519528988cf9185ea867b192cead613c68" dependencies = [ "astral-version-ranges", - "rkyv 0.8.15", + "rkyv", "serde", "tracing", "unicode-width", @@ -6208,7 +5963,7 @@ dependencies = [ "indexmap 2.12.0", "itertools 0.14.0", "regex", - "rkyv 0.8.15", + "rkyv", "rustc-hash", "schemars 1.0.5", "serde", @@ -6249,7 +6004,7 @@ source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192 dependencies = [ "bitflags 2.10.0", "memchr", - "rkyv 0.8.15", + "rkyv", "rustc-hash", "serde", "thiserror 2.0.17", @@ -6279,7 +6034,7 @@ dependencies = [ "mailparse", "petgraph", "regex", - "rkyv 0.8.15", + "rkyv", "rustc-hash", "schemars 1.0.5", "serde", @@ -6412,7 +6167,7 @@ dependencies = [ "owo-colors", "percent-encoding", "petgraph", - "rkyv 0.8.15", + "rkyv", "rustc-hash", "same-file", "schemars 1.0.5", @@ -6540,7 +6295,7 @@ version = "0.0.29" source = "git+https://github.com/astral-sh/uv?rev=988952519528988cf9185ea867b192cead613c68#988952519528988cf9185ea867b192cead613c68" dependencies = [ "arcstr", - "rkyv 0.8.15", + "rkyv", "schemars 1.0.5", "serde", ] @@ -6778,7 +6533,7 @@ dependencies = [ "bumpalo", "proc-macro2", "quote", - "syn 2.0.108", + "syn", "wasm-bindgen-shared", ] @@ -6989,7 +6744,7 @@ checksum = "053e2e040ab57b9dc951b72c264860db7eb3b0200ba345b4e4c3b14f67855ddf" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -7000,7 +6755,7 @@ checksum = "3f316c4a2570ba26bbec722032c4099d8c8bc095efccdc15688708623367e358" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -7315,15 +7070,6 @@ version = "0.6.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9edde0db4769d2dc68579893f2306b26c6ecfbe0ef499b013d731b7b9247e0b9" -[[package]] -name = "wyz" -version = "0.5.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed" -dependencies = [ - "tap", -] - [[package]] name = "xattr" version = "1.6.1" @@ -7368,7 +7114,7 @@ checksum = "b659052874eb698efe5b9e8cf382204678a0086ebf46982b79d6ca3182927e5d" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", "synstructure", ] @@ -7410,7 +7156,7 @@ dependencies = [ "proc-macro-crate", "proc-macro2", "quote", - "syn 2.0.108", + "syn", "zbus_names", "zvariant", "zvariant_utils", @@ -7445,7 +7191,7 @@ checksum = "88d2b8d9c68ad2b9e4340d7832716a4d21a22a1154777ad56ea55c51a9cf3831" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -7465,7 +7211,7 @@ checksum = "d71e5d6e06ab090c67b5e44993ec16b72dcbaabc526db883a360057678b48502" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", "synstructure", ] @@ -7505,7 +7251,7 @@ checksum = "eadce39539ca5cb3985590102671f2567e659fca9666581ad3411d59207951f3" dependencies = [ "proc-macro2", "quote", - "syn 2.0.108", + "syn", ] [[package]] @@ -7594,7 +7340,7 @@ dependencies = [ "proc-macro-crate", "proc-macro2", "quote", - "syn 2.0.108", + "syn", "zvariant_utils", ] @@ -7607,6 +7353,6 @@ dependencies = [ "proc-macro2", "quote", "serde", - "syn 2.0.108", + "syn", "winnow", ] diff --git a/ensembl/Cargo.toml b/ensembl/Cargo.toml index e98ef37..3435cac 100644 --- a/ensembl/Cargo.toml +++ b/ensembl/Cargo.toml @@ -16,4 +16,3 @@ url = { version = "2", features = ["serde"] } [dev-dependencies] env_logger = "0.11" -tokio = { version = "1", features = ["macros", "rt-multi-thread"] } diff --git a/genomes1000/Cargo.toml b/genomes1000/Cargo.toml index 38bd3b6..eabfb28 100755 --- a/genomes1000/Cargo.toml +++ b/genomes1000/Cargo.toml @@ -10,7 +10,6 @@ utile = { path = "../utile" } csv = "1" either = "1" -flate2 = "1" jiff = { version = "0.2", features = ["serde"] } log = "0.4" noodles = { version = "0.98", features = ["core", "fasta", "vcf"] } @@ -19,8 +18,6 @@ serde = { version = "1", features = ["derive"] } url = { version = "2", features = ["serde"] } [dev-dependencies] -pgs_catalog = { path = "../pgs_catalog" } - env_logger = "0.11" tokio = { version = "1", features = ["macros", "rt-multi-thread"] } futures = "0.3" diff --git a/hail/Cargo.toml b/hail/Cargo.toml index af83df1..8b87402 100644 --- a/hail/Cargo.toml +++ b/hail/Cargo.toml @@ -8,7 +8,6 @@ biocore = { path = "../biocore" } resource = { path = "../resource" } utile = { path = "../utile" } -either = "1" log = "0.4" noodles = { version = "0.98", features = ["core", "fasta", "vcf"] } phf = { version = "0.11", features = ["macros"] } @@ -16,8 +15,4 @@ serde = { version = "1", features = ["derive"] } url = { version = "2", features = ["serde"] } [dev-dependencies] -pgs_catalog = { path = "../pgs_catalog" } - env_logger = "0.11" -tokio = { version = "1", features = ["macros", "rt-multi-thread"] } -futures = "0.3" diff --git a/liftover/src/sources.rs b/liftover/src/sources.rs index bb88f97..4d38e73 100755 --- a/liftover/src/sources.rs +++ b/liftover/src/sources.rs @@ -124,7 +124,7 @@ impl UcscResource { pub fn url(&self) -> Url { let key = &self.key; - Url::parse(&format!("https://hgdownload2.cse.ucsc.edu/{key}")).unwrap() + Url::parse(&format!("https://hgdownload2.soe.ucsc.edu/{key}")).unwrap() } fn url_resource(&self) -> UrlResource { diff --git a/pan_ukbb/Cargo.toml b/pan_ukbb/Cargo.toml index a97fcaf..78f4ac1 100755 --- a/pan_ukbb/Cargo.toml +++ b/pan_ukbb/Cargo.toml @@ -10,19 +10,14 @@ categories = ["science"] [dependencies] biocore = { path = "../biocore" } hail = { path = "../hail" } -ids = { path = "../ids" } resource = { path = "../resource" } utile = { path = "../utile" } csv = "1" -flate2 = "1" -log = "0.4" ordered-float = { version = "5", features = ["serde"] } -rust_decimal = "1" serde = { version = "1", features = ["derive"] } serde_json = "1" url = "2" [dev-dependencies] tokio = { version = "1", features = ["full"] } -tokio-test = "0.4" diff --git a/primeedit/Cargo.toml b/primeedit/Cargo.toml index 7d2d3fe..5e0b95e 100644 --- a/primeedit/Cargo.toml +++ b/primeedit/Cargo.toml @@ -14,4 +14,3 @@ serde = { version = "1", features = ["derive"] } [dev-dependencies] proptest = "1.9" -rand = { version = "0.9", features = ["small_rng"] } diff --git a/resource/Cargo.toml b/resource/Cargo.toml index 883a529..ef218ad 100644 --- a/resource/Cargo.toml +++ b/resource/Cargo.toml @@ -6,7 +6,6 @@ edition = "2024" [dependencies] utile = { path = "../utile" } -ahash = "0.8" async-compression = { version = "0.4", default-features = false, features = [ "tokio", "gzip", @@ -19,33 +18,18 @@ flate2 = "1" futures = "0.3" indicatif = { version = "0.17", features = ["tokio"] } log = "0.4" -nohash-hasher = "0.2" pin-project = "1" -plotly = "0.12" -rand = "0.9" -regex = "1" reqwest = { version = "0.12", features = ["blocking", "stream"] } -rmp-serde = "1.3.0" serde = { version = "1", features = ["derive"] } serde_json = "1" -serde_with = "3" tempfile = "3" -thiserror = "2" tokio = { version = "1", features = ["io-util"] } tokio-util = { version = "0.7", features = ["io", "compat"] } -tracing = "0.1" url = { version = "2", features = ["serde"] } -web-time = "1.1.0" [target.'cfg(not(target_arch = "wasm32"))'.dependencies] suppaftp = { version = "6", features = ["async"] } tokio = { version = "1", features = ["fs", "process"] } -[target.'cfg(target_arch = "wasm32")'.dependencies] -gloo-timers = { version = "0.3.0", features = ["futures"] } -wasm-bindgen-futures = "0.4" -getrandom = { version = "0.3", features = ["wasm_js"] } -_getrandom = { version = "0.2", features = ["js"], package = "getrandom" } - [dev-dependencies] tokio = { version = "1", features = ["macros"] } diff --git a/utile/Cargo.toml b/utile/Cargo.toml index 935330e..232a913 100755 --- a/utile/Cargo.toml +++ b/utile/Cargo.toml @@ -10,7 +10,6 @@ nightly = [] [dependencies] ahash = "0.8" -bytes = "1" content_disposition = "0.4" futures = "0.3" log = "0.4" @@ -26,8 +25,6 @@ serde_json = "1" serde_with = "3" thiserror = "2" tokio = { version = "1", features = ["io-util"] } -tokio-util = { version = "0.7", features = ["io", "compat"] } -tracing = "0.1" url = { version = "2", features = ["serde"] } web-time = "1.1.0"