From b88ce145be3362c76801e1c2a1d61b3d9f9389f7 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 16 Oct 2023 13:21:44 +0200 Subject: [PATCH] chore(deps): various dependencies updated --- Cargo.lock | 145 +++++++++++++++++++++++++++++++++++------------------ Cargo.toml | 16 +++--- 2 files changed, 105 insertions(+), 56 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index eed493f7..e2cfc952 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -31,7 +31,7 @@ dependencies = [ "actix-utils", "ahash", "base64", - "bitflags 2.4.0", + "bitflags 2.4.1", "brotli", "bytes", "bytestring", @@ -55,7 +55,7 @@ dependencies = [ "tokio", "tokio-util", "tracing", - "zstd", + "zstd 0.12.4", ] [[package]] @@ -255,9 +255,9 @@ dependencies = [ [[package]] name = "annonars" -version = "0.21.1" +version = "0.23.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3499307cbe9d068afeb1a3edfe415d410f6ed9290f0947f75feef1c137e6199f" +checksum = "17a6e189155aa6d3488e373db9625fc80733ec50cda565e6ed4b160a337760c8" dependencies = [ "actix-web", "anyhow", @@ -276,7 +276,7 @@ dependencies = [ "indicatif", "log", "noodles-bed", - "noodles-bgzf", + "noodles-bgzf 0.25.0", "noodles-core", "noodles-csi", "noodles-tabix", @@ -360,9 +360,9 @@ dependencies = [ [[package]] name = "async-trait" -version = "0.1.73" +version = "0.1.74" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bc00ceb34980c03614e35a3a4e218276a0a824e911d07651cd0d858a51e8c0f0" +checksum = "a66537f1bb974b254c98ed142ff995236e81b9d0fe4db0575f46612cb15eb0f9" dependencies = [ "proc-macro2", "quote", @@ -511,9 +511,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "bitflags" -version = "2.4.0" +version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635" +checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" [[package]] name = "block-buffer" @@ -899,10 +899,11 @@ dependencies = [ [[package]] name = "deranged" -version = "0.3.8" +version = "0.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f2696e8a945f658fd14dc3b87242e6b80cd0f36ff04ea560fa39082368847946" +checksum = "0f32d04922c60427da6f9fef14d042d9edddef64cb9d4ce0d64d0685fbeb1fd3" dependencies = [ + "powerfmt", "serde", ] @@ -1763,10 +1764,10 @@ dependencies = [ "lazy_static", "log", "nom", - "noodles-bgzf", + "noodles-bgzf 0.25.0", "noodles-core", "noodles-csi", - "noodles-fasta", + "noodles-fasta 0.30.0", "noodles-tabix", "noodles-vcf", "parse-display", @@ -1791,7 +1792,7 @@ dependencies = [ "tracing", "tracing-subscriber", "uuid", - "zstd", + "zstd 0.13.0", ] [[package]] @@ -1933,6 +1934,18 @@ dependencies = [ "flate2", ] +[[package]] +name = "noodles-bgzf" +version = "0.25.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7d578e5a173cbfac77295db4188c959966ce24a3364e009d363170d1ed44066a" +dependencies = [ + "byteorder", + "bytes", + "crossbeam-channel", + "flate2", +] + [[package]] name = "noodles-core" version = "0.12.0" @@ -1941,14 +1954,14 @@ checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a" [[package]] name = "noodles-csi" -version = "0.24.0" +version = "0.25.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1b2bb780250c88bc9ea69b56c1aa9df75decc6b79035f3f5ab10c0cd84d24fc6" +checksum = "f327250086b20edade50756b6aee1851d656a3a5967cf94cbe4d4e10a5ef85d7" dependencies = [ "bit-vec", "byteorder", "indexmap 2.0.2", - "noodles-bgzf", + "noodles-bgzf 0.25.0", "noodles-core", ] @@ -1960,32 +1973,44 @@ checksum = "1012431f881aad1912f9650a8d33e7f7493c6202bc2e889949ec1bc26a55f26d" dependencies = [ "bytes", "memchr", - "noodles-bgzf", + "noodles-bgzf 0.24.0", + "noodles-core", +] + +[[package]] +name = "noodles-fasta" +version = "0.30.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "310dcfb61e8e2cafb65d9da4b329a98a390f2b570c17599a7f4639328cfb3e2c" +dependencies = [ + "bytes", + "memchr", + "noodles-bgzf 0.25.0", "noodles-core", ] [[package]] name = "noodles-tabix" -version = "0.29.0" +version = "0.30.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "056e394ddb4c64bcc9806551a69833294062159600aa8ecf7167a922512bda4f" +checksum = "f69786c5eaa25460ae5ea61215f8869edd7eb1728c043f314420cea0bbe59ed3" dependencies = [ "bit-vec", "byteorder", - "noodles-bgzf", + "noodles-bgzf 0.25.0", "noodles-core", "noodles-csi", ] [[package]] name = "noodles-vcf" -version = "0.40.0" +version = "0.41.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dcd62cddca514dd04a13d3f4bf4ff83b5c7bca63c8e6b9ae0de2186ea6517a48" +checksum = "a0c31d3f5fd3bef22fcca702e2a85ab93f1c076a9e34cb94bc0c21874d2f4e02" dependencies = [ "indexmap 2.0.2", "memchr", - "noodles-bgzf", + "noodles-bgzf 0.25.0", "noodles-core", "noodles-csi", "noodles-tabix", @@ -2241,6 +2266,12 @@ dependencies = [ "postgres-protocol", ] +[[package]] +name = "powerfmt" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391" + [[package]] name = "ppv-lite86" version = "0.2.17" @@ -2504,25 +2535,25 @@ dependencies = [ [[package]] name = "regex" -version = "1.10.0" +version = "1.10.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d119d7c7ca818f8a53c300863d4f87566aac09943aef5b355bb83969dae75d87" +checksum = "aaac441002f822bc9705a681810a4dd2963094b9ca0ddc41cb963a4c189189ea" dependencies = [ "aho-corasick", "memchr", "regex-automata", - "regex-syntax 0.8.1", + "regex-syntax 0.8.2", ] [[package]] name = "regex-automata" -version = "0.4.1" +version = "0.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "465c6fc0621e4abc4187a2bda0937bfd4f722c2730b29562e19689ea796c9a4b" +checksum = "5011c7e263a695dc8ca064cddb722af1be54e517a280b12a5356f98366899e5d" dependencies = [ "aho-corasick", "memchr", - "regex-syntax 0.8.1", + "regex-syntax 0.8.2", ] [[package]] @@ -2533,9 +2564,9 @@ checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da" [[package]] name = "regex-syntax" -version = "0.8.1" +version = "0.8.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "56d84fdd47036b038fc80dd333d10b6aab10d5d31f4a366e20014def75328d33" +checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" [[package]] name = "relative-path" @@ -2608,7 +2639,7 @@ version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "549b9d036d571d42e6e85d1c1425e2ac83491075078ca9a15be021c56b1641f2" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "fallible-iterator", "fallible-streaming-iterator", "hashlink", @@ -2666,7 +2697,7 @@ version = "0.38.19" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "745ecfa778e66b2b63c88a61cb36e0eea109e803b0b86bf9879fbc77c70e86ed" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "errno", "libc", "linux-raw-sys 0.4.10", @@ -2719,9 +2750,9 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "94b3579efbd2915e936798fb9f52629feec3cbeef1ef23eb556d49d89ff31455" dependencies = [ "chrono", - "noodles-bgzf", + "noodles-bgzf 0.24.0", "noodles-core", - "noodles-fasta", + "noodles-fasta 0.29.0", "rusqlite", "thiserror", "tracing", @@ -2960,9 +2991,9 @@ dependencies = [ [[package]] name = "strum_macros" -version = "0.25.2" +version = "0.25.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ad8d03b598d3d0fff69bf533ee3ef19b8eeb342729596df84bcc7e1f96ec4059" +checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0" dependencies = [ "heck", "proc-macro2", @@ -3075,12 +3106,13 @@ dependencies = [ [[package]] name = "time" -version = "0.3.29" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "426f806f4089c493dcac0d24c29c01e2c38baf8e30f1b716ee37e83d200b18fe" +checksum = "c4a34ab300f2dee6e562c10a046fc05e358b29f9bf92277f30c3c8d82275f6f5" dependencies = [ "deranged", "itoa", + "powerfmt", "serde", "time-core", "time-macros", @@ -3175,11 +3207,10 @@ dependencies = [ [[package]] name = "tracing" -version = "0.1.37" +version = "0.1.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8ce8c33a8d48bd45d624a6e523445fd21ec13d3653cd51f681abf67418f54eb8" +checksum = "ee2ef2af84856a50c1d430afce2fdded0a4ec7eda868db86409b4543df0797f9" dependencies = [ - "cfg-if", "log", "pin-project-lite", "tracing-attributes", @@ -3188,9 +3219,9 @@ dependencies = [ [[package]] name = "tracing-attributes" -version = "0.1.26" +version = "0.1.27" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5f4f31f56159e98206da9efd823404b79b6ef3143b4a7ab76e67b1751b25a4ab" +checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7" dependencies = [ "proc-macro2", "quote", @@ -3199,9 +3230,9 @@ dependencies = [ [[package]] name = "tracing-core" -version = "0.1.31" +version = "0.1.32" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0955b8137a1df6f1a2e9a37d8a6656291ff0297c1a97c24e0d8425fe2312f79a" +checksum = "c06d3da6113f116aaee68e4d601191614c9053067f9ab7f6edbcb161237daa54" dependencies = [ "once_cell", "valuable", @@ -3627,7 +3658,16 @@ version = "0.12.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c" dependencies = [ - "zstd-safe", + "zstd-safe 6.0.6", +] + +[[package]] +name = "zstd" +version = "0.13.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110" +dependencies = [ + "zstd-safe 7.0.0", ] [[package]] @@ -3640,6 +3680,15 @@ dependencies = [ "zstd-sys", ] +[[package]] +name = "zstd-safe" +version = "7.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e" +dependencies = [ + "zstd-sys", +] + [[package]] name = "zstd-sys" version = "2.0.9+zstd.1.5.5" diff --git a/Cargo.toml b/Cargo.toml index 232e341d..1e017c68 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -27,7 +27,7 @@ path = "src/main.rs" [dependencies] actix-web = "4.4" -annonars = "0.21" +annonars = "0.23" anyhow = "1.0" bgzip = "0.3" bio = "1.3" @@ -47,12 +47,12 @@ jsonl = "4.0" lazy_static = "1.4" log = "0.4" nom = "7.1" -noodles-bgzf = "0.24" +noodles-bgzf = "0.25" noodles-core = "0.12" -noodles-csi = "0.24" -noodles-fasta = "0.29" -noodles-tabix = "0.29" -noodles-vcf = "0.40" +noodles-csi = "0.25" +noodles-fasta = "0.30" +noodles-tabix = "0.30" +noodles-vcf = "0.41" parse-display = "0.8" procfs = "0.15" prost = "0.12" @@ -64,14 +64,14 @@ rustc-hash = "1.1" seqrepo = "0.8" serde_json = "1.0" serde = { version = "1.0", features = ["derive"] } -serde_with = "3.3" +serde_with = { version = "3.3", features = ["indexmap_2"] } strum = { version = "0.25", features = ["derive"] } tempdir = "0.3" thousands = "0.2" tracing-subscriber = "0.3" tracing = { version = "0.1", features = ["log"] } uuid = { version = "1.4", features = ["fast-rng", "serde"] } -zstd = "0.12" +zstd = "0.13" [build-dependencies] prost-build = "0.12"