From 1e182401f919212fbfd2fd516e1c4100c7771a20 Mon Sep 17 00:00:00 2001 From: Virgile Andreani Date: Thu, 26 Sep 2024 16:15:33 -0400 Subject: [PATCH] chore: upgrade dependencies --- Cargo.lock | 259 +++++++++++++++++++++++++++++++---------------------- Cargo.toml | 4 +- 2 files changed, 155 insertions(+), 108 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 2977c6f..8fc4843 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -19,9 +19,9 @@ checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299" [[package]] name = "anstyle" -version = "1.0.7" +version = "1.0.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b" +checksum = "1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1" [[package]] name = "autocfg" @@ -44,6 +44,12 @@ version = "3.16.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c" +[[package]] +name = "byteorder" +version = "1.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b" + [[package]] name = "cast" version = "0.3.0" @@ -52,9 +58,12 @@ checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5" [[package]] name = "cc" -version = "1.1.4" +version = "1.1.21" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9711f33475c22aab363b05564a17d7b789bf3dfec5ebabb586adee56f0e271b5" +checksum = "07b1695e2c7e8fc85310cde85aeaab7e3097f593c91d209d3f9df76c928100f0" +dependencies = [ + "shlex", +] [[package]] name = "cfg-if" @@ -91,18 +100,18 @@ dependencies = [ [[package]] name = "clap" -version = "4.5.9" +version = "4.5.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "64acc1846d54c1fe936a78dc189c34e28d3f5afc348403f28ecf53660b9b8462" +checksum = "b0956a43b323ac1afaffc053ed5c4b7c1f1800bacd1683c353aabbb752515dd3" dependencies = [ "clap_builder", ] [[package]] name = "clap_builder" -version = "4.5.9" +version = "4.5.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6fb8393d67ba2e7bfaf28a23458e4e2b543cc73a99595511eb207fdb8aede942" +checksum = "4d72166dd41634086d5803a47eb71ae740e61d84709c36f3c34110173db3961b" dependencies = [ "anstyle", "clap_lex", @@ -110,9 +119,9 @@ dependencies = [ [[package]] name = "clap_lex" -version = "0.7.1" +version = "0.7.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70" +checksum = "1462739cb27611015575c0c11df5df7601141071f07518d56fcc1be504cbec97" [[package]] name = "criterion" @@ -181,6 +190,17 @@ version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7" +[[package]] +name = "derive_more" +version = "0.99.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5f33878137e4dafd7fa914ad4e259e18a4e8e532b9617a2d0150262bf53abfce" +dependencies = [ + "proc-macro2", + "quote", + "syn", +] + [[package]] name = "either" version = "1.13.0" @@ -216,38 +236,42 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea" [[package]] name = "hermit-abi" -version = "0.3.9" +version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024" +checksum = "fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc" [[package]] name = "iai-callgrind" -version = "0.11.1" +version = "0.13.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "146bf76de95f03c5f4b118f0f2f350ef18df47cc0595755bd29d8f668209466c" +checksum = "4bd871e6374d5ca2d9b48dd23b3c7ef63a4201728621f6d75937dfcc66e91809" dependencies = [ "bincode", + "derive_more", "iai-callgrind-macros", "iai-callgrind-runner", ] [[package]] name = "iai-callgrind-macros" -version = "0.2.0" +version = "0.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e2a4bb39225592c0a28cfca6f70af52ebd8da23f533c2cdd0a3329c1fa252d56" +checksum = "397649417510422ded7033f86132f833cca8c2e5081d0dfbec939b2353da7021" dependencies = [ - "proc-macro-error", + "derive_more", + "proc-macro-error2", "proc-macro2", "quote", - "syn 2.0.71", + "serde", + "serde_json", + "syn", ] [[package]] name = "iai-callgrind-runner" -version = "0.11.1" +version = "0.13.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "60484b2e469ef4f1af6f196af738889ff375151dd11ac223647ed8a97529107d" +checksum = "f3783c337f9e931af702b5d5835ff2a6824bf55e416461a4e042dfb4b8fdbbea" dependencies = [ "serde", ] @@ -260,13 +284,13 @@ checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5" [[package]] name = "is-terminal" -version = "0.4.12" +version = "0.4.13" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b" +checksum = "261f68e344040fbd0edea105bef17c66edf46f984ddb1115b775ce31be948f4b" dependencies = [ "hermit-abi", "libc", - "windows-sys", + "windows-sys 0.52.0", ] [[package]] @@ -286,18 +310,18 @@ checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b" [[package]] name = "js-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d" +checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a" dependencies = [ "wasm-bindgen", ] [[package]] name = "libc" -version = "0.2.155" +version = "0.2.159" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c" +checksum = "561d97a539a36e26a9a5fad1ea11a3039a67714694aaa379433e580854bc3dc5" [[package]] name = "libm" @@ -350,9 +374,9 @@ checksum = "b410bbe7e14ab526a0e86877eb47c6996a2bd7746f027ba551028c925390e4e9" [[package]] name = "plotters" -version = "0.3.6" +version = "0.3.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a15b6eccb8484002195a3e44fe65a4ce8e93a625797a063735536fd59cb01cf3" +checksum = "5aeb6f403d7a4911efb1e33402027fc44f29b5bf6def3effcc22d7bb75f2b747" dependencies = [ "num-traits", "plotters-backend", @@ -363,53 +387,54 @@ dependencies = [ [[package]] name = "plotters-backend" -version = "0.3.6" +version = "0.3.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "414cec62c6634ae900ea1c56128dfe87cf63e7caece0852ec76aba307cebadb7" +checksum = "df42e13c12958a16b3f7f4386b9ab1f3e7933914ecea48da7139435263a4172a" [[package]] name = "plotters-svg" -version = "0.3.6" +version = "0.3.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "81b30686a7d9c3e010b84284bdd26a29f2138574f52f5eb6f794fc0ad924e705" +checksum = "51bae2ac328883f7acdfea3d66a7c35751187f870bc81f94563733a154d7a670" dependencies = [ "plotters-backend", ] [[package]] name = "portable-atomic" -version = "1.6.0" +version = "1.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0" +checksum = "d30538d42559de6b034bc76fd6dd4c38961b1ee5c6c56e3808c50128fdbc22ce" [[package]] name = "ppv-lite86" -version = "0.2.17" +version = "0.2.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de" +checksum = "77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04" +dependencies = [ + "zerocopy", +] [[package]] -name = "proc-macro-error" -version = "1.0.4" +name = "proc-macro-error-attr2" +version = "2.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c" +checksum = "96de42df36bb9bba5542fe9f1a054b8cc87e172759a1868aa05c1f3acc89dfc5" dependencies = [ - "proc-macro-error-attr", "proc-macro2", "quote", - "syn 1.0.109", - "version_check", ] [[package]] -name = "proc-macro-error-attr" -version = "1.0.4" +name = "proc-macro-error2" +version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869" +checksum = "11ec05c52be0a07b08061f7dd003e7d7092e0472bc731b4af7bb1ef876109802" dependencies = [ + "proc-macro-error-attr2", "proc-macro2", "quote", - "version_check", + "syn", ] [[package]] @@ -423,9 +448,9 @@ dependencies = [ [[package]] name = "pyo3" -version = "0.22.1" +version = "0.22.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4e99090d12f6182924499253aaa1e73bf15c69cea8d2774c3c781e35badc3548" +checksum = "15ee168e30649f7f234c3d49ef5a7a6cbf5134289bc46c29ff3155fa3221c225" dependencies = [ "cfg-if", "indoc", @@ -441,9 +466,9 @@ dependencies = [ [[package]] name = "pyo3-build-config" -version = "0.22.1" +version = "0.22.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7879eb018ac754bba32cb0eec7526391c02c14a093121857ed09fbf1d1057d41" +checksum = "e61cef80755fe9e46bb8a0b8f20752ca7676dcc07a5277d8b7768c6172e529b3" dependencies = [ "once_cell", "python3-dll-a", @@ -452,9 +477,9 @@ dependencies = [ [[package]] name = "pyo3-ffi" -version = "0.22.1" +version = "0.22.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ce2baa5559a411fc1cf519295f24c34b53d5d725818bc96b5abf94762da09041" +checksum = "67ce096073ec5405f5ee2b8b31f03a68e02aa10d5d4f565eca04acc41931fa1c" dependencies = [ "libc", "pyo3-build-config", @@ -462,27 +487,27 @@ dependencies = [ [[package]] name = "pyo3-macros" -version = "0.22.1" +version = "0.22.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "049621c20a23f2def20f4fe67978d1da8d8a883d64b9c21362f3b776e254edc7" +checksum = "2440c6d12bc8f3ae39f1e775266fa5122fd0c8891ce7520fa6048e683ad3de28" dependencies = [ "proc-macro2", "pyo3-macros-backend", "quote", - "syn 2.0.71", + "syn", ] [[package]] name = "pyo3-macros-backend" -version = "0.22.1" +version = "0.22.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0e969ee2e025435f1819d31a275ba4bb9cbbdf3ac535227fdbd85b9322ffe144" +checksum = "1be962f0e06da8f8465729ea2cb71a416d2257dff56cbe40a70d3e62a93ae5d1" dependencies = [ "heck", "proc-macro2", "pyo3-build-config", "quote", - "syn 2.0.71", + "syn", ] [[package]] @@ -496,9 +521,9 @@ dependencies = [ [[package]] name = "quote" -version = "1.0.36" +version = "1.0.37" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7" +checksum = "b5b9d34b8991d19d98081b46eacdd8eb58c6f2b201139f7c5f643cc155a633af" dependencies = [ "proc-macro2", ] @@ -576,9 +601,9 @@ dependencies = [ [[package]] name = "regex" -version = "1.10.5" +version = "1.10.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f" +checksum = "4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619" dependencies = [ "aho-corasick", "memchr", @@ -620,50 +645,47 @@ dependencies = [ [[package]] name = "serde" -version = "1.0.204" +version = "1.0.210" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12" +checksum = "c8e3592472072e6e22e0a54d5904d9febf8508f65fb8552499a1abc7d1078c3a" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.204" +version = "1.0.210" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222" +checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f" dependencies = [ "proc-macro2", "quote", - "syn 2.0.71", + "syn", ] [[package]] name = "serde_json" -version = "1.0.120" +version = "1.0.128" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5" +checksum = "6ff5456707a1de34e7e37f2a6fd3d3f808c318259cbd01ab6377795054b483d8" dependencies = [ "itoa", + "memchr", "ryu", "serde", ] [[package]] -name = "syn" -version = "1.0.109" +name = "shlex" +version = "1.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237" -dependencies = [ - "proc-macro2", - "unicode-ident", -] +checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64" [[package]] name = "syn" -version = "2.0.71" +version = "2.0.77" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b146dcf730474b4bcd16c311627b31ede9ab149045db4d6088b3becaea046462" +checksum = "9f35bcdf61fd8e7be6caf75f429fdca8beb3ed76584befb503b1569faee373ed" dependencies = [ "proc-macro2", "quote", @@ -672,9 +694,9 @@ dependencies = [ [[package]] name = "target-lexicon" -version = "0.12.15" +version = "0.12.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4873307b7c257eddcb50c9bedf158eb669578359fb28428bef438fec8e6ba7c2" +checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1" [[package]] name = "tinytemplate" @@ -688,9 +710,9 @@ dependencies = [ [[package]] name = "unicode-ident" -version = "1.0.12" +version = "1.0.13" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" +checksum = "e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe" [[package]] name = "unindent" @@ -698,12 +720,6 @@ version = "0.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce" -[[package]] -name = "version_check" -version = "0.9.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" - [[package]] name = "walkdir" version = "2.5.0" @@ -722,34 +738,35 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" [[package]] name = "wasm-bindgen" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8" +checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5" dependencies = [ "cfg-if", + "once_cell", "wasm-bindgen-macro", ] [[package]] name = "wasm-bindgen-backend" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da" +checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b" dependencies = [ "bumpalo", "log", "once_cell", "proc-macro2", "quote", - "syn 2.0.71", + "syn", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-macro" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726" +checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf" dependencies = [ "quote", "wasm-bindgen-macro-support", @@ -757,28 +774,28 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro-support" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7" +checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836" dependencies = [ "proc-macro2", "quote", - "syn 2.0.71", + "syn", "wasm-bindgen-backend", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-shared" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484" [[package]] name = "web-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" +checksum = "26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0" dependencies = [ "js-sys", "wasm-bindgen", @@ -786,11 +803,11 @@ dependencies = [ [[package]] name = "winapi-util" -version = "0.1.8" +version = "0.1.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b" +checksum = "cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb" dependencies = [ - "windows-sys", + "windows-sys 0.59.0", ] [[package]] @@ -802,6 +819,15 @@ dependencies = [ "windows-targets", ] +[[package]] +name = "windows-sys" +version = "0.59.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b" +dependencies = [ + "windows-targets", +] + [[package]] name = "windows-targets" version = "0.52.6" @@ -865,3 +891,24 @@ name = "windows_x86_64_msvc" version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec" + +[[package]] +name = "zerocopy" +version = "0.7.35" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0" +dependencies = [ + "byteorder", + "zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.35" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e" +dependencies = [ + "proc-macro2", + "quote", + "syn", +] diff --git a/Cargo.toml b/Cargo.toml index e26424c..9a99248 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -11,7 +11,7 @@ description = "A fast stochastic simulator for chemical reaction networks" keywords = ["gillespie-algorithm", "systems-biology", "stochastic", "scientific-computing"] [dependencies] -pyo3 = { version = "0.22.1", features = ["extension-module"] } +pyo3 = { version = "0.22.3", features = ["extension-module"] } rand = { version = "0.8.5", features = ["small_rng"] } rand_distr = "0.4.3" @@ -21,7 +21,7 @@ generate-import-lib = ["pyo3/generate-import-lib"] [dev-dependencies] criterion = "0.5.1" -iai-callgrind = "0.11.1" +iai-callgrind = "0.13.4" [lib] path = "src/lib.rs"