diff --git a/.github/workflows/build-test-rust-fakeminimap2.yaml b/.github/workflows/build-test-rust-fakeminimap2.yaml index 4be92f0..1a25e41 100644 --- a/.github/workflows/build-test-rust-fakeminimap2.yaml +++ b/.github/workflows/build-test-rust-fakeminimap2.yaml @@ -1,4 +1,4 @@ -name: Rust +name: fakeminimap2 on: pull_request: diff --git a/.github/workflows/build-test-rust-minimap2-sys.yml b/.github/workflows/build-test-rust-minimap2-sys.yml index c93114f..212dcec 100644 --- a/.github/workflows/build-test-rust-minimap2-sys.yml +++ b/.github/workflows/build-test-rust-minimap2-sys.yml @@ -1,4 +1,4 @@ -name: Rust +name: minimap2-sys on: pull_request: diff --git a/.github/workflows/build-test-rust-minimap2.yaml b/.github/workflows/build-test-rust-minimap2.yaml index 6ecdae2..1a4cf14 100644 --- a/.github/workflows/build-test-rust-minimap2.yaml +++ b/.github/workflows/build-test-rust-minimap2.yaml @@ -1,4 +1,4 @@ -name: Rust +name: minimap2-rs on: pull_request: diff --git a/.github/workflows/build-test-rust-minimappers2.yaml b/.github/workflows/build-test-rust-minimappers2.yaml index 9ac4d58..adc931b 100644 --- a/.github/workflows/build-test-rust-minimappers2.yaml +++ b/.github/workflows/build-test-rust-minimappers2.yaml @@ -1,4 +1,4 @@ -name: Rust +name: minimappers2 on: pull_request: @@ -34,7 +34,7 @@ jobs: env: RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma with: - rust-toolchain: nightly-2023-01-19 - maturin-version: '0.14.10' + rust-toolchain: nightly-2023-10-15 + maturin-version: '1.4.0' command: build args: -m minimappers2/Cargo.toml diff --git a/Cargo.toml b/Cargo.toml index 5035b35..54828bc 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -22,13 +22,12 @@ exclude = [ [workspace] -members = [ - "fakeminimap2", - "minimap2-sys" -] +members = [] exclude = [ - "minimappers2" + "minimappers2", + "fakeminimap2", + "minimap2-sys" ] [dependencies] @@ -38,8 +37,8 @@ flate2 = { version = "1.0.27", default-features = false } fffx = { version = "0.1.3", optional = true } # Dep for development -minimap2-sys = { path = "./minimap2-sys" } -#minimap2-sys = "0.1.16" +#minimap2-sys = { path = "./minimap2-sys" } +minimap2-sys = "0.1.16" rust-htslib = { version = "0.44.1", optional = true } # [profile.release] diff --git a/fakeminimap2/Cargo.lock b/fakeminimap2/Cargo.lock index 83ef6a2..9acda96 100644 --- a/fakeminimap2/Cargo.lock +++ b/fakeminimap2/Cargo.lock @@ -23,17 +23,6 @@ dependencies = [ "libc", ] -[[package]] -name = "atty" -version = "0.2.14" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8" -dependencies = [ - "hermit-abi 0.1.19", - "libc", - "winapi", -] - [[package]] name = "autocfg" version = "1.1.0" @@ -42,9 +31,9 @@ checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" [[package]] name = "bitflags" -version = "2.3.3" +version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "630be753d4e58660abd17930c71b647fe46c27ea6b63cc59e1e3851406972e42" +checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" [[package]] name = "buffer-redux" @@ -58,15 +47,15 @@ dependencies = [ [[package]] name = "bumpalo" -version = "3.13.0" +version = "3.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1" +checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec" [[package]] name = "bytecount" -version = "0.6.3" +version = "0.6.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c" +checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205" [[package]] name = "bytelines" @@ -97,9 +86,12 @@ dependencies = [ [[package]] name = "cc" -version = "1.0.79" +version = "1.0.83" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f" +checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0" +dependencies = [ + "libc", +] [[package]] name = "cfg-if" @@ -109,23 +101,23 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "chrono" -version = "0.4.26" +version = "0.4.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ec837a71355b28f6556dbd569b37b3f363091c0bd4b2e735674521b4c5fd9bc5" +checksum = "7f2c685bad3eb3d45a01354cedb7d5faa66194d1d58ba6e267a8de788f79db38" dependencies = [ "android-tzdata", "iana-time-zone", "num-traits", - "winapi", + "windows-targets 0.48.5", ] [[package]] name = "colored" -version = "1.9.3" +version = "1.9.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f4ffc801dacf156c5854b9df4f425a626539c3a6ef7893cc0c5084a23f0b6c59" +checksum = "5a5f741c91823341bebf717d4c71bda820630ce065443b58bd1b7451af008355" dependencies = [ - "atty", + "is-terminal", "lazy_static", "winapi", ] @@ -138,14 +130,14 @@ checksum = "2674ec482fbc38012cf31e6c42ba0177b431a0cb6f15fe40efa5aab1bda516f6" dependencies = [ "is-terminal", "lazy_static", - "windows-sys", + "windows-sys 0.48.0", ] [[package]] name = "core-foundation-sys" -version = "0.8.4" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa" +checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f" [[package]] name = "crc32fast" @@ -172,9 +164,9 @@ dependencies = [ [[package]] name = "crossbeam-channel" -version = "0.5.6" +version = "0.5.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c2dd04ddaf88237dc3b8d8f9a3c1004b506b54b3313403944054d23c0870c521" +checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200" dependencies = [ "cfg-if", "crossbeam-utils", @@ -182,9 +174,9 @@ dependencies = [ [[package]] name = "crossbeam-deque" -version = "0.8.2" +version = "0.8.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "715e8152b692bba2d374b53d4875445368fdf21a94751410af607a5ac677d1fc" +checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef" dependencies = [ "cfg-if", "crossbeam-epoch", @@ -193,9 +185,9 @@ dependencies = [ [[package]] name = "crossbeam-epoch" -version = "0.9.11" +version = "0.9.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f916dfc5d356b0ed9dae65f1db9fc9770aa2851d2662b988ccf4fe3516e86348" +checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7" dependencies = [ "autocfg", "cfg-if", @@ -206,9 +198,9 @@ dependencies = [ [[package]] name = "crossbeam-queue" -version = "0.3.6" +version = "0.3.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1cd42583b04998a5363558e5f9291ee5a5ff6b49944332103f251e7479a82aa7" +checksum = "d1cfb3ea8a53f37c40dea2c7bedcbd88bdfae54f5e2175d6ecaff1c988353add" dependencies = [ "cfg-if", "crossbeam-utils", @@ -216,32 +208,21 @@ dependencies = [ [[package]] name = "crossbeam-utils" -version = "0.8.12" +version = "0.8.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "edbafec5fa1f196ca66527c1b12c2ec4745ca14b50f1ad8f9f6f720b55d11fac" +checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294" dependencies = [ "cfg-if", ] [[package]] name = "errno" -version = "0.3.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a" -dependencies = [ - "errno-dragonfly", - "libc", - "windows-sys", -] - -[[package]] -name = "errno-dragonfly" -version = "0.1.2" +version = "0.3.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" +checksum = "a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245" dependencies = [ - "cc", "libc", + "windows-sys 0.52.0", ] [[package]] @@ -264,7 +245,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d9f0c14694cbd524c8720dd69b0e3179344f04ebb5f90f2e4a440c6ea3b2f1ee" dependencies = [ "chrono", - "colored 1.9.3", + "colored 1.9.4", "log", ] @@ -282,9 +263,9 @@ dependencies = [ [[package]] name = "flate2" -version = "1.0.25" +version = "1.0.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a8a2db397cb1c8772f31494cb8917e48cd1e64f0fa7efac59fbd741a0a8ce841" +checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e" dependencies = [ "crc32fast", "libz-sys", @@ -293,18 +274,9 @@ dependencies = [ [[package]] name = "hermit-abi" -version = "0.1.19" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33" -dependencies = [ - "libc", -] - -[[package]] -name = "hermit-abi" -version = "0.3.2" +version = "0.3.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b" +checksum = "d77f7ec81a6d05a3abb01ab6eb7590f6083d08449fe5a1c8b1e620283546ccb7" [[package]] name = "humantime" @@ -314,16 +286,16 @@ checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" [[package]] name = "iana-time-zone" -version = "0.1.57" +version = "0.1.58" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fad5b825842d2b38bd206f3e81d6957625fd7f0a361e345c30e01a0ae2dd613" +checksum = "8326b86b6cff230b97d0d312a6c40a60726df3332e721f72a1b035f451663b20" dependencies = [ "android_system_properties", "core-foundation-sys", "iana-time-zone-haiku", "js-sys", "wasm-bindgen", - "windows", + "windows-core", ] [[package]] @@ -341,16 +313,16 @@ version = "0.4.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b" dependencies = [ - "hermit-abi 0.3.2", + "hermit-abi", "rustix", - "windows-sys", + "windows-sys 0.48.0", ] [[package]] name = "js-sys" -version = "0.3.64" +version = "0.3.66" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a" +checksum = "cee9c64da59eae3b50095c18d3e74f8b73c0b86d2792824ff01bbce68ba229ca" dependencies = [ "wasm-bindgen", ] @@ -363,15 +335,15 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" [[package]] name = "libc" -version = "0.2.147" +version = "0.2.150" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3" +checksum = "89d92a4743f9a61002fae18374ed11e7973f530cb3a3255fb354818118b2203c" [[package]] name = "libz-sys" -version = "1.1.9" +version = "1.1.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "56ee889ecc9568871456d42f603d6a0ce59ff328d291063a45cbdf0036baf6db" +checksum = "d97137b25e321a73eef1418d1d5d2eda4d77e12813f8e6dead84bc52c5870a7b" dependencies = [ "cc", "libc", @@ -381,15 +353,15 @@ dependencies = [ [[package]] name = "linux-raw-sys" -version = "0.4.3" +version = "0.4.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "09fc20d2ca12cb9f044c93e3bd6d32d523e6e2ec3db4f7b2939cd99026ecd3f0" +checksum = "c4cd1a83af159aa67994778be9070f0ae1bd732942279cabb14f86f986a21456" [[package]] name = "log" -version = "0.4.19" +version = "0.4.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4" +checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f" [[package]] name = "lzma-sys" @@ -404,23 +376,24 @@ dependencies = [ [[package]] name = "memchr" -version = "2.5.0" +version = "2.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d" +checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167" [[package]] name = "memoffset" -version = "0.6.5" +version = "0.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce" +checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c" dependencies = [ "autocfg", ] [[package]] name = "minimap2" -version = "0.1.14+minimap2.2.26" -source = "git+https://github.com/jguhlin/minimap2-rs?branch=static#a0952eee7a0147a59bd5ea796912432617b8080d" +version = "0.1.16+minimap2.2.26" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a6cb7c4c240401901de9c5bdfbebbcd8a43a2beb980a00c3b7c558d922ec089" dependencies = [ "fffx", "flate2", @@ -431,20 +404,20 @@ dependencies = [ [[package]] name = "minimap2-sys" -version = "0.1.14+minimap2.2.26" -source = "git+https://github.com/jguhlin/minimap2-rs?branch=static#a0952eee7a0147a59bd5ea796912432617b8080d" +version = "0.1.16+minimap2.2.26" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b3116fd091e0b499cd370475c6d03f8c333aa956b1769140dfd07e1a42101c8a" dependencies = [ "cc", - "libc", "libz-sys", "pkg-config", ] [[package]] name = "miniz_oxide" -version = "0.6.2" +version = "0.7.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b275950c28b37e794e8c55d88aeb5e139d0ce23fdbbeda68f8d7174abdf9e8fa" +checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7" dependencies = [ "adler", ] @@ -465,54 +438,54 @@ dependencies = [ [[package]] name = "num-traits" -version = "0.2.15" +version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd" +checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c" dependencies = [ "autocfg", ] [[package]] name = "once_cell" -version = "1.15.0" +version = "1.18.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e82dad04139b71a90c080c8463fe0dc7902db5192d939bd0950f074d014339e1" +checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d" [[package]] name = "pkg-config" -version = "0.3.26" +version = "0.3.27" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6ac9a59f73473f1b8d852421e59e64809f025994837ef743615c6d0c5b305160" +checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964" [[package]] name = "proc-macro2" -version = "1.0.63" +version = "1.0.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7b368fba921b0dce7e60f5e04ec15e565b3303972b42bcfde1d0713b881959eb" +checksum = "39278fbbf5fb4f646ce651690877f89d1c5811a3d4acb27700c1cb3cdb78fd3b" dependencies = [ "unicode-ident", ] [[package]] name = "quote" -version = "1.0.29" +version = "1.0.33" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "573015e8ab27661678357f27dc26460738fd2b6c86e46f386fde94cb5d913105" +checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae" dependencies = [ "proc-macro2", ] [[package]] name = "rustix" -version = "0.38.3" +version = "0.38.26" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ac5ffa1efe7548069688cd7028f32591853cd7b5b756d41bcffd2353e4fc75b4" +checksum = "9470c4bf8246c8daf25f9598dca807fb6510347b1e1cfa55749113850c79d88a" dependencies = [ "bitflags", "errno", "libc", "linux-raw-sys", - "windows-sys", + "windows-sys 0.52.0", ] [[package]] @@ -523,9 +496,9 @@ checksum = "ef703b7cb59335eae2eb93ceb664c0eb7ea6bf567079d843e09420219668e072" [[package]] name = "scopeguard" -version = "1.1.0" +version = "1.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd" +checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49" [[package]] name = "simdutf8" @@ -541,9 +514,9 @@ checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" [[package]] name = "syn" -version = "2.0.23" +version = "2.0.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "59fb7d6d8281a51045d62b8eb3a7d1ce347b76f312af50cd3dc0af39c87c1737" +checksum = "23e78b90f2fcf45d3e842032ce32e3f2d1545ba6636271dcbf24fa306d87be7a" dependencies = [ "proc-macro2", "quote", @@ -552,9 +525,9 @@ dependencies = [ [[package]] name = "unicode-ident" -version = "1.0.4" +version = "1.0.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dcc811dc4066ac62f84f11307873c4850cb653bfa9b1719cee2bd2204a4bc5dd" +checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" [[package]] name = "vcpkg" @@ -564,9 +537,9 @@ checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426" [[package]] name = "wasm-bindgen" -version = "0.2.87" +version = "0.2.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342" +checksum = "0ed0d4f68a3015cc185aff4db9506a015f4b96f95303897bfa23f846db54064e" dependencies = [ "cfg-if", "wasm-bindgen-macro", @@ -574,9 +547,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-backend" -version = "0.2.87" +version = "0.2.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd" +checksum = 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+[[package]] +name = "windows_x86_64_msvc" +version = "0.52.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a" +checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04" [[package]] name = "xz2" diff --git a/fakeminimap2/Cargo.toml b/fakeminimap2/Cargo.toml index 4b38028..9bec08d 100644 --- a/fakeminimap2/Cargo.toml +++ b/fakeminimap2/Cargo.toml @@ -6,14 +6,13 @@ edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -minimap2 = { path = ".."} -# minimap2 = { git = "https://github.com/jguhlin/minimap2-rs", branch = "static", features = ["static"] } +minimap2 = "0.1.16+minimap2.2.26" crossbeam = "0.8.2" needletail = "0.5.1" fern = { version = "0.6.2", features = ["colored", "chrono"] } humantime = "2.1.0" -log = "0.4.17" -colored = { version = "2.0.0", features = ["no-color"] } +log = "0.4.20" +colored = { version = "2.0.4", features = ["no-color"] } [profile.release] opt-level = 3 diff --git a/minimap2-sys/Cargo.toml b/minimap2-sys/Cargo.toml index 832879e..11d7536 100644 --- a/minimap2-sys/Cargo.toml +++ b/minimap2-sys/Cargo.toml @@ -40,7 +40,7 @@ pkg-config = "0.3.27" [build-dependencies.bindgen] optional = true -version = "0.68.1" +version = "0.69.1" default-features = false features = ["which-rustfmt", "runtime"] diff --git a/minimappers2/Cargo.lock b/minimappers2/Cargo.lock index 39ffcf8..5c40b0d 100644 --- a/minimappers2/Cargo.lock +++ b/minimappers2/Cargo.lock @@ -2,15 +2,6 @@ # It is not intended for manual editing. version = 3 -[[package]] -name = "addr2line" -version = "0.21.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb" -dependencies = [ - "gimli", -] - [[package]] name = "adler" version = "1.0.2" @@ -19,14 +10,15 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.3" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" +checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" dependencies = [ "cfg-if", "getrandom", "once_cell", "version_check", + "zerocopy", ] [[package]] @@ -84,46 +76,6 @@ dependencies = [ "serde", ] -[[package]] -name = "arrow2" -version = "0.17.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "59c468daea140b747d781a1da9f7db5f0a8e6636d4af20cc539e43d05b0604fa" -dependencies = [ - "ahash", - "arrow-format", - "bytemuck", - "chrono", - "dyn-clone", - "either", - "ethnum", - "foreign_vec", - "futures", - "getrandom", - "hash_hasher", - "lexical-core", - "lz4", - "multiversion", - "num-traits", - "regex", - "regex-syntax 0.6.29", - "rustc_version", - "simdutf8", - "strength_reduce", - "zstd", -] - -[[package]] -name = "async-trait" -version = "0.1.73" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bc00ceb34980c03614e35a3a4e218276a0a824e911d07651cd0d858a51e8c0f0" -dependencies = [ - "proc-macro2", - "quote", - "syn 2.0.29", -] - [[package]] name = "atoi" version = "2.0.0" @@ -134,25 +86,16 @@ dependencies = [ ] [[package]] -name = "autocfg" -version = "1.1.0" +name = "atoi_simd" +version = "0.15.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" +checksum = "ccfc14f5c3e34de57539a7ba9c18ecde3d9bbde48d232ea1da3e468adb307fd0" [[package]] -name = "backtrace" -version = "0.3.69" +name = "autocfg" +version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2089b7e3f35b9dd2d0ed921ead4f6d318c27680d4a5bd167b3ee120edb105837" -dependencies = [ - "addr2line", - "cc", - "cfg-if", - "libc", - "miniz_oxide", - "object", - "rustc-demangle", -] +checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" [[package]] name = "bitflags" @@ -195,7 +138,7 @@ checksum = "fdde5c9cd29ebd706ce1b35600920a33550e402fc998a2e53ad3b42c3c47a192" dependencies = [ "proc-macro2", "quote", - "syn 2.0.29", + "syn 2.0.39", ] [[package]] @@ -222,14 +165,14 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "chrono" -version = "0.4.26" +version = "0.4.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ec837a71355b28f6556dbd569b37b3f363091c0bd4b2e735674521b4c5fd9bc5" +checksum = "7f2c685bad3eb3d45a01354cedb7d5faa66194d1d58ba6e267a8de788f79db38" dependencies = [ "android-tzdata", "iana-time-zone", "num-traits", - "winapi", + "windows-targets", ] [[package]] @@ -372,7 +315,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.29", + "syn 2.0.39", ] [[package]] @@ -422,95 +365,6 @@ version = 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= "1e186cfbae8084e513daff4240b4797e342f988cecda4fb6c939150f96315fd8" [[package]] name = "itoa" @@ -637,79 +473,6 @@ dependencies = [ "wasm-bindgen", ] -[[package]] -name = "lexical" -version = "6.1.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c7aefb36fd43fef7003334742cbf77b243fcd36418a1d1bdd480d613a67968f6" -dependencies = [ - "lexical-core", -] - -[[package]] -name = "lexical-core" -version = "0.8.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2cde5de06e8d4c2faabc400238f9ae1c74d5412d03a7bd067645ccbc47070e46" -dependencies = [ - "lexical-parse-float", - "lexical-parse-integer", - "lexical-util", - "lexical-write-float", - "lexical-write-integer", -] - -[[package]] -name = "lexical-parse-float" -version = "0.8.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "683b3a5ebd0130b8fb52ba0bdc718cc56815b6a097e28ae5a6997d0ad17dc05f" -dependencies = [ - "lexical-parse-integer", - 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[[package]] name = "mimalloc" -version = "0.1.37" +version = "0.1.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4e2894987a3459f3ffb755608bd82188f8ed00d0ae077f1edea29c068d639d98" +checksum = "fa01922b5ea280a911e323e4d2fd24b7fe5cc4042e0d2cda3c40775cdc4bdc9c" dependencies = [ "libmimalloc-sys", ] @@ -921,25 +684,6 @@ dependencies = [ "libm", ] -[[package]] -name = "num_cpus" -version = "1.16.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43" -dependencies = [ - "hermit-abi", - "libc", -] - -[[package]] -name = "object" -version = "0.32.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77ac5bbd07aea88c60a577a1ce218075ffd59208b2d7ca97adf9bfc5aeb21ebe" -dependencies = [ - "memchr", -] - [[package]] name = "once_cell" version = "1.18.0" @@ -970,16 +714,10 @@ dependencies = [ ] [[package]] -name = "pin-project-lite" -version = 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source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f967c901fa5da4ca7f64e813d1268488ba97e9b3004cefc579ff851c197a1138" +checksum = "dd503430a6d9779b07915d858865fe998317ef3cfef8973881f578ac5d4baae7" dependencies = [ - "arrow2", + "ahash", + "arrow-format", + "atoi_simd", + "bytemuck", + "chrono", + "dyn-clone", + "either", + "ethnum", + "fast-float", + "foreign_vec", + "getrandom", "hashbrown", + "itoa", + "lz4", "multiversion", "num-traits", "polars-error", - "thiserror", - "version_check", + "polars-utils", + "rustc_version", + "ryu", + "simdutf8", + "streaming-iterator", + "strength_reduce", + "zstd", ] [[package]] name = "polars-core" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b24f92fc5b167f668ff85ab9607dfa72e2c09664cacef59297ee8601dee60126" +checksum = "ae73d5b8e55decde670caba1cc82b61f14bfb9a72503198f0997d657a98dcfd6" dependencies = [ "ahash", - "arrow2", "bitflags 2.4.0", + "bytemuck", "chrono", "comfy-table", "either", @@ -1059,35 +814,34 @@ dependencies = [ [[package]] name = "polars-error" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "40d09c3a7337e53b38c37b57999038440fa39c6801b9ba48afaecd8e16f7ac0a" +checksum = "eb0520d68eaa9993ae0c741409d1526beff5b8f48e1d73e4381616f8152cf488" dependencies = [ - "arrow2", + "arrow-format", "regex", + "simdutf8", "thiserror", ] [[package]] name = "polars-io" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "92cab0df9f2a35702fa5aec99edfaabf9ae8e9cdd0acf69e143ad2d132f34f9c" +checksum = "96e10a0745acd6009db64bef0ceb9e23a70b1c27b26a0a6517c91f3e6363bc06" dependencies = [ "ahash", - "arrow2", - "async-trait", + "atoi_simd", "bytes", "chrono", "fast-float", - "futures", "home", - "lexical", - "lexical-core", + "itoa", "memchr", "memmap2", "num-traits", "once_cell", + "percent-encoding", "polars-arrow", "polars-core", "polars-error", @@ -1095,15 +849,16 @@ dependencies = [ "polars-utils", "rayon", "regex", + "ryu", "simdutf8", - "tokio", + "smartstring", ] [[package]] name = "polars-lazy" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c33762ec2a55e01c9f8776b34db86257c70a0a3b3929bd4eb91a52aacf61456" +checksum = "3555f759705be6dd0d3762d16a0b8787b2dc4da73b57465f3b2bf1a070ba8f20" dependencies = [ "ahash", "bitflags 2.4.0", @@ -1124,28 +879,36 @@ dependencies = [ [[package]] name = "polars-ops" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e825575c96302d2daedfc205a0062180033c92c55bcd6aafc4e109d4d8849ed0" +checksum = "1a7eb218296aaa7f79945f08288ca32ca3cf25fa505649eeee689ec21eebf636" dependencies = [ + "ahash", "argminmax", - "arrow2", + "bytemuck", "either", + "hashbrown", "indexmap", "memchr", + "num-traits", "polars-arrow", "polars-core", + "polars-error", "polars-utils", + "rayon", + "regex", "smartstring", "version_check", ] [[package]] name = "polars-pipe" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1f2bc9a12da9ed043fb0cb51dbcb87b365e4845b7ab6399d7a81e838460c6974" +checksum = "66094e7df64c932a9a7bdfe7df0c65efdcb192096e11a6a765a9778f78b4bdec" dependencies = [ + "crossbeam-channel", + "crossbeam-queue", "enum_dispatch", "hashbrown", "num-traits", @@ -1163,13 +926,14 @@ dependencies = [ [[package]] name = "polars-plan" -version = "0.32.1" +version = "0.35.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fb67b014f0295e8e9dbb84404a91d666d477b3bc248a2ed51bc442833b16da35" +checksum = "10e32a0958ef854b132bad7f8369cb3237254635d5e864c99505bc0bc1035fbc" dependencies = [ "ahash", - "arrow2", + "bytemuck", "once_cell", + "percent-encoding", "polars-arrow", "polars-core", "polars-io", @@ -1185,25 +949,27 @@ 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"947dc12175c254889edc0c02e399476c2f652b4b9ebd123aa655c224de259536" +checksum = "7774b5a8282bd4f25f803b1f0d945120be959a36c72e08e7cd031c792fdfd424" dependencies = [ + "heck", "proc-macro2", "quote", - "syn 1.0.109", + "syn 2.0.39", ] [[package]] name = "pyo3-polars" -version = "0.6.0" +version = "0.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6a01adbc2ca44212d81af1feb1be6d5d659f67a2941092bb5664980848de27c2" +checksum = "e37da190c68036cb620bbde9a8933839addfa4b66e9903b9b1dc751b2b00e7d7" dependencies = [ - "arrow2", "polars", "polars-core", "pyo3", @@ -1384,9 +1152,9 @@ dependencies = [ [[package]] name = "rayon" -version = "1.7.0" +version = "1.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1d2df5196e37bcc87abebc0053e20787d73847bb33134a69841207dd0a47f03b" +checksum = "9c27db03db7734835b3f53954b534c91069375ce6ccaa2e065441e07d9b6cdb1" dependencies = [ "either", "rayon-core", @@ -1394,14 +1162,12 @@ dependencies = [ [[package]] name = "rayon-core" -version = "1.11.0" +version = "1.12.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4b8f95bd6966f5c87776639160a66bd8ab9895d9d4ab01ddba9fc60661aebe8d" +checksum = "5ce3fb6ad83f861aac485e76e1985cd109d9a3713802152be56c3b1f0e0658ed" dependencies = [ - "crossbeam-channel", "crossbeam-deque", "crossbeam-utils", - "num_cpus", ] [[package]] @@ -1422,7 +1188,7 @@ dependencies = [ "aho-corasick", "memchr", "regex-automata", - "regex-syntax 0.7.4", + "regex-syntax", ] [[package]] @@ -1433,27 +1199,15 @@ checksum = "fed1ceff11a1dddaee50c9dc8e4938bd106e9d89ae372f192311e7da498e3b69" dependencies = [ "aho-corasick", "memchr", - "regex-syntax 0.7.4", + "regex-syntax", ] -[[package]] -name = "regex-syntax" -version = "0.6.29" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" - [[package]] name = "regex-syntax" version = "0.7.4" source = 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"dc59dfdcbad1437773485e0367fea4b090a2e0a16d9ffc46af47764536a298ec" +checksum = "43576ca501357b9b071ac53cdc7da8ef0cbd9493d8df094cd821777ea6e894d3" dependencies = [ "proc-macro2", "quote", - "syn 2.0.29", + "syn 2.0.39", ] [[package]] @@ -1554,15 +1308,6 @@ version = "0.1.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a" -[[package]] -name = "slab" -version = "0.4.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8f92a496fb766b417c996b9c5e57daf2f7ad3b0bebe1ccfca4856390e3d3bb67" -dependencies = [ - "autocfg", -] - [[package]] name = "smallvec" version = "1.11.0" @@ -1580,21 +1325,11 @@ dependencies = [ "version_check", ] -[[package]] -name = "socket2" -version = "0.5.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2538b18701741680e0322a2302176d3253a35388e2e62f172f64f4f16605f877" -dependencies = [ - "libc", - "windows-sys", -] - [[package]] name = "sqlparser" -version = "0.36.1" +version = "0.39.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2eaa1e88e78d2c2460d78b7dc3f0c08dbb606ab4222f9aff36f420d36e307d87" +checksum = "743b4dc2cbde11890ccb254a8fc9d537fa41b36da00de2a1c5e9848c9bc42bd7" dependencies = [ "log", ] @@ -1605,6 +1340,12 @@ version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" +[[package]] +name = "streaming-iterator" +version = "0.1.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2b2231b7c3057d5e4ad0156fb3dc807d900806020c5ffa3ee6ff2c8c76fb8520" + [[package]] name = "strength_reduce" version = "0.2.4" @@ -1640,7 +1381,7 @@ dependencies = [ "proc-macro2", "quote", "rustversion", - "syn 2.0.29", + "syn 2.0.39", ] [[package]] @@ -1656,9 +1397,9 @@ dependencies = [ [[package]] name = "syn" -version = "2.0.29" +version = "2.0.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c324c494eba9d92503e6f1ef2e6df781e78f6a7705a0202d9801b198807d518a" +checksum = "23e78b90f2fcf45d3e842032ce32e3f2d1545ba6636271dcbf24fa306d87be7a" dependencies = [ "proc-macro2", "quote", @@ -1708,21 +1449,7 @@ checksum = "6bb623b56e39ab7dcd4b1b98bb6c8f8d907ed255b18de254088016b27a8ee19b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.29", -] - -[[package]] -name = "tokio" -version = "1.32.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "17ed6077ed6cd6c74735e21f37eb16dc3935f96878b1fe961074089cc80893f9" -dependencies = [ - "backtrace", - "libc", - "mio", - "pin-project-lite", - "socket2", - "windows-sys", + "syn 2.0.39", ] [[package]] @@ -1739,9 +1466,9 @@ checksum = "c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b" [[package]] name = "unindent" -version = "0.1.11" +version = "0.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c" +checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce" [[package]] name = "vcpkg" @@ -1782,7 +1509,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.29", + "syn 2.0.39", "wasm-bindgen-shared", ] @@ -1804,7 +1531,7 @@ checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.29", + "syn 2.0.39", "wasm-bindgen-backend", "wasm-bindgen-shared", ] @@ -1918,22 +1645,41 @@ version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "735a71d46c4d68d71d4b24d03fdc2b98e38cea81730595801db779c04fe80d70" +[[package]] +name = "zerocopy" +version = "0.7.28" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7d6f15f7ade05d2a4935e34a457b936c23dc70a05cc1d97133dc99e7a3fe0f0e" +dependencies = [ + "zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.28" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dbbad221e3f78500350ecbd7dfa4e63ef945c05f4c61cb7f4d3f84cd0bba649b" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.39", +] + [[package]] name = "zstd" -version = "0.12.4" +version = "0.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c" +checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110" dependencies = [ "zstd-safe", ] [[package]] name = "zstd-safe" -version = "6.0.6" +version = "7.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ee98ffd0b48ee95e6c5168188e44a54550b1564d9d530ee21d5f0eaed1069581" +checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e" dependencies = [ - "libc", "zstd-sys", ] diff --git a/minimappers2/Cargo.toml b/minimappers2/Cargo.toml index 1874c43..0753d1e 100644 --- a/minimappers2/Cargo.toml +++ b/minimappers2/Cargo.toml @@ -8,18 +8,14 @@ name = "minimappers2" crate-type = ["cdylib", "rlib"] [dependencies] -# fffx = "0.1.2" - minimap2 = { version = "0.1.16", features = ["simde"] } minimap2-sys = { version = "0.1.16", features = ["simde"] } -#minimap2 = { path = "../", features = ["simde"] } -#minimap2-sys = { path = "../minimap2-sys", features = ["simde"] } crossbeam = "0.8.2" -mimalloc = {version = "0.1.34", default-features = false } +mimalloc = {version = "0.1.39", default-features = false } -pyo3 = { version = "0.19.2" } -polars = "0.32.1" -pyo3-polars = "0.6.0" +pyo3 = { version = "0.20.0" } +polars = "0.35.4" +pyo3-polars = "0.9.0" [profile.release] opt-level = 3 diff --git a/minimappers2/README.md b/minimappers2/README.md index 40a749d..e6e47fd 100644 --- a/minimappers2/README.md +++ b/minimappers2/README.md @@ -86,15 +86,15 @@ As this is a very-early stage library, error checking is not yet implemented. Wh ## Compatability -* Windows: Unlikely -* Linux: Likely +* Linux: Yes * Mac: Unknown +* Windows: Unlikely -* x86_64: Likely -* aarch64: Unknown +* x86_64: Yes +* aarch64: Unknown (open an issue) * neon: No (Open an issue) -* Google Colab: No, not sure why though. +* Google Colab: Yes # Performance Effort has been made to make this as performant as possible, but if you need more performance, please use minimap2 directly and import the results. @@ -112,7 +112,8 @@ and/or: # Changelog ## 0.1.4 -* Update pyo3, polars, and minimap2-rs deps +* Update pyo3, polars, minimap2-rs, and mimalloc deps + ## 0.1.1 * Update pyo3 and polars deps * Add with_seq for indexing TODO