From a96b81bd9d417909a6fd9464ce77e6249c5ab067 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 1 Nov 2024 13:42:34 -0700 Subject: [PATCH] benchmarks now kinda working --- Cargo.lock | 215 +++++++++++++++++++++++++++++++++++++++++++++++++++++ Cargo.toml | 22 +++++- Makefile | 5 +- src/lib.rs | 4 +- 4 files changed, 241 insertions(+), 5 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 0f0e425..e94c2dd 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -38,6 +38,12 @@ dependencies = [ "libc", ] +[[package]] +name = "anes" +version = "0.1.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299" + [[package]] name = "anstream" version = "0.6.15" @@ -193,6 +199,12 @@ dependencies = [ "serde", ] +[[package]] +name = "cast" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5" + [[package]] name = "cc" version = "1.1.15" @@ -224,6 +236,58 @@ dependencies = [ "windows-targets", ] +[[package]] +name = "ciborium" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e" +dependencies = [ + "ciborium-io", + "ciborium-ll", + "serde", +] + +[[package]] +name = "ciborium-io" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757" + +[[package]] +name = "ciborium-ll" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9" +dependencies = [ + "ciborium-io", + "half", +] + +[[package]] +name = "clap" +version = "4.5.20" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b97f376d85a664d5837dbae44bf546e6477a679ff6610010f17276f686d867e8" +dependencies = [ + "clap_builder", +] + +[[package]] +name = "clap_builder" +version = "4.5.20" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "19bc80abd44e4bed93ca373a0704ccbd1b710dc5749406201bb018272808dc54" +dependencies = [ + "anstyle", + "clap_lex", +] + +[[package]] +name = "clap_lex" +version = "0.7.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1462739cb27611015575c0c11df5df7601141071f07518d56fcc1be504cbec97" + [[package]] name = "codepage-437" version = "0.1.0" @@ -263,6 +327,42 @@ dependencies = [ "cfg-if", ] +[[package]] +name = "criterion" +version = "0.5.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f2b12d017a929603d80db1831cd3a24082f8137ce19c69e6447f54f5fc8d692f" +dependencies = [ + "anes", + "cast", + "ciborium", + "clap", + "criterion-plot", + "is-terminal", + "itertools 0.10.5", + "num-traits", + "once_cell", + "oorandom", + "plotters", + "rayon", + "regex", + "serde", + "serde_derive", + "serde_json", + "tinytemplate", + "walkdir", +] + +[[package]] +name = "criterion-plot" +version = "0.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6b50826342786a51a89e2da3a28f1c32b06e387201bc2d19791f622c673706b1" +dependencies = [ + "cast", + "itertools 0.10.5", +] + [[package]] name = "crossbeam-deque" version = "0.8.5" @@ -288,6 +388,12 @@ version = "0.8.20" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80" +[[package]] +name = "crunchy" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7" + [[package]] name = "csv" version = "1.3.0" @@ -391,6 +497,16 @@ dependencies = [ "syn", ] +[[package]] +name = "half" +version = "2.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888" +dependencies = [ + "cfg-if", + "crunchy", +] + [[package]] name = "heck" version = "0.4.1" @@ -403,6 +519,12 @@ version = "0.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea" +[[package]] +name = "hermit-abi" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc" + [[package]] name = "histogram" version = "0.11.0" @@ -456,12 +578,32 @@ dependencies = [ "smallvec", ] +[[package]] +name = "is-terminal" +version = "0.4.13" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "261f68e344040fbd0edea105bef17c66edf46f984ddb1115b775ce31be948f4b" +dependencies = [ + "hermit-abi", + "libc", + "windows-sys", +] + [[package]] name = "is_terminal_polyfill" version = "1.70.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf" +[[package]] +name = "itertools" +version = "0.10.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473" +dependencies = [ + "either", +] + [[package]] name = "itertools" version = "0.12.1" @@ -719,6 +861,12 @@ version = "1.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92" +[[package]] +name = "oorandom" +version = "11.1.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b410bbe7e14ab526a0e86877eb47c6996a2bd7746f027ba551028c925390e4e9" + [[package]] name = "ouroboros" version = "0.18.4" @@ -749,6 +897,7 @@ name = "oxli" version = "0.3.0" dependencies = [ "anyhow", + "criterion", "env_logger", "log", "niffler", @@ -787,6 +936,34 @@ version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec" +[[package]] +name = "plotters" +version = "0.3.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5aeb6f403d7a4911efb1e33402027fc44f29b5bf6def3effcc22d7bb75f2b747" +dependencies = [ + "num-traits", + "plotters-backend", + "plotters-svg", + "wasm-bindgen", + "web-sys", +] + +[[package]] +name = "plotters-backend" +version = "0.3.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "df42e13c12958a16b3f7f4386b9ab1f3e7933914ecea48da7139435263a4172a" + +[[package]] +name = "plotters-svg" +version = "0.3.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "51bae2ac328883f7acdfea3d66a7c35751187f870bc81f94563733a154d7a670" +dependencies = [ + "plotters-backend", +] + [[package]] name = "portable-atomic" version = "1.7.0" @@ -1054,6 +1231,15 @@ dependencies = [ "bytemuck", ] +[[package]] +name = "same-file" +version = "1.0.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502" +dependencies = [ + "winapi-util", +] + [[package]] name = "serde" version = "1.0.213" @@ -1227,6 +1413,16 @@ dependencies = [ "syn", ] +[[package]] +name = "tinytemplate" +version = "1.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc" +dependencies = [ + "serde", + "serde_json", +] + [[package]] name = "twox-hash" version = "1.6.3" @@ -1303,6 +1499,16 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a" +[[package]] +name = "walkdir" +version = "2.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b" +dependencies = [ + "same-file", + "winapi-util", +] + [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" @@ -1384,6 +1590,15 @@ dependencies = [ "safe_arch", ] +[[package]] +name = "winapi-util" +version = "0.1.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb" +dependencies = [ + "windows-sys", +] + [[package]] name = "windows-core" version = "0.52.0" diff --git a/Cargo.toml b/Cargo.toml index 76260e2..f5da038 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -6,15 +6,31 @@ edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [lib] name = "oxli" -crate-type = ["cdylib"] +crate-type = ["cdylib", "rlib"] +bench = false + +[[bench]] +name = "consume" +harness = false [dependencies] anyhow = "1.0.91" +criterion = "0.5.1" env_logger = "0.11.5" log = "0.4.22" niffler = "2.6.0" -pyo3 = { version="0.22.5", features = ["extension-module", "anyhow"] } +# pyo3 = { version="0.22.5", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.213", features = ["derive"] } serde_json = "1.0.132" -sourmash = "0.16.0" \ No newline at end of file +sourmash = "0.16.0" + +[dependencies.pyo3] +version = "0.22.5" + +[features] +extension-module = ["pyo3/extension-module"] +anyhow = ["pyo3/anyhow"] + +[profile.bench] +debug = true diff --git a/Makefile b/Makefile index b339d81..82fbd93 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,10 @@ PYTHON ?= python all: - maturin develop + maturin develop --all-features + +bench: + cargo bench --features anyhow install: $(PYTHON) -m pip install -e . diff --git a/src/lib.rs b/src/lib.rs index 3b86f91..3b80bc4 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,3 +1,5 @@ +// #![feature(test)] + // Standard library imports use std::cmp::{max, Ord}; use std::collections::hash_map::IntoIter; @@ -77,7 +79,7 @@ impl Hash for HashIntoType { #[pyclass] #[derive(Serialize, Deserialize, Debug)] /// Basic KmerCountTable struct, mapping hashes to counts. -struct KmerCountTable { +pub struct KmerCountTable { counts: HashMap, pub ksize: u8, version: String,