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chore: update dependencies and adapt to updated crate APIs

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Bumps core dependencies including ndarray, rand, hashbrown, niffler, ureq, sysinfo, indicatif, lru, and remove_dir_all. Adapts source code to accommodate breaking changes by migrating RNG initialization, adjusting HTTP response handling, and replacing the fs4 crate with standard library file locking. Adds a planning document for query benchmarking and sparse index regression tests.
This commit is contained in:
Eric Coissac
2026-08-20 13:45:41 +02:00
parent 32bcbd1465
commit 5a9d903e51
15 changed files with 365 additions and 511 deletions
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src/Cargo.lock
Generated
+247 -479
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File diff suppressed because it is too large Load Diff
src/obicompactvec/Cargo.toml
+1 -1
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@@ -6,7 +6,7 @@ edition = "2024"
[dependencies]
common_traits = "0.11"
memmap2 = "0.9"
ndarray = "0.16"
ndarray = "0.17"
rayon = "1"
tempfile = "3"
src/obidebruinj/Cargo.toml
+1 -1
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@@ -7,7 +7,7 @@ edition = "2021"
obikseq = { path = "../obikseq" }
obifastwrite = { path = "../obifastwrite" }
ahash = "0.8"
hashbrown = { version = "0.14", features = ["rayon"] }
hashbrown = { version = "0.17", features = ["rayon"] }
rayon = "1"
crossbeam-channel = "0.5"
xxhash-rust = { version = "0.8.15", features = ["xxh3", "const_xxh3"] }
src/obikindex/Cargo.toml
+2 -2
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@@ -11,12 +11,12 @@ obiskio = { path = "../obiskio" }
obisys = { path = "../obisys" }
obicompactvec = { path = "../obicompactvec" }
obilayeredmap = { path = "../obilayeredmap" }
ndarray = "0.16"
ndarray = "0.17"
rayon = "1"
crossbeam-channel = "0.5"
serde = { version = "1", features = ["derive"] }
serde_json = "1"
indicatif = "0.17"
indicatif = "0.18"
tracing = "0.1.44"
hwlocality = { version = "1.0.0-alpha.11", features = ["vendored"], optional = true }
src/obikpartitionner/Cargo.toml
+3 -3
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@@ -11,7 +11,7 @@ obikrope = { path = "../obikrope" }
[dependencies]
niffler = "3.0.0"
remove_dir_all = "0.8"
remove_dir_all = "1.0"
obikseq = { path = "../obikseq" }
obikentropy = { path = "../obikentropy" }
obiskbuilder = { path = "../obiskbuilder" }
@@ -19,7 +19,7 @@ obiskio = { path = "../obiskio" }
obidebruinj = { path = "../obidebruinj" }
obilayeredmap = { path = "../obilayeredmap" }
rayon = "1"
sysinfo = "0.33"
sysinfo = "0.39"
serde = { version = "1", features = ["derive"] }
serde_json = "1"
tracing = "0.1.44"
@@ -28,6 +28,6 @@ epserde = "0.8"
memmap2 = "0.9.10"
obicompactvec = { path = "../obicompactvec" }
ptr_hash = "1.1"
indicatif = "0.17"
indicatif = "0.18"
obisys = { path = "../obisys" }
obipipeline = { path = "../obipipeline" }
src/obikphylo/Cargo.toml
+2 -2
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@@ -14,8 +14,8 @@ obilayeredmap = { path = "../obilayeredmap" }
obiskbuilder = { path = "../obiskbuilder" }
obipipeline = { path = "../obipipeline" }
memmap2 = "0.9"
ndarray = "0.16"
rand = "0.8"
ndarray = "0.17"
rand = "0.10"
rayon = "1"
tracing = "0.1.44"
src/obikphylo/src/siblings/subsample.rs
+5 -5
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@@ -22,7 +22,7 @@
use std::collections::HashSet;
use std::path::{Path, PathBuf};
use rand::Rng;
use rand::RngExt;
use rayon::prelude::*;
use obikindex::{KmerIndex, OKIError, OKIResult};
@@ -97,7 +97,7 @@ fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet
let mut reservoir: Vec<usize> = Vec::with_capacity(n_layer);
let mut seen: u64 = 0;
let mut family_idx: usize = 0;
let mut rng = rand::thread_rng();
let mut rng = rand::rng();
for slot in 0..annex.len() {
let Some(mask) = annex.get(slot) else { continue };
if !mask.is_minorant() {
@@ -111,7 +111,7 @@ fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet
if reservoir.len() < n_layer {
reservoir.push(this_family_idx);
} else {
let j = rng.gen_range(0..=seen);
let j = rng.random_range(0..=seen);
if j < n_layer as u64 {
reservoir[j as usize] = this_family_idx;
}
@@ -188,7 +188,7 @@ fn entropy_biased_sample_layer(layer_dir: &Path, p0: f64, bias: EntropyBias) ->
let entropy_annex = EntropyAnnex::open(&layer_dir.join(ENTROPY_ANNEX_FILE_NAME)).map_err(OKIError::Io)?;
let mut selected = HashSet::new();
let mut family_idx: usize = 0;
let mut rng = rand::thread_rng();
let mut rng = rand::rng();
for slot in 0..annex.len() {
let Some(mask) = annex.get(slot) else { continue };
if !mask.is_minorant() {
@@ -207,7 +207,7 @@ fn entropy_biased_sample_layer(layer_dir: &Path, p0: f64, bias: EntropyBias) ->
let Some(entropy) = entropy_annex.get(this_family_idx) else { continue };
let d = (entropy as f64 - bias.mu) / bias.sigma;
let w = (-0.5 * d * d).exp();
if rng.r#gen::<f64>() < p0 * w {
if rng.random::<f64>() < p0 * w {
selected.insert(this_family_idx);
}
}
src/obilayeredmap/Cargo.toml
+1 -1
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@@ -11,7 +11,7 @@ ptr_hash = "1.1"
cacheline-ef = "1.1"
epserde = "0.8"
rayon = "1"
ndarray = "0.16"
ndarray = "0.17"
bitvec = "1"
memmap2 = "0.9"
serde = { version = "1", features = ["derive"] }
src/obiread/Cargo.toml
+9 -5
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@@ -5,11 +5,15 @@ edition = "2024"
[dependencies]
obikrope = { path = "../obikrope" }
niffler = { version = "2", default-features = false, features = ["gz", "bz2", "lzma", "zstd"] }
bzip2-sys = { version = "0.1", features = ["static"] }
liblzma-sys = { version = "0.3", features = ["static"] }
ureq = "2"
niffler = { version = "3", default-features = false, features = ["gz", "bz2", "lzma", "zstd"] }
# `niffler`'s plain "bz2" feature only pulls the `bzip2` crate, without
# picking a backend — its own "default" feature is what forwards
# "bzip2/default" (the pure-Rust libbz2-rs-sys backend). Depend on it
# directly, default features on, purely to select that backend.
bzip2 = "0.6"
liblzma = { version = "0.4", features = ["static"] }
ureq = "3"
tracing = "0.1.44"
tracing-subscriber = { version = "0.3.23", features = ["fmt", "env-filter"] }
infer = "0.19.0"
infer = "0.22.0"
regex = "1"
src/obiread/src/xopen.rs
+1 -1
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@@ -52,7 +52,7 @@ fn http_reader(url: &str) -> io::Result<Box<dyn Read + Send>> {
ureq::get(url)
.call()
.map_err(|e| io::Error::new(io::ErrorKind::Other, e.to_string()))
.map(|resp| -> Box<dyn Read + Send> { Box::new(resp.into_reader()) })
.map(|resp| -> Box<dyn Read + Send> { Box::new(resp.into_body().into_reader()) })
}
fn decompress(raw: Box<dyn Read + Send>) -> io::Result<Box<dyn Read + Send>> {
src/obiskio/Cargo.toml
+1 -1
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@@ -6,7 +6,7 @@ edition = "2024"
[dependencies]
niffler = "3.0.0"
rustix = { version = "1.1.4", features = ["process"] }
lru = "0.12"
lru = "0.18"
serde = { version = "1", features = ["derive"] }
serde_json = "1"
src/obisys/Cargo.toml
+2 -3
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@@ -5,7 +5,6 @@ edition = "2024"
[dependencies]
libc = "0.2"
sysinfo = "0.33"
indicatif = "0.17"
sysinfo = "0.39"
indicatif = "0.18"
tracing = "0.1"
fs4 = "0.9"
src/obisys/src/lock.rs
+5 -7
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@@ -11,9 +11,9 @@ use tracing::info;
/// only needs to lock the destination.
///
/// Uses the OS's advisory file lock (`flock` on Unix, `LockFileEx` on
/// Windows) via `fs4`, not a hand-rolled PID file: the OS releases it
/// automatically on process exit, including a crash — no stale-lock cleanup
/// logic needed.
/// Windows) via `std::fs::File::lock`/`try_lock`, not a hand-rolled PID
/// file: the OS releases it automatically on process exit, including a
/// crash — no stale-lock cleanup logic needed.
pub struct DirLock {
_file: std::fs::File,
}
@@ -23,8 +23,6 @@ impl DirLock {
/// and the lock file within it if needed). Logs once if the wait is
/// non-trivial, so a blocked command doesn't look silently hung.
pub fn acquire(dir: &std::path::Path) -> std::io::Result<Self> {
use fs4::fs_std::FileExt;
std::fs::create_dir_all(dir)?;
let lock_path = dir.join(".obikmer.lock");
let file = std::fs::OpenOptions::new()
@@ -33,9 +31,9 @@ impl DirLock {
.write(true)
.open(&lock_path)?;
if file.try_lock_exclusive().is_err() {
if file.try_lock().is_err() {
info!(dir = %dir.display(), "waiting for another obikmer process to release this index");
file.lock_exclusive()?;
file.lock()?;
}
Ok(Self { _file: file })
}