chore: update dependencies and adapt to updated crate APIs

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.

src/obikphylo/Cargo.toml

@@ -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

@@ -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);
         }
     }