Update rand to 0.9, which changes what a seed means

webgestalt_lib/Cargo.toml

@@ -13,7 +13,7 @@ repository = "https://github.com/bzhanglab/webgestalt_rust"
 [dependencies]
 csv = "1.3.0"
 serde = { version = "1.0.190", features = ["std", "derive"] }
-rand = { version = "0.8.5", features = ["small_rng"] }
+rand = { version = "0.9.3", features = ["small_rng"] }
 rayon = "1.8.0"
 statrs = "0.16.0"
 ahash = "0.8.6"

webgestalt_lib/src/methods/gsea.rs

@@ -421,9 +421,17 @@ pub fn gsea(
 /// ```
 pub fn make_permutations(permutations: i32, max: usize, seed: Option<u64>) -> Vec<Vec<usize>> {
     let mut temp_permutations: Vec<Vec<usize>> = Vec::new();
+    // `from_os_rng` is rand 0.9's name for what was `from_entropy`.
+    //
+    // Note that 0.9 changed what a seed *means*: it reimplemented
+    // `SmallRng::seed_from_u64` and replaced the `shuffle` algorithm, both listed under
+    // "Reproducibility-breaking changes". A given seed therefore produces different
+    // permutations here than it did under 0.8, and so different p-values. Verified rather
+    // than assumed — seed 42 gives [16, 2, 5, 14, …] under 0.8 and [16, 17, 19, 6, …] here.
+    // Seeds are comparable within a version of this crate, not across versions.
     let mut smallrng = match seed {
         Some(s) => rand::rngs::SmallRng::seed_from_u64(s),
-        None => rand::rngs::SmallRng::from_entropy(),
+        None => rand::rngs::SmallRng::from_os_rng(),
     };
     (0..permutations).for_each(|_i| {
         // get random permutations that are shared for all analyte sets