deps: update rand to v0.9 and rand_distr to v0.5

Armavica · Jan 29, 2025 · 1af8025 · 1af8025
1 parent 4926deb
commit 1af8025
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Showing 5 changed files with 65 additions and 25 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -12,8 +12,8 @@ keywords = ["gillespie-algorithm", "systems-biology", "stochastic", "scientific-
 
 [dependencies]
 pyo3 = { version = "0.23.3", features = ["extension-module"] }
-rand = { version = "0.8.5", features = ["small_rng"] }
-rand_distr = "0.4.3"
+rand = "0.9.0"
+rand_distr = "0.5.0"
 winnow = "0.6.24"
 
 [features]

diff --git a/src/gillespie.rs b/src/gillespie.rs
@@ -150,7 +150,7 @@ impl Gillespie {
             species: species.as_ref().to_vec(),
             t: 0.,
             reactions: Vec::new(),
-            rng: SmallRng::from_entropy(),
+            rng: SmallRng::from_os_rng(),
             sparse,
         }
     }
@@ -251,7 +251,7 @@ impl Gillespie {
             return;
         }
         self.t += self.rng.sample::<f64, _>(Exp1) / total_rate;
-        let chosen_rate = total_rate * self.rng.gen::<f64>();
+        let chosen_rate = total_rate * self.rng.random::<f64>();
 
         // let ireaction = choose_rate_sum(chosen_rate, &rates);
         // let ireaction = choose_rate_for(chosen_rate, &rates);
@@ -297,7 +297,7 @@ impl Gillespie {
                 self.t = tmax;
                 return;
             }
-            let chosen_rate = total_rate * self.rng.gen::<f64>();
+            let chosen_rate = total_rate * self.rng.random::<f64>();
 
             //let ireaction = choose_rate_sum(chosen_rate, &rates);
             //let ireaction = choose_rate_for(chosen_rate, &rates);

diff --git a/src/gillespie_macro.rs b/src/gillespie_macro.rs
@@ -73,7 +73,7 @@ macro_rules! define_system {
                     $($species: 0,)*
                     $($param: f64::NAN,)*
                     t: 0.,
-                    rng: $crate::rand::rngs::SmallRng::from_entropy()
+                    rng: $crate::rand::rngs::SmallRng::from_os_rng()
                 }
             }
             /// Seeds the random number generator.
@@ -90,7 +90,7 @@ macro_rules! define_system {
                     $($species: 0,)*
                     $($param,)*
                     t: 0.,
-                    rng: $crate::rand::rngs::SmallRng::from_entropy()
+                    rng: $crate::rand::rngs::SmallRng::from_os_rng()
                 }
             }
             /// Simulates the problem until `t = tmax`.
@@ -113,7 +113,7 @@ macro_rules! define_system {
                         self.t = tmax;
                         return
                     }
-                    let reaction_choice = total_rate * self.rng.gen::<f64>();
+                    let reaction_choice = total_rate * self.rng.random::<f64>();
                     $crate::_choice!(self reaction_choice 0.;
                         $($rname:
                             $($($nr)? $r)? $(+ $($tnr)? $tr)* =>

diff --git a/tests/test_rebop.py b/tests/test_rebop.py
@@ -32,8 +32,8 @@ def test_fixed_seed() -> None:
     ds = sir.run({"S": 999, "I": 1}, tmax=250, nb_steps=250, rng=42)
 
     assert ds.S[-1] == 0
-    assert ds.I[-1] == 182
-    assert ds.R[-1] == 818
+    assert ds.I[-1] == 227
+    assert ds.R[-1] == 773
 
 
 @pytest.mark.parametrize("seed", range(10))