feat: Bump pharmsol and update examples

Cargo.toml

@@ -28,7 +28,7 @@ tracing-subscriber = { version = "0.3.19", features = [
     "time",
 ] }
 faer = "0.24.0"
-pharmsol = "=0.25"
+pharmsol = "=0.26"
 rand = "0.9.0"
 anyhow = "1.0.100"
 rayon = "1.10.0"

benches/bimodal_ke.rs

@@ -18,7 +18,6 @@ fn create_equation() -> equation::ODE {
             y[1] = x[0] / v;
         },
     )
-    .with_default_cache()
 }
 
 fn create_parameters() -> Parameters {

examples/bestdose.rs

@@ -16,8 +16,7 @@ fn main() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    }
-    .with_default_cache();
+    };
 
     let params = Parameters::new()
         .add("ke", 0.001, 3.0)

examples/bestdose_auc.rs

@@ -19,8 +19,7 @@ fn main() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    }
-    .with_default_cache();
+    };
 
     // Minimal parameter ranges
     let params = Parameters::new()

examples/bestdose_bounds.rs

@@ -19,8 +19,7 @@ fn main() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    }
-    .with_default_cache();
+    };
 
     let params = Parameters::new()
         .add("ke", 0.001, 3.0)

examples/bimodal_ke/main.rs

@@ -13,8 +13,7 @@ fn main() -> Result<()> {
             y[1] = x[0] / v;
         },
     }
-    .with_solver(OdeSolver::ExplicitRk(ExplicitRkTableau::Tsit45))
-    .with_default_cache();
+    .with_solver(OdeSolver::ExplicitRk(ExplicitRkTableau::Tsit45));
 
     let params = Parameters::new()
         .add("ke", 0.001, 3.0)

examples/drusano/main.rs

@@ -69,8 +69,7 @@ fn main() -> Result<()> {
             y[3] = x[3].log10();
             y[4] = x[4].log10();
         },
-    }
-    .with_default_cache();
+    };
 
     let params = Parameters::new()
         .add("v1", 5.0, 160.0)

examples/iov/main.rs

@@ -29,8 +29,7 @@ fn main() -> Result<()> {
     )
     .with_nstates(2)
     .with_ndrugs(1)
-    .with_nout(1)
-    .with_default_cache();
+    .with_nout(1);
 
     let params = Parameters::new().add("ke0", 0.001, 2.0);
 

examples/meta/main.rs

@@ -26,8 +26,7 @@ fn main() {
             y[1] = x[0] / v;
             y[2] = x[1] / v2;
         },
-    }
-    .with_default_cache();
+    };
 
     let params = Parameters::new()
         .add("cls", 0.1, 10.0)

examples/neely/main.rs

@@ -45,8 +45,7 @@ fn main() {
             y[2] = x[2] / vm1;
             y[3] = x[3] / vm2;
         },
-    }
-    .with_default_cache();
+    };
 
     let params = Parameters::new()
         .add("cls", 0.0, 0.4)

examples/new_iov/main.rs

@@ -29,8 +29,7 @@ fn main() {
     )
     .with_nstates(2)
     .with_ndrugs(1)
-    .with_nout(1)
-    .with_default_cache();
+    .with_nout(1);
 
     let params = Parameters::new()
         .add("ke0", 0.0001, 2.4)

examples/theophylline/main.rs

@@ -11,8 +11,7 @@ fn main() {
             fetch_params!(p, _ka, _ke, v);
             y[0] = x[1] * 1000.0 / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new()
         .add("ka", 0.001, 3.0)

examples/two_eq_lag/main.rs

@@ -20,8 +20,7 @@ fn main() {
             fetch_params!(p, _ka, _ke, _tlag, v);
             y[1] = x[1] / v;
         },
-    }
-    .with_default_cache();
+    };
     // let eq = Equation::new_analytical(
     //     one_compartment_with_absorption,
     //     |_p, _cov| {},

examples/vanco.rs

@@ -12,8 +12,7 @@ fn main() {
         out: |x, _p, _t, _cov, y| {
             y[0] = x[1];
         },
-    }
-    .with_default_cache();
+    };
     // same eq but analytical
     // let eq = Equation::new_analytical(
     //     two_compartments,

examples/vanco_sde/main.rs

@@ -27,8 +27,7 @@ fn main() {
             y[0] = x[1] / (vol * wt);
         },
         100,
-    )
-    .with_default_cache();
+    );
 
     // let ode = equation::ODE::new(
     //     |x, p, _t, dx, _rateiv, _cov| {

tests/bestdose_tests.rs

@@ -21,8 +21,7 @@ fn test_infusion_mask_inclusion() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
 
@@ -137,8 +136,7 @@ fn test_fixed_infusion_preservation() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new()
         .add("ke", 0.001, 3.0)
@@ -231,8 +229,7 @@ fn test_dose_count_validation() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
     let ems = AssayErrorModels::new().add(
@@ -302,8 +299,7 @@ fn test_empty_observations_validation() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
     let ems = AssayErrorModels::new().add(
@@ -363,8 +359,7 @@ fn test_basic_auc_mode() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
 
@@ -449,8 +444,7 @@ fn test_infusion_auc_mode() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
 
@@ -554,8 +548,7 @@ fn test_multi_outeq_auc_mode() -> Result<()> {
             y[0] = x[0] / v; // outeq 0: concentration
             y[1] = x[0]; // outeq 1: amount
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
 
@@ -625,8 +618,7 @@ fn test_multi_outeq_auc_optimization() -> Result<()> {
             y[0] = x[0] / v;
             y[1] = x[0];
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
     let error_model = AssayErrorModel::additive(ErrorPoly::new(0.0, 5.0, 0.0, 0.0), 0.0);
@@ -711,8 +703,7 @@ fn test_auc_from_zero_single_dose() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.2, 0.4).add("v", 40.0, 60.0);
 
@@ -796,8 +787,7 @@ fn test_auc_from_last_dose_maintenance() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.2, 0.4).add("v", 40.0, 60.0);
 
@@ -885,8 +875,7 @@ fn test_auc_modes_comparison() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.3, 0.3).add("v", 50.0, 50.0);
 
@@ -1015,8 +1004,7 @@ fn test_auc_from_last_dose_multiple_observations() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.2, 0.4).add("v", 40.0, 60.0);
 
@@ -1110,8 +1098,7 @@ fn test_auc_from_last_dose_no_prior_dose() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.2, 0.4).add("v", 40.0, 60.0);
 
@@ -1200,8 +1187,7 @@ fn test_dose_range_bounds_respected() -> Result<()> {
             fetch_params!(p, _ke, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     let params = Parameters::new().add("ke", 0.1, 0.5).add("v", 40.0, 60.0);
 
@@ -1295,7 +1281,6 @@ fn one_compartment_model() -> pharmsol::ODE {
             y[0] = x[0] / v;
         },
     )
-    .with_default_cache()
 }
 
 /// Helper to build minimal settings for tests (no posterior refinement)

tests/onecomp.rs

@@ -16,8 +16,7 @@ fn test_one_compartment_npag() -> Result<()> {
             fetch_params!(p, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     // Define parameters
     let params = Parameters::new().add("ke", 0.1, 1.0).add("v", 1.0, 20.0);
@@ -84,8 +83,7 @@ fn test_one_compartment_npod() -> Result<()> {
             fetch_params!(p, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     // Define parameters
     let params = Parameters::new().add("ke", 0.1, 1.0).add("v", 1.0, 20.0);
@@ -152,8 +150,7 @@ fn test_one_compartment_postprob() -> Result<()> {
             fetch_params!(p, v);
             y[0] = x[0] / v;
         },
-    )
-    .with_default_cache();
+    );
 
     // Define parameters
     let params = Parameters::new().add("ke", 0.1, 1.0).add("v", 1.0, 20.0);