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feat: Rework trait definitions #277

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1246a51
Expanding the documentation for the macro-based entrypoints and the O…
Siel Jun 17, 2026
bf66058
rework traits
Siel Jun 17, 2026
d85f347
fmt
Siel Jun 17, 2026
356cf2f
Trying to fix compilation on Ubuntu
Siel Jun 18, 2026
a225aa8
answering copilot's comments
Siel Jun 18, 2026
c46ce7d
force SDEs to use the standard loop
Siel Jun 18, 2026
74493d5
fix benchmarks
Siel Jun 18, 2026
7a94f67
Merge branch 'main' into feature/traits_rework
Siel Jun 18, 2026
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14 changes: 6 additions & 8 deletions benches/common/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,15 @@
#![allow(dead_code)]

use ndarray::Array2;
use pharmsol::metadata::{self, ModelMetadata};
use pharmsol::prelude::*;
use pharmsol::simulator::equation::analytical::{
use pharmsol::simulator::backends::analytical::{
one_compartment_with_absorption, two_compartments,
};
use pharmsol::{
equation::{self, Route},
Analytical, ResidualErrorModel, ResidualErrorModels, ODE, SDE,
};
use pharmsol::{backends::Route, Analytical, ResidualErrorModel, ResidualErrorModels, ODE, SDE};

/// `ModelMetadata` for handwritten factories so route/output labels resolve like the macro/DSL paths.
fn model_metadata(workload: Workload, kind: SolverKind) -> equation::ModelMetadata {
fn model_metadata(workload: Workload, kind: SolverKind) -> ModelMetadata {
let name = match (workload, kind) {
(Workload::Short, SolverKind::Ode) => "bench_one_cpt_po_ode",
(Workload::Short, SolverKind::Analytical) => "bench_one_cpt_po_analytical",
Expand All @@ -37,7 +35,7 @@ fn model_metadata(workload: Workload, kind: SolverKind) -> equation::ModelMetada
SolverKind::Sde => &["ka", "ke", "v", "sigma_ke"],
_ => &["ka", "ke", "v"],
};
equation::metadata::new(name)
metadata::new(name)
.parameters(params.iter().copied())
.states(["depot", "central"])
.outputs(["plasma"])
Expand All @@ -52,7 +50,7 @@ fn model_metadata(workload: Workload, kind: SolverKind) -> equation::ModelMetada
SolverKind::Sde => &["ke", "kcp", "kpc", "v", "sigma_ke"],
_ => &["ke", "kcp", "kpc", "v"],
};
equation::metadata::new(name)
metadata::new(name)
.parameters(params.iter().copied())
.states(["central", "peripheral"])
.outputs(["plasma"])
Expand Down
14 changes: 7 additions & 7 deletions benches/dsl_matrix.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ use pharmsol::dsl::{
NativeAotCompileOptions, NativeOdeModel, NativeSdeModel, RuntimeCompilationTarget,
};
use pharmsol::prelude::*;
use pharmsol::{Cache, Parameters};
use pharmsol::Parameters;

mod common;
use common::{
Expand Down Expand Up @@ -245,7 +245,7 @@ fn predictions_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_ode(workload, backend, &aot),
CacheState::Cold => {
compile_ode(workload, backend, &aot).disable_cache()
compile_ode(workload, backend, &aot).without_cache()
}
};
let theta = ode_parameters(&model, workload);
Expand All @@ -266,7 +266,7 @@ fn predictions_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_analytical(workload, backend, &aot),
CacheState::Cold => {
compile_analytical(workload, backend, &aot).disable_cache()
compile_analytical(workload, backend, &aot).without_cache()
}
};
let theta = analytical_parameters(&model, workload);
Expand All @@ -287,7 +287,7 @@ fn predictions_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_sde(workload, backend, &aot),
CacheState::Cold => {
compile_sde(workload, backend, &aot).disable_cache()
compile_sde(workload, backend, &aot).without_cache()
}
};
let theta = sde_parameters(&model, workload);
Expand Down Expand Up @@ -339,7 +339,7 @@ fn log_likelihood_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_ode(workload, backend, &aot),
CacheState::Cold => {
compile_ode(workload, backend, &aot).disable_cache()
compile_ode(workload, backend, &aot).without_cache()
}
};
let theta = ode_parameters(&model, workload);
Expand All @@ -361,7 +361,7 @@ fn log_likelihood_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_analytical(workload, backend, &aot),
CacheState::Cold => {
compile_analytical(workload, backend, &aot).disable_cache()
compile_analytical(workload, backend, &aot).without_cache()
}
};
let theta = analytical_parameters(&model, workload);
Expand All @@ -383,7 +383,7 @@ fn log_likelihood_group(c: &mut Criterion) {
let model = match cache {
CacheState::Hot => compile_sde(workload, backend, &aot),
CacheState::Cold => {
compile_sde(workload, backend, &aot).disable_cache()
compile_sde(workload, backend, &aot).without_cache()
}
};
let theta = sde_parameters(&model, workload);
Expand Down
26 changes: 13 additions & 13 deletions benches/native_matrix.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ use std::time::Duration;

use criterion::{criterion_group, criterion_main, BenchmarkId, Criterion, SamplingMode};
use pharmsol::prelude::*;
use pharmsol::{Analytical, Cache, Parameters, ODE, SDE};
use pharmsol::{Analytical, Parameters, ODE, SDE};

mod common;
use common::{
Expand Down Expand Up @@ -113,7 +113,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Ode, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_ode(workload).disable_cache();
let model = handwritten_ode(workload).without_cache();
let theta = ode_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -141,7 +141,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Ode, Authoring::Macro, CacheState::Cold) => {
let model = macro_ode(workload).disable_cache();
let model = macro_ode(workload).without_cache();
let theta = ode_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -169,7 +169,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Analytical, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_analytical(workload).disable_cache();
let model = handwritten_analytical(workload).without_cache();
let theta = analytical_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -197,7 +197,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Analytical, Authoring::Macro, CacheState::Cold) => {
let model = macro_analytical(workload).disable_cache();
let model = macro_analytical(workload).without_cache();
let theta = analytical_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -225,7 +225,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Sde, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_sde(workload).disable_cache();
let model = handwritten_sde(workload).without_cache();
let theta = sde_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -253,7 +253,7 @@ fn predictions_group(c: &mut Criterion) {
});
}
(SolverKind::Sde, Authoring::Macro, CacheState::Cold) => {
let model = macro_sde(workload).disable_cache();
let model = macro_sde(workload).without_cache();
let theta = sde_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -304,7 +304,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Ode, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_ode(workload).disable_cache();
let model = handwritten_ode(workload).without_cache();
let theta = ode_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -334,7 +334,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Ode, Authoring::Macro, CacheState::Cold) => {
let model = macro_ode(workload).disable_cache();
let model = macro_ode(workload).without_cache();
let theta = ode_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -364,7 +364,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Analytical, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_analytical(workload).disable_cache();
let model = handwritten_analytical(workload).without_cache();
let theta = analytical_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -394,7 +394,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Analytical, Authoring::Macro, CacheState::Cold) => {
let model = macro_analytical(workload).disable_cache();
let model = macro_analytical(workload).without_cache();
let theta = analytical_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -424,7 +424,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Sde, Authoring::Handwritten, CacheState::Cold) => {
let model = handwritten_sde(workload).disable_cache();
let model = handwritten_sde(workload).without_cache();
let theta = sde_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down Expand Up @@ -454,7 +454,7 @@ fn log_likelihood_group(c: &mut Criterion) {
});
}
(SolverKind::Sde, Authoring::Macro, CacheState::Cold) => {
let model = macro_sde(workload).disable_cache();
let model = macro_sde(workload).without_cache();
let theta = sde_parameters(&model, workload);
b.iter(|| {
black_box(
Expand Down
4 changes: 2 additions & 2 deletions examples/compare_solvers.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ use pharmsol::{prelude::*, Parameters};
// between runs; the declaration-first `ode!` surface and the generated
// metadata stay the same.

fn two_cpt(solver: OdeSolver) -> equation::ODE {
fn two_cpt(solver: OdeSolver) -> backends::ODE {
ode! {
name: "two_cpt",
params: [ke, kcp, kpc, v],
Expand Down Expand Up @@ -74,7 +74,7 @@ fn main() {
)
.expect("valid named parameters");

let results: Vec<(&str, equation::ODE)> = vec![
let results: Vec<(&str, backends::ODE)> = vec![
("Bdf", bdf),
("Sdirk(TrBdf2)", trbdf2),
("Sdirk(Esdirk34)", esdirk34),
Expand Down
10 changes: 5 additions & 5 deletions examples/macro_vs_handwritten_one_cpt.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

use pharmsol::{prelude::*, Parameters};

fn macro_model() -> equation::ODE {
fn macro_model() -> backends::ODE {
ode! {
name: "one_cpt_macro_parity",
params: [ke, v],
Expand All @@ -24,8 +24,8 @@ fn macro_model() -> equation::ODE {
}
}

fn handwritten_model() -> equation::ODE {
equation::ODE::new(
fn handwritten_model() -> backends::ODE {
backends::ODE::new(
|x, p, _t, dx, _bolus, rateiv, _cov| {
fetch_params!(p, ke, _v);
dx[0] = rateiv[0] - ke * x[0];
Expand All @@ -42,12 +42,12 @@ fn handwritten_model() -> equation::ODE {
.with_ndrugs(1)
.with_nout(1)
.with_metadata(
equation::metadata::new("one_cpt_macro_parity")
pharmsol::metadata::new("one_cpt_macro_parity")
.parameters(["ke", "v"])
.states(["central"])
.outputs(["cp"])
.route(
equation::Route::infusion("iv")
backends::Route::infusion("iv")
.to_state("central")
.inject_input_to_destination(),
),
Expand Down
12 changes: 6 additions & 6 deletions examples/macro_vs_handwritten_two_cpt.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

use pharmsol::{prelude::*, Parameters};

fn macro_model() -> equation::ODE {
fn macro_model() -> backends::ODE {
ode! {
name: "two_cpt_shared_input_parity",
params: [ke, kcp, kpc, v],
Expand All @@ -27,8 +27,8 @@ fn macro_model() -> equation::ODE {
}
}

fn handwritten_model() -> equation::ODE {
equation::ODE::new(
fn handwritten_model() -> backends::ODE {
backends::ODE::new(
|x, p, _t, dx, bolus, rateiv, _cov| {
fetch_params!(p, ke, kcp, kpc, _v);
dx[0] = -ke * x[0] - kcp * x[0] + kpc * x[1] + rateiv[0] + bolus[0];
Expand All @@ -46,15 +46,15 @@ fn handwritten_model() -> equation::ODE {
.with_ndrugs(1)
.with_nout(1)
.with_metadata(
equation::metadata::new("two_cpt_shared_input_parity")
pharmsol::metadata::new("two_cpt_shared_input_parity")
.parameters(["ke", "kcp", "kpc", "v"])
.states(["central", "peripheral"])
.outputs(["cp"])
.routes([
equation::Route::bolus("load")
backends::Route::bolus("load")
.to_state("central")
.inject_input_to_destination(),
equation::Route::infusion("iv")
backends::Route::infusion("iv")
.to_state("central")
.inject_input_to_destination(),
]),
Expand Down
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