merge with local changes

.gitignore

@@ -12,7 +12,13 @@ r.csv
 posterior.csv
 simulation_output.csv
 meta*.csv
+/examples/rosuva/*
+/examples/iohexol/*
+/examples/vori/*
+/examples/data/iohexol*
+/examples/data/rosuva*
+/examples/data/vori*
 /.idea
 stop
 .vscode
-*.f90
+*.f90

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "npcore"
-version = "0.1.1"
+version = "0.1.2"
 edition = "2021"
 authors = [
     "Julián D. Otálvaro <juliandavid347@gmail.com>",
@@ -28,7 +28,7 @@ ndarray-stats = "0.5.1"
 linfa-linalg = "0.1.0"
 rayon = "1.8.0"
 eyre = "0.6.8"
-ratatui = { version = "0.24.0", features = ["crossterm"] }
+ratatui = { version = "0.25.0", features = ["crossterm"] }
 crossterm = "0.27.0"
 tokio = { version = "1.32.0", features = ["sync", "rt"] }
 ndarray-csv = "0.5.2"
@@ -37,7 +37,7 @@ argmin = { version = "0.8.1", features = [] }
 itertools = "0.12.0"
 faer-core = { version = "0.15.0", features = [] }
 # faer-lu = "0.9"
-faer-qr = "0.15.0"
+faer-qr = "0.16.0"
 # faer-cholesky = "0.9"
 # faer-svd = "0.9"
 argmin-math = { version = "0.3.0", features = ["ndarray_v0_15-nolinalg-serde"] }
@@ -47,6 +47,12 @@ tracing = "0.1.40"
 tracing-subscriber = { version = "0.3.17", features = ["env-filter", "fmt", "time"] }
 chrono = "0.4"
 
+[dev-dependencies]
+criterion = "0.5"
+
+[[bench]]
+name = "benchmarks" 
+harness = false
 
 [profile.release]
 codegen-units = 1

README.md

@@ -1,6 +1,7 @@
 # NPcore
 [![Build](https://github.com/LAPKB/NPcore/actions/workflows/rust.yml/badge.svg)](https://github.com/LAPKB/NPcore/actions/workflows/rust.yml)
 [![Security Audit](https://github.com/LAPKB/NPcore/actions/workflows/security_audit.yml/badge.svg)](https://github.com/LAPKB/NPcore/actions/workflows/security_audit.yml)
+![crates.io](https://img.shields.io/crates/v/npcore.svg)
 
 Rust library with the building blocks to create and implement new non-parametric algorithms and their integration with [Pmetrics](https://github.com/LAPKB/Pmetrics).
 

benches/benchmarks.rs

@@ -0,0 +1,23 @@
+use criterion::{black_box, criterion_group, criterion_main, Criterion};
+
+/// Benchmark the Sobol initialization routine using 1000 points in 10 dimensions
+fn benchmark_sobol(c: &mut Criterion) {
+    c.bench_function("sobol", |b| {
+        b.iter(|| {
+            let _ = npcore::routines::initialization::sobol::generate(
+                black_box(1000),
+                black_box(&vec![(0.0, 1.0); 10]),
+                black_box(22),
+            );
+        });
+    });
+}
+
+criterion_group! {
+    name = benches;
+    config = Criterion::default()
+        .measurement_time(std::time::Duration::from_secs(10)) // Measure for 10 seconds
+        .noise_threshold(0.10); // Performance changes less than 10% will be ignored
+    targets = benchmark_sobol
+}
+criterion_main!(benches);

examples/bimodal_ke/config.toml

@@ -6,13 +6,13 @@ log_out = "log/bimodal_ke.log"
 [config]
 cycles = 1024
 engine = "NPAG"
-init_points = 2129
+init_points = 10000
 seed = 347
-tui = true
+tui = false
 pmetrics_outputs = true
 cache = true
 idelta = 0.1
-log_level = "info"
+log_level = "debug"
 
 [random]
 Ke = [0.001, 3.0]

examples/bimodal_ke/main.rs

@@ -63,8 +63,10 @@ impl<'a> Predict<'a> for Ode {
             scenario.reorder_with_lag(vec![(0.0, 1)]),
         )
     }
-    fn get_output(&self, _time: f64, x: &Self::State, system: &Self::Model, outeq: usize) -> f64 {
+    fn get_output(&self, time: f64, x: &Self::State, system: &Self::Model, outeq: usize) -> f64 {
         let v = system.get_param("v");
+        #[allow(unused_variables)]
+        let t = time;
         match outeq {
             1 => x[0] / v,
             _ => panic!("Invalid output equation"),