cleaning up the API a bit

benches/compare.rs

@@ -1,7 +1,6 @@
 use pmcore::prelude::{
     data::read_pmetrics, models::one_compartment_with_absorption, simulator::Equation, *,
 };
-use std::path::Path;
 
 // type V = nalgebra::DVector<f64>;
 // type V = nalgebra::SVector<f64, 3>;
@@ -51,7 +50,7 @@ fn main() -> std::io::Result<()> {
 //     });
 // }
 pub fn analytical_ns(bencher: Bencher, len: usize) {
-    let data = read_pmetrics(Path::new(PATH)).unwrap();
+    let data = read_pmetrics(PATH).unwrap();
     let subjects = data.get_subjects();
     let first_subject = subjects.first().unwrap();
 
@@ -79,7 +78,7 @@ pub fn analytical_ns(bencher: Bencher, len: usize) {
 }
 
 pub fn diffsol_ns(bencher: Bencher, len: usize) {
-    let data = read_pmetrics(Path::new(PATH)).unwrap();
+    let data = read_pmetrics(PATH).unwrap();
     let subjects = data.get_subjects();
     let first_subject = subjects.first().unwrap();
 

examples/bimodal_ke/main.rs

@@ -1,6 +1,3 @@
-use std::path::Path;
-
-use data::read_pmetrics;
 use pmcore::prelude::{models::one_compartment, simulator::Equation, *};
 
 fn main() {
@@ -39,7 +36,7 @@ fn main() {
         _ => panic!("Method not found"),
     };
 
-    let settings = read_settings("examples/bimodal_ke/config.toml".to_string()).unwrap();
-    let data = read_pmetrics(Path::new("examples/bimodal_ke/bimodal_ke.csv")).unwrap();
+    let settings = settings::read("examples/bimodal_ke/config.toml").unwrap();
+    let data = data::read_pmetrics("examples/bimodal_ke/bimodal_ke.csv").unwrap();
     let _result = fit(eq, data, settings);
 }

examples/meta/main.rs

@@ -3,7 +3,6 @@
 #![allow(unused_imports)]
 use std::path::Path;
 
-use data::read_pmetrics;
 use pmcore::prelude::{models::one_compartment, simulator::Equation, *};
 
 fn main() {
@@ -33,7 +32,7 @@ fn main() {
         },
         (2, 2),
     );
-    let settings = read_settings("examples/meta/config.toml".to_string()).unwrap();
-    let data = read_pmetrics(Path::new("examples/meta/meta.csv")).unwrap();
+    let settings = settings::read("examples/meta/config.toml").unwrap();
+    let data = data::read_pmetrics("examples/meta/meta.csv").unwrap();
     let _result = fit(eq, data, settings);
 }

examples/theophylline/main.rs

@@ -1,6 +1,3 @@
-use std::path::Path;
-
-use data::read_pmetrics;
 use pmcore::prelude::{models::one_compartment_with_absorption, simulator::Equation, *};
 
 fn main() {
@@ -32,7 +29,7 @@ fn main() {
         },
         (2, 1),
     );
-    let settings = read_settings("examples/theophylline/config.toml".to_string()).unwrap();
-    let data = read_pmetrics(Path::new("examples/theophylline/theophylline.csv")).unwrap();
+    let settings = settings::read("examples/theophylline/config.toml").unwrap();
+    let data = data::read_pmetrics("examples/theophylline/theophylline.csv").unwrap();
     let _result = fit(eq, data, settings);
 }

examples/tmp.rs

@@ -17,7 +17,7 @@ fn main() {
         (1, 1),
     );
 
-    let data = read_pmetrics(std::path::Path::new("examples/bimodal_ke/bimodal_ke.csv")).unwrap();
+    let data = read_pmetrics("examples/bimodal_ke/bimodal_ke.csv").unwrap();
     let theta = data.estimate_theta(&eq, &array![1.5, 125.0]);
     dbg!(theta);
 }

examples/toml.rs

@@ -1,10 +1,9 @@
 use pmcore::prelude::*;
-use settings::read_settings;
 
 fn main() {
     let path = "examples/bimodal_ke/config.toml".to_string();
     for i in 0..10 {
-        let s = read_settings(path.clone()).unwrap();
+        let s = settings::read(path.clone()).unwrap();
         let keys: Vec<&String> = s.random.parameters.keys().collect();
         // let values = s.random.parameters.values();
         println!("{}: {:?}", i, keys);

examples/two_eq_lag/main.rs

@@ -42,7 +42,7 @@ fn main() {
     //     (2, 1),
     // );
 
-    let settings = read_settings("examples/two_eq_lag/config.toml".to_string()).unwrap();
-    let data = read_pmetrics(Path::new("examples/two_eq_lag/two_eq_lag.csv")).unwrap();
+    let settings = settings::read("examples/two_eq_lag/config.toml").unwrap();
+    let data = data::read_pmetrics("examples/two_eq_lag/two_eq_lag.csv").unwrap();
     let _result = fit(eq, data, settings);
 }

src/lib.rs

@@ -108,7 +108,7 @@ pub mod prelude {
     pub use crate::routines::expansion::*;
     pub use crate::routines::initialization::*;
     pub use crate::routines::optimization;
-    pub use crate::routines::settings::read_settings;
+    pub use crate::routines::settings::*;
     pub use crate::routines::*;
     pub use crate::tui::ui::*;
     //Alma re-exports

src/routines/settings.rs

@@ -480,8 +480,8 @@ impl Output {
 /// This function parses the settings from a TOML configuration file. The settings are validated, and a copy of the settings is written to file.
 ///
 /// Entries in the TOML file may be overridden by environment variables. The environment variables must be prefixed with `PMCORE__`, and the TOML entry must be in uppercase. For example, the TUI may be disabled by setting the environment variable `PMCORE__CONFIG__TUI=false` Note that a double underscore, `__`, is used as the separator, as some settings may contain a single underscore, such as `PMCORE__CONFIG__LOG_LEVEL`.
-pub fn read_settings(path: String) -> Result<Settings, anyhow::Error> {
-    let settings_path = path;
+pub fn read(path: impl Into<String>) -> Result<Settings, anyhow::Error> {
+    let settings_path = path.into();
 
     let parsed = eConfig::builder()
         .add_source(config::File::with_name(&settings_path).format(config::FileFormat::Toml))