chore: Use Rust 2024

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "pmcore"
 version = "0.10.0"
-edition = "2021"
+edition = "2024"
 authors = [
     "Julián D. Otálvaro <[email protected]>",
     "Markus Hovd",

benches/bimodal_ke.rs

@@ -1,5 +1,5 @@
 use anyhow::Result;
-use criterion::{criterion_group, criterion_main, Criterion};
+use criterion::{Criterion, criterion_group, criterion_main};
 use pmcore::prelude::*;
 
 fn create_equation() -> equation::ODE {

src/algorithms/mod.rs

@@ -204,11 +204,11 @@ pub trait Algorithms<E: Equation>: Sync {
             }
 
             return Err(anyhow::anyhow!(
-                    "The probability of {}/{} subjects is zero given the model. Affected subjects: {:?}",
-                    indices.len(),
-                    self.psi().matrix().nrows(),
-                    zero_probability_subjects
-                ));
+                "The probability of {}/{} subjects is zero given the model. Affected subjects: {:?}",
+                indices.len(),
+                self.psi().matrix().nrows(),
+                zero_probability_subjects
+            ));
         }
 
         Ok(())

src/algorithms/npag.rs

@@ -5,11 +5,11 @@ pub use crate::routines::evaluation::qr;
 use crate::routines::settings::Settings;
 
 use crate::routines::output::{CycleLog, NPCycle, NPResult};
-use crate::structs::psi::{calculate_psi, Psi};
+use crate::structs::psi::{Psi, calculate_psi};
 use crate::structs::theta::Theta;
 
-use anyhow::bail;
 use anyhow::Result;
+use anyhow::bail;
 use pharmsol::prelude::{
     data::{Data, ErrorModel, ErrorType},
     simulator::Equation,

src/algorithms/npod.rs

@@ -8,26 +8,26 @@ use crate::{
         },
     },
     structs::{
-        psi::{calculate_psi, Psi},
+        psi::{Psi, calculate_psi},
         theta::Theta,
     },
 };
-use anyhow::bail;
 use anyhow::Result;
+use anyhow::bail;
 use faer_ext::IntoNdarray;
 use pharmsol::{
+    Subject,
     prelude::{
         data::{Data, ErrorModel},
         simulator::Equation,
     },
-    Subject,
 };
 
 use faer::Col;
 
 use ndarray::{
-    parallel::prelude::{IntoParallelRefMutIterator, ParallelIterator},
     Array, Array1, ArrayBase, Dim, OwnedRepr,
+    parallel::prelude::{IntoParallelRefMutIterator, ParallelIterator},
 };
 
 use crate::routines::{initialization, optimization::SppOptimizer};
@@ -404,7 +404,8 @@ impl<E: Equation> NPOD<E> {
                 indices.iter().map(|&i| subject[i].id()).collect();
 
             return Err(anyhow::anyhow!(
-                "The probability of one or more subjects, given the model, is zero. The following subjects have zero probability: {:?}", zero_probability_subjects
+                "The probability of one or more subjects, given the model, is zero. The following subjects have zero probability: {:?}",
+                zero_probability_subjects
             ));
         }
 

src/algorithms/postprob.rs

@@ -1,7 +1,7 @@
 use crate::{
     prelude::algorithms::Algorithms,
     structs::{
-        psi::{calculate_psi, Psi},
+        psi::{Psi, calculate_psi},
         theta::Theta,
     },
 };

src/lib.rs

@@ -66,8 +66,8 @@ pub mod prelude {
     pub use super::HashMap;
     pub use super::Result;
     pub use crate::algorithms;
-    pub use crate::algorithms::dispatch_algorithm;
     pub use crate::algorithms::Algorithm;
+    pub use crate::algorithms::dispatch_algorithm;
     pub use crate::routines;
     pub use crate::routines::logger;
 
@@ -89,15 +89,15 @@ pub mod prelude {
     }
 
     //traits
+    pub use pharmsol::ODE;
+    pub use pharmsol::SDE;
     pub use pharmsol::data::*;
     pub use pharmsol::equation::Equation;
     pub use pharmsol::equation::EquationTypes;
     pub use pharmsol::equation::Predictions;
     pub use pharmsol::equation::*;
     pub use pharmsol::prelude::*;
     pub use pharmsol::simulator::*;
-    pub use pharmsol::ODE;
-    pub use pharmsol::SDE;
 
     //macros
     pub use pharmsol::fa;

src/routines/evaluation/qr.rs

@@ -1,6 +1,6 @@
 use crate::structs::psi::Psi;
-use faer::linalg::solvers::ColPivQr;
 use faer::Mat;
+use faer::linalg::solvers::ColPivQr;
 
 pub fn calculate_r(psi: &Psi) -> (Mat<f64>, Vec<usize>) {
     // Clone the matrix, as we will modify it

src/routines/initialization/latin.rs

@@ -1,8 +1,8 @@
 use anyhow::Result;
 use faer::Mat;
+use rand::Rng;
 use rand::prelude::*;
 use rand::rngs::StdRng;
-use rand::Rng;
 
 use crate::prelude::Parameters;
 use crate::structs::theta::Theta;

src/routines/initialization/mod.rs

@@ -1,7 +1,7 @@
 use std::fs::File;
 
 use crate::structs::theta::Theta;
-use anyhow::{bail, Context, Result};
+use anyhow::{Context, Result, bail};
 use faer::Mat;
 use serde::{Deserialize, Serialize};
 
@@ -66,8 +66,8 @@ pub fn sample_space(settings: &Settings) -> Result<Theta> {
     let prior = match settings.prior() {
         Prior::Sobol(points, seed) => sobol::generate(settings.parameters(), *points, *seed)?,
         Prior::Latin(points, seed) => latin::generate(settings.parameters(), *points, *seed)?,
-        Prior::File(ref path) => parse_prior(path, settings)?,
-        Prior::Theta(ref theta) => {
+        Prior::File(path) => parse_prior(path, settings)?,
+        Prior::Theta(theta) => {
             // If a custom prior is provided, return it directly
             return Ok(theta.clone());
         }

src/routines/logger.rs

@@ -3,12 +3,12 @@ use std::time::Instant;
 use crate::routines::output::OutputFile;
 use crate::routines::settings::Settings;
 use anyhow::Result;
+use tracing_subscriber::EnvFilter;
 use tracing_subscriber::fmt::time::FormatTime;
 use tracing_subscriber::fmt::{self};
 use tracing_subscriber::prelude::__tracing_subscriber_SubscriberExt;
 use tracing_subscriber::registry::Registry;
 use tracing_subscriber::util::SubscriberInitExt;
-use tracing_subscriber::EnvFilter;
 
 /// Setup logging for the library
 ///

src/routines/optimization/mod.rs

@@ -6,7 +6,7 @@ use ndarray::{Array1, Axis};
 
 use pharmsol::prelude::{
     data::{Data, ErrorModel},
-    simulator::{psi, Equation},
+    simulator::{Equation, psi},
 };
 
 pub struct SppOptimizer<'a, E: Equation> {

src/routines/output.rs

@@ -1,7 +1,7 @@
 use crate::prelude::*;
 use crate::structs::psi::Psi;
 use crate::structs::theta::Theta;
-use anyhow::{bail, Context, Result};
+use anyhow::{Context, Result, bail};
 use csv::WriterBuilder;
 use faer::linalg::zip::IntoView;
 use faer_ext::IntoNdarray;
@@ -12,7 +12,7 @@ use serde::Serialize;
 // use pharmsol::Cache;
 use crate::routines::settings::Settings;
 use faer::{Col, Mat};
-use std::fs::{create_dir_all, File, OpenOptions};
+use std::fs::{File, OpenOptions, create_dir_all};
 use std::path::{Path, PathBuf};
 
 /// Defines the result objects from an NPAG run
@@ -810,7 +810,12 @@ pub fn posterior_mean_median(
 
     // Check for compatible sizes
     if theta.nrows() != w.len() || theta.nrows() != psi.ncols() || psi.ncols() != w.len() {
-        bail!("Number of parameters and number of weights do not match, theta.nrows(): {}, w.len(): {}, psi.ncols(): {}", theta.nrows(), w.len(), psi.ncols());
+        bail!(
+            "Number of parameters and number of weights do not match, theta.nrows(): {}, w.len(): {}, psi.ncols(): {}",
+            theta.nrows(),
+            w.len(),
+            psi.ncols()
+        );
     }
 
     // Normalize psi to get probabilities of each spp for each id

src/routines/settings.rs

@@ -1,7 +1,7 @@
 use crate::algorithms::Algorithm;
 use crate::routines::initialization::Prior;
 use crate::routines::output::OutputFile;
-use anyhow::{bail, Result};
+use anyhow::{Result, bail};
 use pharmsol::prelude::data::ErrorType;
 use serde::{Deserialize, Serialize};
 use serde_json;

src/structs/psi.rs

@@ -2,10 +2,10 @@ use faer::Mat;
 use faer_ext::IntoFaer;
 use faer_ext::IntoNdarray;
 use ndarray::{Array2, ArrayView2};
-use pharmsol::prelude::simulator::psi;
 use pharmsol::Data;
 use pharmsol::Equation;
 use pharmsol::ErrorModel;
+use pharmsol::prelude::simulator::psi;
 
 use super::theta::Theta;