From 975ab20d813e0dcb8d06976ec70cc8cf4c462a6b Mon Sep 17 00:00:00 2001
From: Markus <markushh@uio.no>
Date: Sun, 23 Feb 2025 14:36:09 +0100
Subject: [PATCH] chore: Update dependencies

faer-ext has been held back, as it uses an older version of faer, which causes an import collision.
---
 Cargo.toml                       | 10 +++++-----
 src/routines/evaluation/ipm.rs   |  2 +-
 src/routines/evaluation/qr.rs    | 14 ++++++++------
 src/routines/optimization/mod.rs | 12 ++++++------
 4 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 12fb8037d..251ba5570 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -16,12 +16,12 @@ exclude = [".github/*", ".vscode/*"]
 
 [dependencies]
 csv = "1.2.1"
-ndarray = { version = "0.15.6", features = ["rayon"] }
+ndarray = { version = "0.16.1", features = ["rayon"] }
 serde = "1.0.188"
 serde_json = "1.0.66"
 sobol_burley = "0.5.0"
-ndarray-stats = "0.5.1"
-linfa-linalg = "0.1.0"
+ndarray-stats = "0.6.0"
+linfa-linalg = "0.2.0"
 argmin = { version = "0.10.0", features = [] }
 argmin-math = { version = "0.4.0", features = ["ndarray_v0_15-nolinalg"] }
 tracing = "0.1.40"
@@ -31,8 +31,8 @@ tracing-subscriber = { version = "0.3.17", features = [
     "time",
 ] }
 config = { version = "0.15", features = ["preserve_order"] }
-faer = "0.19.3"
-faer-ext = { version = "0.2.0", features = ["nalgebra", "ndarray"] }
+faer = "0.20.2"
+faer-ext = { version = "0.4.1", features = ["nalgebra", "ndarray"] }
 pharmsol = "0.7.6"
 rand = "0.9.0"
 anyhow = "1.0.86"
diff --git a/src/routines/evaluation/ipm.rs b/src/routines/evaluation/ipm.rs
index 2554d63a8..febfb6a9e 100644
--- a/src/routines/evaluation/ipm.rs
+++ b/src/routines/evaluation/ipm.rs
@@ -97,7 +97,7 @@ pub fn burke(
         let uph = uph.t();
         let smuyinv = smu * (&ecol / &y);
         let rhsdw = &erow / &w - (psi.dot(&smuyinv));
-        let a = rhsdw.clone().into_shape((rhsdw.len(), 1))?;
+        let a = rhsdw.clone().into_shape_with_order((rhsdw.len(), 1))?;
 
         let x = uph
             .t()
diff --git a/src/routines/evaluation/qr.rs b/src/routines/evaluation/qr.rs
index bda68f3b8..e8b75b502 100644
--- a/src/routines/evaluation/qr.rs
+++ b/src/routines/evaluation/qr.rs
@@ -1,18 +1,20 @@
-// use faer::{FaerMat, IntoFaer, IntoNdarray};
 use faer_ext::*;
 use ndarray::parallel::prelude::*;
 use ndarray::{Array2, Axis};
 
+use faer::MatRef;
+
 pub fn calculate_r(x: &Array2<f64>) -> (Array2<f64>, Vec<usize>) {
     let mut n_x = x.clone();
     n_x.axis_iter_mut(Axis(0))
         .into_par_iter()
         .for_each(|mut row| row /= row.sum());
-    let mat_x = n_x.view().into_faer();
-    let qr = mat_x.col_piv_qr();
-    let r_mat = qr.compute_r();
+    let mat_x: MatRef<'_, f64> = n_x.view().into_faer();
+    let qr: faer::sparse::solvers::ColPivQr<f64> = mat_x.col_piv_qr();
+    let r_mat: faer::Mat<f64> = qr.compute_r();
     let (forward, _inverse) = qr.col_permutation().arrays();
-    let r = r_mat.as_ref().into_ndarray().to_owned();
-    let perm = Vec::from(forward);
+    let r: ndarray::ArrayBase<ndarray::OwnedRepr<f64>, ndarray::Dim<[usize; 2]>> =
+        r_mat.as_ref().into_ndarray().to_owned();
+    let perm: Vec<usize> = Vec::from(forward);
     (r, perm)
 }
diff --git a/src/routines/optimization/mod.rs b/src/routines/optimization/mod.rs
index 973c6df42..e7566bd1e 100644
--- a/src/routines/optimization/mod.rs
+++ b/src/routines/optimization/mod.rs
@@ -17,10 +17,10 @@ pub struct SppOptimizer<'a, E: Equation> {
 }
 
 impl<'a, E: Equation> CostFunction for SppOptimizer<'a, E> {
-    type Param = Array1<f64>;
+    type Param = Vec<f64>;
     type Output = f64;
     fn cost(&self, spp: &Self::Param) -> Result<Self::Output, Error> {
-        let theta = spp.to_owned().insert_axis(Axis(0));
+        let theta = Array1::from(spp.clone()).insert_axis(Axis(0));
 
         let psi = psi(self.equation, self.data, &theta, self.sig, false, false);
 
@@ -53,17 +53,17 @@ impl<'a, E: Equation> SppOptimizer<'a, E> {
         }
     }
     pub fn optimize_point(self, spp: Array1<f64>) -> Result<Array1<f64>, Error> {
-        let simplex = create_initial_simplex(&spp);
+        let simplex = create_initial_simplex(&spp.to_vec());
         let solver = NelderMead::new(simplex).with_sd_tolerance(1e-2)?;
         let res = Executor::new(self, solver)
             .configure(|state| state.max_iters(5))
             // .add_observer(SlogLogger::term(), ObserverMode::Always)
             .run()?;
-        Ok(res.state.best_param.unwrap())
+        Ok(Array1::from(res.state.best_param.unwrap()))
     }
 }
 
-fn create_initial_simplex(initial_point: &Array1<f64>) -> Vec<Array1<f64>> {
+fn create_initial_simplex(initial_point: &[f64]) -> Vec<Vec<f64>> {
     let num_dimensions = initial_point.len();
     let perturbation_percentage = 0.008;
 
@@ -71,7 +71,7 @@ fn create_initial_simplex(initial_point: &Array1<f64>) -> Vec<Array1<f64>> {
     let mut vertices = Vec::new();
 
     // Add the initial point to the vertices
-    vertices.push(initial_point.to_owned());
+    vertices.push(initial_point.to_vec());
 
     // Calculate perturbation values for each component
     for i in 0..num_dimensions {