Fixing clippy suggestions

src/dspsa.rs

@@ -1,18 +1,18 @@
 use rand::Rng;
 
-pub fn phi(v: &Vec<f64>) -> Vec<f64> {
+pub fn phi(v: &[f64]) -> Vec<f64> {
     v.iter().enumerate().map(|(i, value)| {
         if i == 0 || value.lt(&0.0) {
             0.0
         } else if value.gt(&(i as f64)) {
             (i as f64) - 0.001
         } else {
-            *value as f64
+            *value
         }
     }).collect()
 }
 
-pub fn piv(v: &Vec<f64>) -> Vec<f64> {
+pub fn piv(v: &[f64]) -> Vec<f64> {
     let mut pivec: Vec<f64> = phi(v).iter().map(|el| el.floor() + 0.5).collect();
     pivec[0] = 0.0;
     pivec

src/gen_list.rs

@@ -104,19 +104,17 @@ pub fn char_to_mutation(e: &char) -> Mutation {
 // }
 
 pub fn combine_lists(
-    seq1: &Vec<Mutation>,
-    seq2: &Vec<Mutation>,
+    seq1: &[Mutation],
+    seq2: &[Mutation],
     branchlengths: (f64, f64),
     rate_matrix: &na::Matrix4<f64>,
 ) -> Vec<Mutation> {
-
-    let mut out: Vec<Mutation> = Vec::new();
 
     // Probability matrices
     let p1 = na::Matrix::exp(&(rate_matrix * branchlengths.0));
     let p2 = na::Matrix::exp(&(rate_matrix * branchlengths.1));
 
-    out = seq1.iter()
+    let out: Vec<Mutation> = seq1.iter()
     .zip(seq2.iter())
     .map(|(b1, b2)| b1.child_log_likelihood(&p1)
                                             .sum(b2.child_log_likelihood(&p2)))

src/lib.rs

@@ -101,7 +101,7 @@ pub fn main() {
 
             let ak = a / (1.0 + A + k as f64).powf(alpha);
 
-            theta = theta.iter().zip(ghat.iter()).map(|(theta, g)| *theta as f64 - ak * g).collect();
+            theta = theta.iter().zip(ghat.iter()).map(|(theta, g)| *theta - ak * g).collect();
 
             llvec.push(x1);
 

src/likelihoods.rs

@@ -10,7 +10,7 @@ impl Tree {
     pub fn update_likelihood(&mut self, rate_matrix: &na::Matrix4<f64>) {
 
         if self.changes.is_empty() {
-            return ()
+            return
         }
 
         let max_depth: usize = *self.changes.keys().max().unwrap();

src/phylo2vec.rs

@@ -8,7 +8,7 @@ use rand::{seq::SliceRandom, thread_rng, Rng};
 pub fn phylo2vec_quad(v: Vec<usize>) -> Tree {
     let mut tree = Tree::new(v);
     let k = tree.tree_vec.len();
-    let mut not_processed = vec![true].repeat(k);
+    let mut not_processed = [true].repeat(k);
     let mut M = Array2::<usize>::zeros((k, 3));
     let mut labels = Array2::<usize>::zeros((k + 1, k + 1));
 

src/tree.rs

@@ -82,8 +82,8 @@ impl Tree {
                                 .collect();
 
         for i in &x {
-            match temp.get(&i) {
-                Some(_) => temp.remove(&i),
+            match temp.get(i) {
+                Some(_) => temp.remove(i),
                 None => temp.insert(*i),
             };
         };
@@ -360,19 +360,6 @@ impl<'a> Iterator for Preorder<'a> {
                     None => None,
                     Some(node) => node,
                 };
-                if self.next_node.is_some() {
-                    match self.next_node.unwrap().parent {
-                        Some(x) if x == output.unwrap().index => {
-                        },
-                        Some(x) => {
-                        },
-                        None => {
-
-                        }
-                    }
-                } else {
-
-                }
             }
             _ => {
                 panic!("Iterator has found a node with only a right child")