refactor: lint

Author: ivan-aksamentov

packages/treetime-utils/src/file.rs

@@ -4,7 +4,7 @@ use eyre::{Report, WrapErr};
 use log::info;
 use std::fs::File;
 use std::io::{BufRead, BufReader, BufWriter, Write, stdin, stdout};
-use std::path::{Path, PathBuf};
+use std::path::Path;
 
 pub const DEFAULT_FILE_BUF_SIZE: usize = 256 * 1024;
 
@@ -57,12 +57,12 @@ pub fn create_file_or_stdout(filepath: impl AsRef<Path>) -> Result<Box<dyn Write
 
 pub fn is_path_stdin(filepath: impl AsRef<Path>) -> bool {
   let filepath = filepath.as_ref();
-  filepath == PathBuf::from("-") || filepath == PathBuf::from("/dev/stdin")
+  filepath == "-" || filepath == "/dev/stdin"
 }
 
 pub fn is_path_stdout(filepath: impl AsRef<Path>) -> bool {
   let filepath = filepath.as_ref();
-  filepath == PathBuf::from("-") || filepath == PathBuf::from("/dev/stdout")
+  filepath == "-" || filepath == "/dev/stdout"
 }
 
 #[cfg(not(target_arch = "wasm32"))]

packages/treetime/src/commands/ancestral/anc_args.rs

@@ -6,18 +6,14 @@ use std::path::PathBuf;
 
 #[derive(Copy, Debug, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum)]
 #[value(rename_all = "kebab-case")]
+#[derive(Default)]
 pub enum MethodAncestral {
+  #[default]
   Joint,
   Marginal,
   Parsimony,
 }
 
-impl Default for MethodAncestral {
-  fn default() -> Self {
-    Self::Joint
-  }
-}
-
 #[derive(Parser, Debug)]
 pub struct TreetimeAncestralArgs {
   /// Path to one or multiple FASTA files with aligned input sequences

packages/treetime/src/commands/timetree/args.rs

@@ -8,49 +8,37 @@ use std::path::PathBuf;
 
 #[derive(Copy, Debug, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum)]
 #[value(rename_all = "kebab-case")]
+#[derive(Default)]
 pub enum BranchLengthMode {
+  #[default]
   Auto,
   Input,
   Joint,
   Marginal,
 }
 
-impl Default for BranchLengthMode {
-  fn default() -> Self {
-    Self::Auto
-  }
-}
-
 #[derive(Copy, Debug, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum)]
 #[value(rename_all = "kebab-case")]
+#[derive(Default)]
 pub enum TimeMarginalMode {
+  #[default]
   Never,
   Always,
   OnlyFinal,
 }
 
-impl Default for TimeMarginalMode {
-  fn default() -> Self {
-    Self::Never
-  }
-}
-
 #[derive(Copy, Debug, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum)]
 #[value(rename_all = "kebab-case")]
+#[derive(Default)]
 pub enum RerootMode {
+  #[default]
   LeastSquares,
   MinDev,
   Oldest,
   ClockFilter,
   Mrca,
 }
 
-impl Default for RerootMode {
-  fn default() -> Self {
-    Self::LeastSquares
-  }
-}
-
 #[derive(Parser, Debug, SmartDefault)]
 pub struct TreetimeTimetreeArgs {
   /// Path to one or multiple FASTA files with aligned input sequences

packages/treetime/src/distribution/distribution_convolution.rs

@@ -84,7 +84,7 @@ fn convolution_range_function(r: &DistributionRange<f64>, f: &DistributionFuncti
   // - a point distribution (taking care of the shift + amplitude)
   // - an interval centered on zero and of a fixed width (taking care of the smoothing)
 
-  let shift = (r.start() + r.end()) / 2.0;
+  let shift = f64::midpoint(r.start(), r.end());
   let amplitude = r.amplitude();
   let width = r.end() - r.start();