Merge pull request #168 from neherlab/chore/upgrade-rust

Author: ivan-aksamentov

Cargo.lock

@@ -61,7 +61,6 @@ indicatif-log-bridge = "0.2.3"
 indoc = "=2.0.5"
 intervallum = "=1.4.1"
 itertools = "=0.14.0"
-lazy_static = "=1.5.0"
 log = "=0.4.26"
 maplit = "=1.0.2"
 ndarray = { version = "=0.16.1", features = ["rayon", "serde", "blas", "approx"] }
@@ -234,6 +233,7 @@ pub_use = "allow"
 pub_with_shorthand = "allow"
 question_mark_used = "allow"
 redundant_closure_for_method_calls = "allow"
+redundant_test_prefix = "allow"
 renamed_function_params = "allow"
 self_named_module_files = "allow"
 semicolon_inside_block = "allow"

Cargo.toml

@@ -387,7 +387,7 @@ impl Minimap2RawRegs {
 
     // SAFETY: calling unsafe function. The `mm_map()` allocates memory for results array and the `.p` field each of
     // its elements' using `malloc()`. This memory needs to be deallocated using `free()`.
-    let regs: *mut mm_reg1_t = unsafe { mm_map(mi, l_seq, seq, &mut n_regs, buf.get_mut(), map_opt, name) };
+    let regs: *mut mm_reg1_t = unsafe { mm_map(mi, l_seq, seq, &raw mut n_regs, buf.get_mut(), map_opt, name) };
 
     Ok(Self {
       regs,

packages/minimap2/src/map.rs

@@ -69,15 +69,15 @@ impl Minimap2Options {
   }
 
   pub(crate) fn idx_opt_mut(&mut self) -> *mut mm_idxopt_t {
-    &mut self.idx_opt
+    &raw mut self.idx_opt
   }
 
   pub(crate) fn map_opt(&self) -> &mm_mapopt_t {
     &self.map_opt
   }
 
   pub(crate) fn map_opt_mut(&mut self) -> *mut mm_mapopt_t {
-    &mut self.map_opt
+    &raw mut self.map_opt
   }
 }
 

packages/minimap2/src/options.rs

@@ -43,7 +43,6 @@ indicatif-log-bridge = { workspace = true }
 indoc = { workspace = true }
 intervallum = { workspace = true }
 itertools = { workspace = true }
-lazy_static = { workspace = true }
 log = { workspace = true }
 maplit = { workspace = true }
 minimap2 = { workspace = true }

packages/pangraph/Cargo.toml

@@ -115,7 +115,7 @@ pub fn create_alignment_band(
 
   // loop over remaining seeds in chain
   for next_seed in chain.iter().skip(1) {
-    let mean_offset = (next_seed.offset + current_seed.offset) / 2; // offset of gap seed
+    let mean_offset = isize::midpoint(next_seed.offset, current_seed.offset); // offset of gap seed
     let shift = abs_shift(current_seed, next_seed) / 2; // distance from mean offset
     look_forward_length = shift + excess_bandwidth;
 

packages/pangraph/src/align/nextclade/align/seed_alignment.rs

@@ -81,13 +81,11 @@ mod tests {
   use crate::commands::build::build_args::PangraphBuildArgs;
   use crate::o;
   use eyre::Report;
-  use lazy_static::lazy_static;
   use pretty_assertions::assert_eq;
   use rstest::rstest;
+  use std::sync::LazyLock;
 
-  lazy_static! {
-    static ref EXTRA_BANDWIDTH: usize = PangraphBuildArgs::default().extra_band_width;
-  }
+  static EXTRA_BANDWIDTH: LazyLock<usize> = LazyLock::new(|| PangraphBuildArgs::default().extra_band_width);
 
   #[rstest]
   fn test_align_with_nextclade_general_case() -> Result<(), Report> {

packages/pangraph/src/align/nextclade/align_with_nextclade.rs

@@ -178,14 +178,14 @@ fn check_sequence_reconstruction(
     if seq != new_seq {
       warn!("seq1: {}", e1.apply(block_1.consensus())?);
       warn!("cons1: {}", block_1.consensus());
-      warn!("e1: {:?}", e1);
+      warn!("e1: {e1:?}");
       warn!("seq2: {}", e2.apply(block_2.consensus())?);
       warn!("cons2: {}", block_2.consensus());
-      warn!("e2: {:?}", e2);
+      warn!("e2: {e2:?}");
 
-      warn!("new_seq: {}", new_seq);
+      warn!("new_seq: {new_seq}");
       warn!("new_cons: {}", new_block.consensus());
-      warn!("new_e: {:?}", new_e);
+      warn!("new_e: {new_e:?}");
     }
     debug_assert_eq!(seq, new_seq);
   }

packages/pangraph/src/circularize/merge_blocks.rs

@@ -12,14 +12,11 @@ use clap::{CommandFactory, Parser, Subcommand, ValueEnum};
 use clap_complete::{Shell, generate};
 use clap_complete_fig::Fig;
 use eyre::{Report, eyre};
-use lazy_static::lazy_static;
 use num_cpus;
 use std::fmt::Debug;
 use std::io;
 
-lazy_static! {
-  pub static ref SHELLS: Vec<&'static str> = ["bash", "elvish", "fish", "fig", "powershell", "zsh"].to_vec();
-}
+const SHELLS: &[&str] = &["bash", "elvish", "fish", "fig", "powershell", "zsh"];
 
 fn styles() -> styling::Styles {
   styling::Styles::styled()
@@ -90,7 +87,7 @@ pub enum PangraphCommands {
   ///
   Completions {
     /// Name of the shell to generate appropriate completions
-    #[clap(value_name = "SHELL", default_value_t = String::from("bash"), value_parser = SHELLS.clone())]
+    #[clap(value_name = "SHELL", default_value_t = String::from("bash"), value_parser = SHELLS.to_vec())]
     shell: String,
   },
 

packages/pangraph/src/commands/root_args.rs

@@ -8,7 +8,7 @@ use flate2::write::GzEncoder;
 use num::Integer;
 use num_traits::NumCast;
 use std::env;
-use std::io::{ErrorKind, Read, Write};
+use std::io::{Read, Write};
 use std::path::Path;
 use std::str::FromStr;
 
@@ -123,7 +123,7 @@ impl Read for Decompressor<'_> {
           .header("Filename")
       })
       .with_section(|| self.compression_type.clone().header("Decompressor"))
-      .map_err(|report| std::io::Error::new(ErrorKind::Other, report_to_string(&report)))
+      .map_err(|report| std::io::Error::other(report_to_string(&report)))
   }
 }
 
@@ -182,7 +182,7 @@ impl Write for Compressor<'_> {
           .header("Filename")
       })
       .with_section(|| self.compression_type.clone().header("Compressor"))
-      .map_err(|report| std::io::Error::new(ErrorKind::Other, report_to_string(&report)))
+      .map_err(|report| std::io::Error::other(report_to_string(&report)))
   }
 
   fn flush(&mut self) -> std::io::Result<()> {
@@ -198,7 +198,7 @@ impl Write for Compressor<'_> {
           .header("Filename")
       })
       .with_section(|| self.compression_type.clone().header("Compressor"))
-      .map_err(|report| std::io::Error::new(ErrorKind::Other, report_to_string(&report)))
+      .map_err(|report| std::io::Error::other(report_to_string(&report)))
   }
 }