Update rust to 1.65 (#210)

Fix new clippy lints.

Update to maintained github actions.

Author: adam-azarchs

.github/workflows/test.yml

@@ -15,40 +15,39 @@ jobs:
   rust:
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions-rs/toolchain@v1
+      - uses: dtolnay/rust-toolchain@master
         with:
-          toolchain: 1.63.0
+          toolchain: 1.65.0
           components: rustfmt, clippy
-          default: true
       - name: Checkout git repository
         uses: actions/checkout@master
       - name: Check Rust formatting
         run: cargo fmt -- --check
       - name: Install cargo-deny
         run: |
-          wget https://github.com/EmbarkStudios/cargo-deny/releases/download/0.12.2/cargo-deny-0.12.2-x86_64-unknown-linux-musl.tar.gz
-          tar -xvf cargo-deny-0.12.2-x86_64-unknown-linux-musl.tar.gz
+          wget https://github.com/EmbarkStudios/cargo-deny/releases/download/0.13.5/cargo-deny-0.13.5-x86_64-unknown-linux-musl.tar.gz
+          tar -xvf cargo-deny-0.13.5-x86_64-unknown-linux-musl.tar.gz
           mkdir -p ~/bin/
-          cp cargo-deny-0.12.2-x86_64-unknown-linux-musl/cargo-deny ~/bin/
+          cp cargo-deny-0.13.5-x86_64-unknown-linux-musl/cargo-deny ~/bin/
           rm -r cargo-deny-*
           echo "$HOME/bin" >> $GITHUB_PATH
       - name: Cache cargo registry
         uses: actions/cache@v3
         with:
           path: ~/.cargo/registry
-          key: ${{runner.os}}-cargo-registry-${{hashFiles('**/*.rs')}}
+          key: ${{runner.os}}-cargo-registry-${{hashFiles('Cargo.lock')}}
           restore-keys: ${{runner.os}}-cargo-registry-
       - name: Cache cargo git index
         uses: actions/cache@v3
         with:
           path: ~/.cargo/git
-          key: ${{runner.os}}-cargo-git-${{hashFiles('**/*.rs')}}
+          key: ${{runner.os}}-cargo-git-${{hashFiles('Cargo.lock')}}
           restore-keys: ${{runner.os}}-cargo-git-
       - name: Cache cargo build --release --all-targets
         uses: actions/cache@v3
         with:
           path: target
-          key: ${{runner.os}}-cargo-target-${{hashFiles('**/*.rs')}}
+          key: ${{runner.os}}-cargo-target-${{hashFiles('Cargo.lock')}}-${{hashFiles('**/Cargo.toml')}}
           restore-keys: |
             ${{runner.os}}-cargo-target-
       - name: Remove the Cargo target directory

fasta_tools/src/lib.rs

@@ -39,7 +39,7 @@ pub fn read_fasta_to_vec_vec_u8(f: impl AsRef<Path>) -> Vec<Vec<u8>> {
             x.push(last.as_bytes().to_vec());
         }
         _ => {
-            let gz = MultiGzDecoder::new(std::fs::File::open(&f).unwrap());
+            let gz = MultiGzDecoder::new(std::fs::File::open(f).unwrap());
             let fin = std::io::BufReader::new(gz);
             let mut last: String = String::new();
             let mut first = true;
@@ -99,7 +99,7 @@ pub fn read_fasta_into_vec_dna_string_plus_headers(
             dv.push(DnaString::from_dna_string(&last));
         }
         _ => {
-            let gz = MultiGzDecoder::new(std::fs::File::open(&f).unwrap());
+            let gz = MultiGzDecoder::new(std::fs::File::open(f).unwrap());
             let fin = std::io::BufReader::new(gz);
             let mut last: String = String::new();
             let mut first = true;

io_utils/src/lib.rs

@@ -16,7 +16,7 @@ use string_utils::TextUtils;
 // ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
 
 pub fn dir_list(d: &str) -> Vec<String> {
-    let x = fs::read_dir(&d).unwrap_or_else(|_| panic!("failed to read directory {}", d));
+    let x = fs::read_dir(d).unwrap_or_else(|_| panic!("failed to read directory {}", d));
     let mut y = Vec::<String>::new();
     for f in x {
         let s: String = f.unwrap().file_name().into_string().unwrap();

mirror_sparse_matrix/src/lib.rs

@@ -65,14 +65,14 @@ pub struct MirrorSparseMatrix {
 
 pub fn get_code_version_from_file(f: &str) -> u32 {
     assert_eq!(std::mem::size_of::<usize>(), 8); // for the usize at the beginning of the file
-    let mut ff = std::fs::File::open(&f).unwrap();
+    let mut ff = std::fs::File::open(f).unwrap();
     let mut x = vec![0_u32; 11];
     binary_read_to_ref::<u32>(&mut ff, &mut x[0], 11).unwrap();
     x[10]
 }
 
 pub fn read_from_file(s: &mut MirrorSparseMatrix, f: &str) {
-    let mut ff = std::fs::File::open(&f).unwrap();
+    let mut ff = std::fs::File::open(f).unwrap();
     binary_read_vec::<u8>(&mut ff, &mut s.x).unwrap();
     if s.code_version() != 0 && s.code_version() != 1 {
         panic!(
@@ -91,7 +91,7 @@ pub fn read_from_file(s: &mut MirrorSparseMatrix, f: &str) {
 pub fn write_to_file(s: &MirrorSparseMatrix, f: &str) {
     assert!(s.code_version() > 0);
     let mut ff =
-        std::fs::File::create(&f).unwrap_or_else(|_| panic!("Failed to create file {}.", f));
+        std::fs::File::create(f).unwrap_or_else(|_| panic!("Failed to create file {}.", f));
     binary_write_vec::<u8>(&mut ff, &s.x).unwrap();
 }
 

pretty_trace/examples/bad_traceback.rs

@@ -13,5 +13,5 @@ use std::fs;
 fn main() {
     PrettyTrace::new().on();
     let not = "file_that_does_not_exist";
-    let _ = fs::read_to_string(&not).unwrap();
+    let _ = fs::read_to_string(not).unwrap();
 }

pretty_trace/src/lib.rs

@@ -946,7 +946,7 @@ fn force_pretty_trace_fancy(
                      █ a string.  This is weird and might result in a defective traceback.\n\n";
                     }
                     Some(ex) => {
-                        let f = File::open(&ex);
+                        let f = File::open(ex);
                         if f.is_err() {
                             out +=
                             "█ WARNING.  Your executable file could not be opened for reading.\n\
@@ -1249,7 +1249,7 @@ fn prettify_traceback(bt: &[u8], whitelist: &[String], pack: bool) -> String {
             // Don't allow blocklets whose first line has the form ... main(...).
 
             let m = " main (";
-            if s.contains(&m) && s.after(m).contains(')') && !s.between(m, ")").contains('(') {
+            if s.contains(m) && s.after(m).contains(')') && !s.between(m, ")").contains('(') {
                 to_delete[j] = true;
             }
         }

vdj_ann/src/annotate.rs

@@ -2916,7 +2916,7 @@ impl AnnotationUnit {
         let types = vec!["IGH", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG"];
         let mut chain_type = String::new();
         for i in 0..types.len() {
-            if refdata.rheaders[t].contains(&types[i]) {
+            if refdata.rheaders[t].contains(types[i]) {
                 chain_type = types[i].to_string();
                 break;
             }

vdj_ann_ref/src/bin/build_vdj_ref.rs

@@ -991,13 +991,13 @@ fn main() {
                     .expect("gunzip failed");
             }
             Command::new("git")
-                .current_dir(&internal)
+                .current_dir(internal)
                 .arg("add")
                 .arg(&path)
                 .status()
                 .expect("git add failed");
             Command::new("git")
-                .current_dir(&internal)
+                .current_dir(internal)
                 .arg("commit")
                 .arg(path)
                 .status()

vdj_ann_ref/src/bin/build_vdj_ref_exons.rs

@@ -628,13 +628,13 @@ fn main() {
                     .expect("gunzip failed");
             }
             Command::new("git")
-                .current_dir(&internal)
+                .current_dir(internal)
                 .arg("add")
                 .arg(&path)
                 .status()
                 .expect("git add failed");
             Command::new("git")
-                .current_dir(&internal)
+                .current_dir(internal)
                 .arg("commit")
                 .arg(path)
                 .status()