Bump rust to 1.63.

Run cargo clippy --fix.

Author: adam-azarchs

.github/workflows/test.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.62.0
+          toolchain: 1.63.0
           components: rustfmt, clippy
           default: true
       - name: Checkout git repository
@@ -26,10 +26,10 @@ jobs:
         run: cargo fmt -- --check
       - name: Install cargo-deny
         run: |
-          wget https://github.com/EmbarkStudios/cargo-deny/releases/download/0.12.1/cargo-deny-0.12.1-x86_64-unknown-linux-musl.tar.gz
-          tar -xvf cargo-deny-0.12.1-x86_64-unknown-linux-musl.tar.gz
+          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
           mkdir -p ~/bin/
-          cp cargo-deny-0.12.1-x86_64-unknown-linux-musl/cargo-deny ~/bin/
+          cp cargo-deny-0.12.2-x86_64-unknown-linux-musl/cargo-deny ~/bin/
           rm -r cargo-deny-*
           echo "$HOME/bin" >> $GITHUB_PATH
       - name: Cache cargo registry

amino/src/lib.rs

@@ -32,7 +32,8 @@ pub fn have_stop(b: &DnaString, j: usize) -> bool {
 
 pub fn aa3_to_aa(aa3: &[u8]) -> u8 {
     assert!(aa3.len() == 3);
-    let aa = match aa3 {
+
+    match aa3 {
         b"ALA" => b'A',
         b"ARG" => b'R',
         b"ASN" => b'N',
@@ -54,13 +55,13 @@ pub fn aa3_to_aa(aa3: &[u8]) -> u8 {
         b"TYR" => b'Y',
         b"VAL" => b'V',
         _ => panic!("Unexpected three-letter amino acid code {}.", strme(aa3)),
-    };
-    aa
+    }
 }
 
 pub fn codon_to_aa(codon: &[u8]) -> u8 {
     assert!(codon.len() == 3);
-    let aa = match codon {
+
+    match codon {
         b"GGT" => b'G',
         b"GGC" => b'G',
         b"GGA" => b'G',
@@ -126,8 +127,7 @@ pub fn codon_to_aa(codon: &[u8]) -> u8 {
         b"TAA" => b'*',
         b"TGA" => b'*',
         _ => panic!("Unexpected codon {}.", strme(codon)),
-    };
-    aa
+    }
 }
 
 // Convert a given DNA sequence to amino acids, starting at a given position.

bio_edit/src/alphabets/mod.rs

@@ -7,7 +7,7 @@ use std::borrow::Borrow;
 
 use bit_set::BitSet;
 
-#[derive(Debug, PartialEq)]
+#[derive(Debug, PartialEq, Eq)]
 pub struct Alphabet {
     pub symbols: BitSet,
 }

pretty_trace/src/lib.rs

@@ -870,7 +870,7 @@ fn force_pretty_trace_fancy(
         }
         let msg = match info.location() {
             Some(location) => {
-                let loc = &(*location.file());
+                let loc = location.file();
 
                 // Replace long constructs of the form /rustc/......./src/
                 //                                  by /rustc/<stuff>/src/.

vdj_ann/src/annotate.rs

@@ -2794,7 +2794,7 @@ pub fn print_cdr3_using_ann(
 // EXTEND_PENALTY = 1
 // which are copied from cellranger/lib/python/cellranger/vdj/constants.py.
 
-#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
+#[derive(Debug, Serialize, Deserialize, Clone, PartialEq, Eq)]
 pub struct AnnotationFeature {
     pub chain: VdjChain,        // chain type of the reference record, e.g. TRA
     pub display_name: String,   // same as gene_name
@@ -2803,7 +2803,7 @@ pub struct AnnotationFeature {
     pub region_type: VdjRegion, // region type e.g. L-REGION+V-REGION
 }
 
-#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
+#[derive(Debug, Serialize, Deserialize, Clone, PartialEq, Eq)]
 pub struct AnnotationUnit {
     pub contig_match_start: usize,     // start on contig
     pub contig_match_end: usize,       // stop on contig
@@ -2941,7 +2941,7 @@ impl AnnotationUnit {
     }
 }
 
-#[derive(Debug, Serialize, Deserialize, Clone, Default, PartialEq)]
+#[derive(Debug, Serialize, Deserialize, Clone, Default, PartialEq, Eq)]
 pub struct ClonotypeInfo {
     #[serde(default)]
     pub raw_clonotype_id: Option<String>,
@@ -2957,7 +2957,7 @@ impl ClonotypeInfo {
     }
 }
 
-#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
+#[derive(Debug, Serialize, Deserialize, Clone, PartialEq, Eq)]
 pub struct Region {
     pub start: usize,
     pub stop: usize,