chore: updates rustfmt to use version = "Two"

stjude-rust-labs · Dec 21, 2023 · 50c7dcc · 50c7dcc
1 parent bfbcd70
commit 50c7dcc
Show file tree

Hide file tree

Showing 18 changed files with 347 additions and 191 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -8,7 +8,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Update Rust
-        run: rustup update stable && rustup default stable
+        run: rustup update nightly && rustup defaultnightly 
       - name: Install rustfmt
         run: rustup component add rustfmt
       - run: cargo fmt -- --check
@@ -18,7 +18,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Update Rust
-        run: rustup update stable && rustup default stable
+        run: rustup update nightly && rustup defaultnightly 
       - name: Install clippy
         run: rustup component add clippy
       - run: cargo clippy --all-features -- --deny warnings
@@ -28,5 +28,5 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Update Rust
-        run: rustup update stable && rustup default stable
+        run: rustup update nightly && rustup defaultnightly 
       - run: cargo test --all-features
diff --git a/examples/chain_check.rs b/examples/chain_check.rs
@@ -47,10 +47,10 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         .map(BufReader::new)
         .map(chain::Reader::new)?;
 
-    let machine = liftover::machine::builder::Builder::default().try_build_from(chain)?;
+    let machine = liftover::machine::builder::Builder.try_build_from(chain)?;
 
     let mut reference = HashMap::new();
-    for result in fasta::reader::Builder::default()
+    for result in fasta::reader::Builder
         .build_from_path(reference_path)?
         .records()
     {
@@ -59,7 +59,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
     }
 
     let mut query = HashMap::new();
-    for result in fasta::reader::Builder::default()
+    for result in fasta::reader::Builder
         .build_from_path(query_path)?
         .records()
     {
@@ -87,8 +87,8 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         for region in results {
             let query_sequence = query.get(region.query().contig()).unwrap_or_else(|| {
                 panic!(
-                    "query fasta did not contain necessary contig: {}. \
-                    Are the FASTA files and chain file correct?",
+                    "query fasta did not contain necessary contig: {}. Are the FASTA files and \
+                     chain file correct?",
                     region.query().contig()
                 )
             });

diff --git a/examples/liftover.rs b/examples/liftover.rs
@@ -18,7 +18,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
         .map(BufReader::new)
         .map(chain::Reader::new)?;
 
-    let machine = liftover::machine::builder::Builder::default().try_build_from(reader)?;
+    let machine = liftover::machine::builder::Builder.try_build_from(reader)?;
     let results = machine.liftover(&interval);
 
     match results {

diff --git a/rustfmt.toml b/rustfmt.toml
@@ -0,0 +1,15 @@
+# Unstable settings
+condense_wildcard_suffixes = true
+format_code_in_doc_comments = true
+format_macro_matchers = true
+format_strings = true
+group_imports = "StdExternalCrate"
+hex_literal_case = "Upper"
+imports_granularity = "Item"
+newline_style = "Unix"
+normalize_comments = true
+normalize_doc_attributes = true
+reorder_impl_items = true
+use_field_init_shorthand = true
+wrap_comments = true
+version = "Two"
diff --git a/src/core/coordinate.rs b/src/core/coordinate.rs
@@ -1,4 +1,5 @@
-//! A 0-based location within a genome consisting of a contig, a position, and a strand.
+//! A 0-based location within a genome consisting of a contig, a position, and a
+//! strand.
 
 use crate::core::Interval;
 use crate::core::Strand;
@@ -46,11 +47,11 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
+    /// use chain::core::coordinate::Error;
     /// use chain::core::Coordinate;
     /// use chain::core::Position;
     /// use chain::core::Strand;
-    /// use chain::core::coordinate::Error;
+    /// use chainfile as chain;
     ///
     /// // Positive-stranded
     ///
@@ -75,7 +76,8 @@ impl Coordinate {
     ///
     /// // Attempting to create negative-bound on positive strand
     ///
-    /// let err = Coordinate::try_new("seq0", Position::negative_bound(), Strand::Positive).unwrap_err();
+    /// let err =
+    ///     Coordinate::try_new("seq0", Position::negative_bound(), Strand::Positive).unwrap_err();
     /// assert_eq!(err, Error::NegativeBoundOnNonNegativeStrand);
     ///
     /// # Ok::<(), Box<dyn std::error::Error>>(())
@@ -107,10 +109,10 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// let coordinate = Coordinate::negative_bound("seq0");
     /// assert_eq!(coordinate.contig().as_str(), "seq0");
@@ -128,9 +130,9 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Zero-based coordinate
     ///
@@ -153,10 +155,10 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Zero-based coordinate
     ///
@@ -179,9 +181,9 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Zero-based coordinate
     ///
@@ -211,10 +213,10 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Positive-stranded
     ///
@@ -330,10 +332,10 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Positive-stranded
     ///
@@ -430,17 +432,19 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Interval;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Positive-stranded that falls within interval
     ///
     /// let coordinate = Coordinate::try_new("seq0", 0, Strand::Positive)?;
     /// let interval = "seq0:0-1000".parse::<Interval>()?;
-    /// let result = coordinate.move_forward_checked_bounds(10, &interval).unwrap()?;
+    /// let result = coordinate
+    ///     .move_forward_checked_bounds(10, &interval)
+    ///     .unwrap()?;
     ///
     /// assert_eq!(result.contig(), &String::from("seq0"));
     /// assert_eq!(result.position(), &Position::new(10));
@@ -450,7 +454,9 @@ impl Coordinate {
     ///
     /// let coordinate = Coordinate::try_new("seq0", 1000, Strand::Negative)?;
     /// let interval = "seq0:1000-0".parse::<Interval>()?;
-    /// let result = coordinate.move_forward_checked_bounds(10, &interval).unwrap()?;
+    /// let result = coordinate
+    ///     .move_forward_checked_bounds(10, &interval)
+    ///     .unwrap()?;
     ///
     /// assert_eq!(result.contig(), &String::from("seq0"));
     /// assert_eq!(result.position(), &Position::new(990));
@@ -502,17 +508,19 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Interval;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Positive-stranded that falls within interval
     ///
     /// let coordinate = Coordinate::try_new("seq0", 500, Strand::Positive)?;
     /// let interval = "seq0:0-1000".parse::<Interval>()?;
-    /// let result = coordinate.move_backward_checked_bounds(10, &interval).unwrap()?;
+    /// let result = coordinate
+    ///     .move_backward_checked_bounds(10, &interval)
+    ///     .unwrap()?;
     ///
     /// assert_eq!(result.contig(), &String::from("seq0"));
     /// assert_eq!(result.position(), &Position::new(490));
@@ -522,7 +530,9 @@ impl Coordinate {
     ///
     /// let coordinate = Coordinate::try_new("seq0", 500, Strand::Negative)?;
     /// let interval = "seq0:1000-0".parse::<Interval>()?;
-    /// let result = coordinate.move_backward_checked_bounds(10, &interval).unwrap()?;
+    /// let result = coordinate
+    ///     .move_backward_checked_bounds(10, &interval)
+    ///     .unwrap()?;
     ///
     /// assert_eq!(result.contig(), &String::from("seq0"));
     /// assert_eq!(result.position(), &Position::new(510));
@@ -540,7 +550,9 @@ impl Coordinate {
     ///
     /// let coordinate = Coordinate::negative_bound("seq0");
     /// let interval = "seq0:10-$".parse::<Interval>()?;
-    /// let result = coordinate.move_backward_checked_bounds(11, &interval).unwrap()?;
+    /// let result = coordinate
+    ///     .move_backward_checked_bounds(11, &interval)
+    ///     .unwrap()?;
     ///
     /// assert_eq!(result.contig(), &String::from("seq0"));
     /// assert_eq!(result.position(), &Position::new(10));
@@ -581,11 +593,11 @@ impl Coordinate {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Coordinate;
     /// use chain::core::Interval;
     /// use chain::core::Position;
     /// use chain::core::Strand;
+    /// use chainfile as chain;
     ///
     /// // Positive-strand
     /// let coordinate = Coordinate::try_new("seq0", 5, Strand::Positive)?;
@@ -613,16 +625,16 @@ impl Coordinate {
         let position = match self.position() {
             Position::ZeroBased(position) => position,
             Position::NegativeBound => {
-                return Coordinate::try_new(self.contig(), contig_size, self.strand().clone())
+                return Coordinate::try_new(self.contig(), contig_size, self.strand().clone());
             }
         };
 
         let new_position_plus_one = contig_size - position;
         if new_position_plus_one == 0 {
             match self.strand() {
                 Strand::Positive => unreachable!(
-                    "it should never be possible to want to return the negative bound \
-                    if the source coordinate is on the positive strand"
+                    "it should never be possible to want to return the negative bound if the \
+                     source coordinate is on the positive strand"
                 ),
                 Strand::Negative => Ok(Coordinate::negative_bound(self.contig())),
             }

diff --git a/src/core/coordinate/position.rs b/src/core/coordinate/position.rs
@@ -147,12 +147,7 @@ impl std::ops::Sub for &Position {
 
 impl PartialOrd for Position {
     fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
-        match (self, other) {
-            (Position::ZeroBased(a), Position::ZeroBased(b)) => a.partial_cmp(b),
-            (Position::ZeroBased(_), Position::NegativeBound) => Some(std::cmp::Ordering::Greater),
-            (Position::NegativeBound, Position::ZeroBased(_)) => Some(std::cmp::Ordering::Less),
-            (Position::NegativeBound, Position::NegativeBound) => Some(std::cmp::Ordering::Equal),
-        }
+        Some(self.cmp(other))
     }
 }
 
@@ -182,8 +177,8 @@ impl Position {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Position;
+    /// use chainfile as chain;
     ///
     /// let position = Position::new(0);
     /// assert!(matches!(position, Position::ZeroBased(0)));
@@ -197,8 +192,8 @@ impl Position {
     /// # Examples
     ///
     /// ```
-    /// use chainfile as chain;
     /// use chain::core::Position;
+    /// use chainfile as chain;
     ///
     /// let position = Position::negative_bound();
     /// assert!(matches!(position, Position::NegativeBound));