Switch from Travis to Github Actions (#21)

* Switch from Travis to Github Actions * Clippy fixes Co-authored-by: Franklin Delehelle <franklin.delehelle@odena.eu>
rust-bio · Jan 6, 2021 · 27c0e7d · 27c0e7d
1 parent c2206e3
commit 27c0e7d
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Showing 11 changed files with 173 additions and 121 deletions.
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -0,0 +1,109 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: rustfmt
+
+      - name: Check format
+        run: cargo fmt -- --check
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: clippy
+
+      - name: Lint with clippy
+        uses: actions-rs/clippy-check@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+  Testing:
+    needs: Formatting
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        build: [linux, windows, macos]
+        include:
+          - build: macos
+            os: macos-latest
+            rust: stable
+          - build: windows
+            os: windows-latest
+            rust: stable
+          - build: linux
+            os: ubuntu-latest
+            rust: stable
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: ${{ matrix.rust }}
+          override: true
+
+      - name: Install ${{ matrix.rust }} toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: ${{ matrix.rust }}
+          override: true
+
+      - name: Run tests
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all --no-fail-fast
+
+  Coverage:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install nightly toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: nightly
+          override: true
+
+      - name: Install cargo-tarpaulin
+        uses: actions-rs/install@v0.1
+        with:
+          crate: cargo-tarpaulin
+          version: latest
+          use-tool-cache: true
+
+      - name: Coverage with tarpaulin
+        run: cargo tarpaulin --all --all-features --timeout 600 --out Lcov -- --test-threads 1
+
+      - name: Upload coverage
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./lcov.info
diff --git a/.travis.yml b/.travis.yml
diff --git a/Cargo.toml b/Cargo.toml
@@ -8,7 +8,6 @@ repository = "https://github.com/rust-bio/rust-bio"
 documentation = "https://docs.rs/bio"
 readme = "README.md"
 license = "MIT"
-license-file = "LICENSE.md"
 
 
 [dependencies]

diff --git a/src/alignment.rs b/src/alignment.rs
@@ -219,7 +219,7 @@ impl Alignment {
                         x_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[x[x_i]])));
                         x_i += 1;
 
-                        inb_pretty.push_str("|");
+                        inb_pretty.push('|');
 
                         y_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[y[y_i]])));
                         y_i += 1;
@@ -304,13 +304,13 @@ impl Alignment {
         while idx < ml {
             let rng = idx..min(idx + step, ml);
             s.push_str(&x_pretty[rng.clone()]);
-            s.push_str("\n");
+            s.push('\n');
 
             s.push_str(&inb_pretty[rng.clone()]);
-            s.push_str("\n");
+            s.push('\n');
 
             s.push_str(&y_pretty[rng]);
-            s.push_str("\n");
+            s.push('\n');
 
             s.push_str("\n\n");
             idx += step;

diff --git a/src/annot/contig.rs b/src/annot/contig.rs
@@ -63,10 +63,10 @@ impl<R, S> Contig<R, S> {
     /// ```
     pub fn new(refid: R, start: isize, length: usize, strand: S) -> Self {
         Contig {
-            refid: refid,
-            start: start,
-            length: length,
-            strand: strand,
+            refid,
+            start,
+            length,
+            strand,
         }
     }
 
@@ -118,8 +118,8 @@ impl<R, S> Contig<R, S> {
 
             Ok(Contig {
                 refid: pos.refid().clone(),
-                start: start,
-                length: length,
+                start,
+                length,
                 strand: pos.strand(),
             })
         }
@@ -131,7 +131,7 @@ impl<R, S> Contig<R, S> {
             refid: self.refid,
             start: self.start,
             length: self.length,
-            strand: strand,
+            strand,
         }
     }
 }
@@ -313,21 +313,15 @@ where
             static ref CONTIG_RE: Regex = Regex::new(r"^(.*):(\d+)-(\d+)(\([+-]\))?$").unwrap();
         }
 
-        let cap = CONTIG_RE
-            .captures(s)
-            .ok_or_else(|| ParseAnnotError::BadAnnot)?;
+        let cap = CONTIG_RE.captures(s).ok_or(ParseAnnotError::BadAnnot)?;
 
-        let start = cap[2]
-            .parse::<isize>()
-            .map_err(|e| ParseAnnotError::ParseInt(e))?;
-        let end = cap[3]
-            .parse::<isize>()
-            .map_err(|e| ParseAnnotError::ParseInt(e))?;
+        let start = cap[2].parse::<isize>().map_err(ParseAnnotError::ParseInt)?;
+        let end = cap[3].parse::<isize>().map_err(ParseAnnotError::ParseInt)?;
         let strand = cap
             .get(4)
             .map_or("", |m| m.as_str())
             .parse::<S>()
-            .map_err(|e| ParseAnnotError::ParseStrand(e))?;
+            .map_err(ParseAnnotError::ParseStrand)?;
 
         if start <= end {
             Ok(Contig::new(

diff --git a/src/annot/pos.rs b/src/annot/pos.rs
@@ -107,8 +107,8 @@ where
     /// ```
     fn add_assign(&mut self, dist: T) {
         match self.strand {
-            ReqStrand::Forward => self.pos += dist.into(),
-            ReqStrand::Reverse => self.pos -= dist.into(),
+            ReqStrand::Forward => self.pos += dist,
+            ReqStrand::Reverse => self.pos -= dist,
         }
     }
 }
@@ -138,8 +138,8 @@ where
     /// ```
     fn sub_assign(&mut self, dist: T) {
         match self.strand {
-            ReqStrand::Forward => self.pos -= dist.into(),
-            ReqStrand::Reverse => self.pos += dist.into(),
+            ReqStrand::Forward => self.pos -= dist,
+            ReqStrand::Reverse => self.pos += dist,
         }
     }
 }
@@ -169,9 +169,7 @@ impl<R, S> Loc for Pos<R, S> {
         Self::Strand: Into<ReqStrand> + Copy,
         T: Neg<Output = T> + Copy,
     {
-        if self.refid != pos.refid {
-            None
-        } else if self.pos != pos.pos {
+        if (self.refid != pos.refid) || (self.pos != pos.pos) {
             None
         } else {
             Some(Pos::new(
@@ -252,21 +250,17 @@ where
             static ref POS_RE: Regex = Regex::new(r"^(.*):(\d+)(\([+-]\))?$").unwrap();
         }
 
-        let cap = POS_RE
-            .captures(s)
-            .ok_or_else(|| ParseAnnotError::BadAnnot)?;
+        let cap = POS_RE.captures(s).ok_or(ParseAnnotError::BadAnnot)?;
 
         let strand = cap
             .get(3)
             .map_or("", |m| m.as_str())
             .parse::<S>()
-            .map_err(|e| ParseAnnotError::ParseStrand(e))?;
+            .map_err(ParseAnnotError::ParseStrand)?;
 
         Ok(Pos::new(
             R::from(cap[1].to_owned()),
-            cap[2]
-                .parse::<isize>()
-                .map_err(|e| ParseAnnotError::ParseInt(e))?,
+            cap[2].parse::<isize>().map_err(ParseAnnotError::ParseInt)?,
             strand,
         ))
     }

diff --git a/src/annot/refids.rs b/src/annot/refids.rs
@@ -41,6 +41,12 @@ pub struct RefIDSet<R> {
     refids: HashMap<String, R>,
 }
 
+impl<R> Default for RefIDSet<R> {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
 impl<R> RefIDSet<R> {
     /// Create a new, empty table of interned reference names
     pub fn new() -> Self {