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Switch from Travis to Github Actions (#21)
* Switch from Travis to Github Actions * Clippy fixes Co-authored-by: Franklin Delehelle <[email protected]>
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‎.github/workflows/rust.yml‎

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name: CI
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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jobs:
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Formatting:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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override: true
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components: rustfmt
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- name: Check format
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run: cargo fmt -- --check
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Linting:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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override: true
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components: clippy
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- name: Lint with clippy
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uses: actions-rs/clippy-check@v1
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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Testing:
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needs: Formatting
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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build: [linux, windows, macos]
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include:
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- build: macos
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os: macos-latest
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rust: stable
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- build: windows
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os: windows-latest
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rust: stable
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- build: linux
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os: ubuntu-latest
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rust: stable
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- uses: actions-rs/toolchain@v1
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with:
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toolchain: ${{ matrix.rust }}
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override: true
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- name: Install ${{ matrix.rust }} toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: ${{ matrix.rust }}
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override: true
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- name: Run tests
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uses: actions-rs/cargo@v1
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with:
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command: test
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args: --all --no-fail-fast
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Coverage:
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needs: Formatting
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install nightly toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: nightly
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override: true
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- name: Install cargo-tarpaulin
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uses: actions-rs/[email protected]
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with:
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crate: cargo-tarpaulin
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version: latest
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use-tool-cache: true
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- name: Coverage with tarpaulin
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run: cargo tarpaulin --all --all-features --timeout 600 --out Lcov -- --test-threads 1
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- name: Upload coverage
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uses: coverallsapp/github-action@master
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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path-to-lcov: ./lcov.info

‎.travis.yml‎

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This file was deleted.

‎Cargo.toml‎

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@@ -8,7 +8,6 @@ repository = "https://github.com/rust-bio/rust-bio"
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documentation = "https://docs.rs/bio"
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readme = "README.md"
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license = "MIT"
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license-file = "LICENSE.md"
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[dependencies]

‎src/alignment.rs‎

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Original file line numberDiff line numberDiff line change
@@ -219,7 +219,7 @@ impl Alignment {
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x_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[x[x_i]])));
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x_i += 1;
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222-
inb_pretty.push_str("|");
222+
inb_pretty.push('|');
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y_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[y[y_i]])));
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y_i += 1;
@@ -304,13 +304,13 @@ impl Alignment {
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while idx < ml {
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let rng = idx..min(idx + step, ml);
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s.push_str(&x_pretty[rng.clone()]);
307-
s.push_str("\n");
307+
s.push('\n');
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309309
s.push_str(&inb_pretty[rng.clone()]);
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s.push_str("\n");
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s.push('\n');
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312312
s.push_str(&y_pretty[rng]);
313-
s.push_str("\n");
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s.push('\n');
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s.push_str("\n\n");
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idx += step;

‎src/annot/contig.rs‎

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Original file line numberDiff line numberDiff line change
@@ -63,10 +63,10 @@ impl<R, S> Contig<R, S> {
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/// ```
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pub fn new(refid: R, start: isize, length: usize, strand: S) -> Self {
6565
Contig {
66-
refid: refid,
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start: start,
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length: length,
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strand: strand,
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refid,
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start,
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length,
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strand,
7070
}
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}
7272

@@ -118,8 +118,8 @@ impl<R, S> Contig<R, S> {
118118

119119
Ok(Contig {
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refid: pos.refid().clone(),
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start: start,
122-
length: length,
121+
start,
122+
length,
123123
strand: pos.strand(),
124124
})
125125
}
@@ -131,7 +131,7 @@ impl<R, S> Contig<R, S> {
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refid: self.refid,
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start: self.start,
133133
length: self.length,
134-
strand: strand,
134+
strand,
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}
136136
}
137137
}
@@ -313,21 +313,15 @@ where
313313
static ref CONTIG_RE: Regex = Regex::new(r"^(.*):(\d+)-(\d+)(\([+-]\))?$").unwrap();
314314
}
315315

316-
let cap = CONTIG_RE
317-
.captures(s)
318-
.ok_or_else(|| ParseAnnotError::BadAnnot)?;
316+
let cap = CONTIG_RE.captures(s).ok_or(ParseAnnotError::BadAnnot)?;
319317

320-
let start = cap[2]
321-
.parse::<isize>()
322-
.map_err(|e| ParseAnnotError::ParseInt(e))?;
323-
let end = cap[3]
324-
.parse::<isize>()
325-
.map_err(|e| ParseAnnotError::ParseInt(e))?;
318+
let start = cap[2].parse::<isize>().map_err(ParseAnnotError::ParseInt)?;
319+
let end = cap[3].parse::<isize>().map_err(ParseAnnotError::ParseInt)?;
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let strand = cap
327321
.get(4)
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.map_or("", |m| m.as_str())
329323
.parse::<S>()
330-
.map_err(|e| ParseAnnotError::ParseStrand(e))?;
324+
.map_err(ParseAnnotError::ParseStrand)?;
331325

332326
if start <= end {
333327
Ok(Contig::new(

‎src/annot/pos.rs‎

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@@ -107,8 +107,8 @@ where
107107
/// ```
108108
fn add_assign(&mut self, dist: T) {
109109
match self.strand {
110-
ReqStrand::Forward => self.pos += dist.into(),
111-
ReqStrand::Reverse => self.pos -= dist.into(),
110+
ReqStrand::Forward => self.pos += dist,
111+
ReqStrand::Reverse => self.pos -= dist,
112112
}
113113
}
114114
}
@@ -138,8 +138,8 @@ where
138138
/// ```
139139
fn sub_assign(&mut self, dist: T) {
140140
match self.strand {
141-
ReqStrand::Forward => self.pos -= dist.into(),
142-
ReqStrand::Reverse => self.pos += dist.into(),
141+
ReqStrand::Forward => self.pos -= dist,
142+
ReqStrand::Reverse => self.pos += dist,
143143
}
144144
}
145145
}
@@ -169,9 +169,7 @@ impl<R, S> Loc for Pos<R, S> {
169169
Self::Strand: Into<ReqStrand> + Copy,
170170
T: Neg<Output = T> + Copy,
171171
{
172-
if self.refid != pos.refid {
173-
None
174-
} else if self.pos != pos.pos {
172+
if (self.refid != pos.refid) || (self.pos != pos.pos) {
175173
None
176174
} else {
177175
Some(Pos::new(
@@ -252,21 +250,17 @@ where
252250
static ref POS_RE: Regex = Regex::new(r"^(.*):(\d+)(\([+-]\))?$").unwrap();
253251
}
254252

255-
let cap = POS_RE
256-
.captures(s)
257-
.ok_or_else(|| ParseAnnotError::BadAnnot)?;
253+
let cap = POS_RE.captures(s).ok_or(ParseAnnotError::BadAnnot)?;
258254

259255
let strand = cap
260256
.get(3)
261257
.map_or("", |m| m.as_str())
262258
.parse::<S>()
263-
.map_err(|e| ParseAnnotError::ParseStrand(e))?;
259+
.map_err(ParseAnnotError::ParseStrand)?;
264260

265261
Ok(Pos::new(
266262
R::from(cap[1].to_owned()),
267-
cap[2]
268-
.parse::<isize>()
269-
.map_err(|e| ParseAnnotError::ParseInt(e))?,
263+
cap[2].parse::<isize>().map_err(ParseAnnotError::ParseInt)?,
270264
strand,
271265
))
272266
}

‎src/annot/refids.rs‎

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@@ -41,6 +41,12 @@ pub struct RefIDSet<R> {
4141
refids: HashMap<String, R>,
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}
4343

44+
impl<R> Default for RefIDSet<R> {
45+
fn default() -> Self {
46+
Self::new()
47+
}
48+
}
49+
4450
impl<R> RefIDSet<R> {
4551
/// Create a new, empty table of interned reference names
4652
pub fn new() -> Self {

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