update to 2018 edition (#24)

* make serde optional

* update to 2018 edition

* try to cache

* fixes

* add lock

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

.github/workflows/rust.yml

@@ -62,6 +62,14 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
+
       - uses: actions-rs/toolchain@v1
         with:
           toolchain: ${{ matrix.rust }}
@@ -85,11 +93,19 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
+
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
 
       - name: Install nightly toolchain
         uses: actions-rs/toolchain@v1
         with:
-          toolchain: nightly
+          toolchain: stable
           override: true
 
       - name: Install cargo-tarpaulin

Cargo.toml

@@ -8,6 +8,8 @@ repository = "https://github.com/rust-bio/rust-bio"
 documentation = "https://docs.rs/bio"
 readme = "README.md"
 license = "MIT"
+license-file = "LICENSE.md"
+edition = "2018"
 
 
 [dependencies]

src/annot/contig.rs

@@ -14,10 +14,10 @@ use std::str::FromStr;
 
 use regex::Regex;
 
-use annot::loc::Loc;
-use annot::pos::Pos;
-use annot::*;
-use strand::*;
+use crate::annot::loc::Loc;
+use crate::annot::pos::Pos;
+use crate::annot::*;
+use crate::strand::*;
 
 /// Contiguous sequence region on a particular, named sequence (e.g. a
 /// chromosome)

src/annot/loc.rs

@@ -8,10 +8,10 @@
 
 use std::ops::Neg;
 
-use annot::contig::Contig;
-use annot::pos::Pos;
+use crate::annot::contig::Contig;
+use crate::annot::pos::Pos;
 
-use strand::*;
+use crate::strand::*;
 
 /// A trait for a sequence location -- a defined region on a named
 /// chromosome (or other reference sequence), which may also have
@@ -80,7 +80,7 @@ pub trait Loc {
         Self::Strand: Into<ReqStrand> + Copy,
         T: Neg<Output = T> + Copy;
 
-    fn contig_intersection<T>(&self, &Contig<Self::RefID, T>) -> Option<Self>
+    fn contig_intersection<T>(&self, other: &Contig<Self::RefID, T>) -> Option<Self>
     where
         Self: ::std::marker::Sized,
         Self::RefID: PartialEq + Clone,

src/annot/mod.rs

@@ -44,7 +44,7 @@
 //! # fn main() { try_main().unwrap(); }
 //! ```
 
-use strand;
+use crate::strand;
 
 pub mod contig;
 pub mod loc;

src/annot/pos.rs

@@ -14,10 +14,10 @@ use std::str::FromStr;
 
 use regex::Regex;
 
-use annot::contig::Contig;
-use annot::loc::Loc;
-use annot::*;
-use strand::*;
+use crate::annot::contig::Contig;
+use crate::annot::loc::Loc;
+use crate::annot::*;
+use crate::strand::*;
 
 /// Position on a particular, named sequence (e.g. a chromosome).
 ///

src/annot/spliced.rs

@@ -15,11 +15,11 @@ use std::str::FromStr;
 
 use regex::Regex;
 
-use annot::contig::Contig;
-use annot::loc::Loc;
-use annot::pos::Pos;
-use annot::*;
-use strand::*;
+use crate::annot::contig::Contig;
+use crate::annot::loc::Loc;
+use crate::annot::pos::Pos;
+use crate::annot::*;
+use crate::strand::*;
 
 // The spliced location representation inherently cannot represent
 // "bad" splicing structures. Locations comprise a first exon length,

src/strand.rs

@@ -281,7 +281,7 @@ impl Display for NoStrand {
 pub trait Same {
     /// Indicate when two strands are the "same" -- two
     /// unknown/unspecified strands are the "same" but are not equal.
-    fn same(&self, &Self) -> bool;
+    fn same(&self, other: &Self) -> bool;
 }
 
 impl<T> Same for Option<T>

src/variant.rs

@@ -1,5 +1,5 @@
-use genome;
-use sequence::{Base, Sequence};
+use crate::genome;
+use crate::sequence::{Base, Sequence};
 
 #[cfg(feature = "serde")]
 use serde::{Deserialize, Serialize};