Adding feature "serde_feature" to enable support.

.github/workflow/rust.yml

@@ -0,0 +1,112 @@
+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: [beta, stable, windows, macos]
+        include:
+          - build: macos
+            os: macos-latest
+            rust: stable
+          - build: windows
+            os: windows-latest
+            rust: stable
+          - build: beta
+            os: ubuntu-latest
+            rust: beta
+          - build: stable
+            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/[email protected]
+        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

CHANGELOG.md

@@ -0,0 +1,11 @@
+# Change Log
+All notable changes to this project will be documented in this file.
+This project adheres to [Semantic Versioning](http://semver.org/).
+
+## [next]
+- BREAKING: Adding serialization with `serde` as a feature: `serde_feature`.
+- Adding `Debug` and `Serialize`/`Deserialize` traits to a couple of more types.
+- Moving from Travis CI to Github Actions for CI.
+
+## [0.7.0] - 2020-07-02
+No changelog is kept up to and including this version.

Cargo.toml

@@ -7,14 +7,16 @@ homepage = "https://rust-bio.github.io"
 repository = "https://github.com/rust-bio/rust-bio"
 documentation = "https://docs.rs/bio"
 readme = "README.md"
-license = "MIT"
 license-file = "LICENSE.md"
 
+[features]
+serde_feature = ["serde", "serde_derive"]
 
 [dependencies]
-serde = "1.0"
-serde_derive = "1.0"
 quick-error = "1.2"
 regex = "1.0"
 lazy_static = "1.1"
 derive-new = "0.5"
+
+serde = { version = "1.0", optional = true }
+serde_derive = { version = "1.0", optional = true }

src/alignment.rs

@@ -15,7 +15,8 @@ pub type TextSlice<'a> = &'a [u8];
 /// value associated with the clipping operations are the lengths clipped. In case
 /// of standard modes like Global, Semi-Global and Local alignment, the clip operations
 /// are filtered out
-#[derive(Eq, PartialEq, Debug, Copy, Clone, Serialize, Deserialize)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(Eq, PartialEq, Debug, Copy, Clone)]
 pub enum AlignmentOperation {
     Match,
     Subst,
@@ -33,7 +34,8 @@ pub enum AlignmentOperation {
 /// appropriately set.
 ///
 /// The default alignment mode is Global.
-#[derive(Debug, PartialEq, Eq, Copy, Clone, Serialize, Deserialize)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(Debug, PartialEq, Eq, Copy, Clone)]
 pub enum AlignmentMode {
     Local,
     Semiglobal,
@@ -53,7 +55,8 @@ impl Default for AlignmentMode {
 /// lengths of sequences x and y, and the alignment edit operations. The start position
 /// and end position of the alignment does not include the clipped regions. The length
 /// of clipped regions are already encapsulated in the Alignment Operation.
-#[derive(Debug, Eq, PartialEq, Clone, Serialize, Deserialize, Default)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(Debug, Eq, PartialEq, Clone, Default)]
 pub struct Alignment {
     /// Smith-Waterman alignment score
     pub score: i32,

src/annot/contig.rs

@@ -43,6 +43,7 @@ use strand::*;
 /// # }
 /// # fn main() { try_main().unwrap(); }
 /// ```
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Hash, PartialEq, Eq)]
 pub struct Contig<R, S> {
     refid: R,

src/annot/mod.rs

@@ -54,6 +54,7 @@ pub mod spliced;
 
 // Errors that arise in parsing annotations.
 quick_error! {
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone)]
     pub enum ParseAnnotError {
         BadAnnot {
@@ -76,6 +77,7 @@ quick_error! {
 
 // Errors that arise in maniuplating annotations
 quick_error! {
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone)]
     pub enum AnnotError {
         NoStrand {

src/annot/pos.rs

@@ -42,6 +42,7 @@ use strand::*;
 /// # }
 /// # fn main() { try_main().unwrap(); }
 /// ```
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Hash, PartialEq, Eq)]
 pub struct Pos<R, S> {
     refid: R,

src/annot/refids.rs

@@ -37,6 +37,8 @@ use std::ops::Deref;
 ///   assert_eq!(Rc::strong_count(&chr_i), 7);
 /// }
 /// ```
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(Debug)]
 pub struct RefIDSet<R> {
     refids: HashMap<String, R>,
 }

src/annot/spliced.rs

@@ -37,6 +37,7 @@ mod inex {
 
     use super::SplicingError;
 
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone, Hash, PartialEq, Eq)]
     pub struct InEx {
         intron_length: usize,
@@ -69,6 +70,7 @@ mod inex {
 
     // Represent just the start (relative to the start of the location) and length of exons
     // Useful for internal coordinate math
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone, Hash, PartialEq, Eq)]
     pub struct Ex {
         start: usize,
@@ -88,12 +90,15 @@ mod inex {
     }
 
     // Iterator over the Ex exons from lowest to highest coordinate
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+    #[derive(Debug)]
     pub struct Exes<'a> {
         state: ExesState,
         curr_start: usize,
         rest: Iter<'a, InEx>,
     }
 
+    #[derive(Debug)]
     enum ExesState {
         FirstExon(usize),
         LaterExon,
@@ -140,6 +145,7 @@ mod inex {
 
     // Represent just the start (relative to the start of the location) and length of introns
     // Useful for internal coordinate math
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone, Hash, PartialEq, Eq)]
     pub struct In {
         start: usize,
@@ -160,6 +166,8 @@ mod inex {
     }
 
     // Iterator over the Ex introns from lowest to highest coordinate
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+    #[derive(Debug)]
     pub struct Ins<'a> {
         curr_start: usize,
         rest: Iter<'a, InEx>,
@@ -223,6 +231,7 @@ mod inex {
 /// # }
 /// # fn main() { try_main().unwrap(); }
 /// ```
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Hash, PartialEq, Eq)]
 pub struct Spliced<R, S> {
     refid: R,
@@ -687,6 +696,7 @@ pub type SeqSplicedStranded = Spliced<String, ReqStrand>;
 pub type SeqSplicedUnstranded = Spliced<String, NoStrand>;
 
 quick_error! {
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone)]
     pub enum SplicingError {
         IntronLength {

src/genome.rs

@@ -20,7 +20,8 @@ pub trait AbstractInterval {
     }
 }
 
-#[derive(new, Debug, PartialEq, Eq, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(new, Debug, PartialEq, Eq, Clone, Hash)]
 pub struct Interval {
     contig: String,
     range: Range<Position>,
@@ -67,7 +68,8 @@ pub trait AbstractLocus {
     fn pos(&self) -> Position;
 }
 
-#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash)]
 pub struct Locus {
     contig: String,
     pos: Position,

src/lib.rs

@@ -1,4 +1,5 @@
-#[macro_use]
+#[cfg_attr(feature = "serde_feature", macro_use)]
+#[cfg(feature = "serde_feature")]
 extern crate serde_derive;
 #[macro_use]
 extern crate quick_error;

src/strand.rs

@@ -10,6 +10,7 @@ use std::ops::Neg;
 use std::str::FromStr;
 
 /// Strand information.
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Copy)]
 pub enum Strand {
     Forward,
@@ -134,6 +135,7 @@ impl From<NoStrand> for Strand {
 }
 
 /// Strand information for annotations that require a strand.
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Hash, PartialEq, Eq, Ord, PartialOrd, Copy)]
 pub enum ReqStrand {
     Forward,
@@ -243,6 +245,7 @@ impl Neg for ReqStrand {
 
 /// Strand information for annotations that definitively have no
 /// strand information.
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 #[derive(Debug, Clone, Hash, PartialEq, Eq, Ord, PartialOrd, Copy)]
 pub enum NoStrand {
     Unknown,
@@ -302,6 +305,7 @@ where
 }
 
 quick_error! {
+    #[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
     #[derive(Debug, Clone)]
     pub enum StrandError {
         InvalidChar(invalid_char: char) {

src/variant.rs

@@ -7,7 +7,8 @@ pub trait AbstractVariant: genome::AbstractLocus {
 }
 
 /// Possible genomic variants.
-#[derive(Debug, PartialEq, Eq, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
+#[derive(Debug, PartialEq, Eq, Clone, Hash)]
 pub enum Kind {
     SNV(Base),
     MNV(Sequence),