make serde optional (#23)

Co-authored-by: Johannes Köster <[email protected]>

Author: pmarks

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bio-types"
-version = "0.7.1-alpha.0"
+version = "0.8.0-alpha.0"
 authors = ["Johannes Köster <[email protected]>"]
 description = "A collection of common biomedical types for use in rust-bio and rust-htslib."
 homepage = "https://rust-bio.github.io"
@@ -11,8 +11,7 @@ license = "MIT"
 
 
 [dependencies]
-serde = "1.0"
-serde_derive = "1.0"
+serde = { version = "^1", optional = true, features=["derive"] }
 quick-error = "1.2"
 regex = "1.0"
 lazy_static = "1.1"

src/alignment.rs

@@ -5,6 +5,9 @@
 
 //! Types for representing pairwise sequence alignments
 
+#[cfg(feature = "serde")]
+use serde::{Deserialize, Serialize};
+
 pub type TextSlice<'a> = &'a [u8];
 
 /// Alignment operations supported are match, substitution, insertion, deletion
@@ -15,7 +18,8 @@ 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 = "serde", derive(Serialize, Deserialize))]
+#[derive(Eq, PartialEq, Debug, Copy, Clone)]
 pub enum AlignmentOperation {
     Match,
     Subst,
@@ -33,7 +37,8 @@ pub enum AlignmentOperation {
 /// appropriately set.
 ///
 /// The default alignment mode is Global.
-#[derive(Debug, PartialEq, Eq, Copy, Clone, Serialize, Deserialize)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug, PartialEq, Eq, Copy, Clone)]
 pub enum AlignmentMode {
     Local,
     Semiglobal,
@@ -53,7 +58,8 @@ 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 = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug, Eq, PartialEq, Clone, Default)]
 pub struct Alignment {
     /// Smith-Waterman alignment score
     pub score: i32,

src/genome.rs

@@ -1,6 +1,9 @@
 use std::cmp;
 use std::ops::Range;
 
+#[cfg(feature = "serde")]
+use serde::{Deserialize, Serialize};
+
 pub type Position = u64;
 pub type Length = u64;
 
@@ -19,8 +22,8 @@ pub trait AbstractInterval {
             && locus.pos() < self.range().end
     }
 }
-
-#[derive(new, Debug, PartialEq, Eq, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(new, Debug, PartialEq, Eq, Clone, Hash)]
 pub struct Interval {
     contig: String,
     range: Range<Position>,
@@ -67,7 +70,8 @@ pub trait AbstractLocus {
     fn pos(&self) -> Position;
 }
 
-#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash)]
 pub struct Locus {
     contig: String,
     pos: Position,

src/lib.rs

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

src/variant.rs

@@ -1,13 +1,17 @@
 use genome;
 use sequence::{Base, Sequence};
 
+#[cfg(feature = "serde")]
+use serde::{Deserialize, Serialize};
+
 /// A trait for providing variant information. This can e.g. be implemented by file readers.
 pub trait AbstractVariant: genome::AbstractLocus {
     fn kind(&self) -> &Kind;
 }
 
 /// Possible genomic variants.
-#[derive(Debug, PartialEq, Eq, Clone, Hash, Serialize, Deserialize)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug, PartialEq, Eq, Clone, Hash)]
 pub enum Kind {
     SNV(Base),
     MNV(Sequence),