use simd_json instead of serde_json

sourmash-bio · Dec 19, 2024 · a35e64b · a35e64b
1 parent d9aad8e
commit a35e64b
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Showing 8 changed files with 129 additions and 16 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
@@ -55,8 +55,8 @@ rayon = { version = "1.10.0", optional = true }
 rkyv = { version = "0.7.44", optional = true }
 roaring = "0.10.9"
 roots = "0.0.8"
+simd-json = "0.14.3"
 serde = { version = "1.0.216", features = ["derive"] }
-serde_json = "1.0.133"
 statrs = "0.18.0"
 streaming-stats = "0.2.3"
 thiserror = "2.0"

diff --git a/src/core/src/errors.rs b/src/core/src/errors.rs
@@ -68,7 +68,7 @@ pub enum SourmashError {
     StorageError(#[from] crate::storage::StorageError),
 
     #[error(transparent)]
-    SerdeError(#[from] serde_json::error::Error),
+    SerdeError(#[from] simd_json::Error),
 
     #[error(transparent)]
     NifflerError(#[from] niffler::Error),

diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
@@ -576,7 +576,7 @@ impl Signature {
     {
         let (rdr, _format) = niffler::get_reader(Box::new(rdr))?;
 
-        let sigs: Vec<Signature> = serde_json::from_reader(rdr)?;
+        let sigs: Vec<Signature> = simd_json::from_reader(rdr)?;
         Ok(sigs)
     }
 
@@ -787,7 +787,7 @@ impl ToWriter for Signature {
     where
         W: io::Write,
     {
-        serde_json::to_writer(writer, &vec![&self])?;
+        simd_json::to_writer(writer, &vec![&self])?;
         Ok(())
     }
 }
@@ -797,7 +797,7 @@ impl ToWriter for Vec<&Signature> {
     where
         W: io::Write,
     {
-        serde_json::to_writer(writer, &self)?;
+        simd_json::to_writer(writer, &self)?;
         Ok(())
     }
 }

diff --git a/src/core/src/sketch/minhash.rs b/src/core/src/sketch/minhash.rs
@@ -190,7 +190,7 @@ impl ToWriter for KmerMinHash {
     where
         W: io::Write,
     {
-        serde_json::to_writer(writer, &self)?;
+        simd_json::to_writer(writer, &self)?;
         Ok(())
     }
 }
@@ -875,7 +875,7 @@ impl KmerMinHash {
     {
         let (rdr, _format) = niffler::get_reader(Box::new(rdr))?;
 
-        let mh: KmerMinHash = serde_json::from_reader(rdr)?;
+        let mh: KmerMinHash = simd_json::from_reader(rdr)?;
         Ok(mh)
     }
 }
@@ -1140,7 +1140,7 @@ impl ToWriter for KmerMinHashBTree {
     where
         W: io::Write,
     {
-        serde_json::to_writer(writer, &self)?;
+        simd_json::to_writer(writer, &self)?;
         Ok(())
     }
 }
@@ -1633,7 +1633,7 @@ impl KmerMinHashBTree {
     {
         let (rdr, _format) = niffler::get_reader(Box::new(rdr))?;
 
-        let mh: KmerMinHashBTree = serde_json::from_reader(rdr)?;
+        let mh: KmerMinHashBTree = simd_json::from_reader(rdr)?;
         Ok(mh)
     }
 }

diff --git a/src/core/src/wasm.rs b/src/core/src/wasm.rs
@@ -178,7 +178,7 @@ pub enum JsErrors {
     SourmashError(#[from] crate::Error),
 
     #[error(transparent)]
-    SerdeError(#[from] serde_json::error::Error),
+    SerdeError(#[from] simd_json::Error),
 
     #[error(transparent)]
     NifflerError(#[from] niffler::Error),

diff --git a/src/core/tests/minhash.rs b/src/core/tests/minhash.rs
@@ -14,7 +14,6 @@ use sourmash::sketch::minhash::{
 };
 use sourmash::sketch::Sketch;
 use sourmash::ScaledType;
-use sourmash::prelude::ToWriter;
 
 // TODO: use f64::EPSILON when we bump MSRV
 const EPSILON: f64 = 0.01;

diff --git a/src/core/tests/storage.rs b/src/core/tests/storage.rs
@@ -12,9 +12,9 @@ fn zipstorage_load_file() -> Result<(), Box<dyn std::error::Error>> {
 
     let zs = ZipStorage::from_file(filename.to_str().unwrap())?;
 
-    let data = zs.load("v6.sbt.json")?;
+    let mut data = zs.load("v6.sbt.json")?;
 
-    let description: serde_json::Value = serde_json::from_slice(&data[..])?;
+    let description: simd_json::borrowed::Value = simd_json::from_slice(&mut data[..])?;
     assert_eq!(description["version"], 6);
 
     Ok(())