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Replace serde_json with simd_json #3174

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Replace serde_json with simd_json #3174

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d9aad8e
limit usage of serde_json across the codebase
luizirber Dec 19, 2024
a35e64b
use simd_json instead of serde_json
luizirber Dec 19, 2024
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120 changes: 117 additions & 3 deletions Cargo.lock
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2 changes: 1 addition & 1 deletion src/core/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion src/core/src/errors.rs
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Expand Up @@ -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),
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6 changes: 3 additions & 3 deletions src/core/src/signature.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -576,7 +576,7 @@
{
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)
}

Expand Down Expand Up @@ -787,7 +787,7 @@
where
W: io::Write,
{
serde_json::to_writer(writer, &vec![&self])?;
simd_json::to_writer(writer, &vec![&self])?;
Ok(())
}
}
Expand All @@ -797,7 +797,7 @@
where
W: io::Write,
{
serde_json::to_writer(writer, &self)?;
simd_json::to_writer(writer, &self)?;

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Ok(())
}
}
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8 changes: 4 additions & 4 deletions src/core/src/sketch/minhash.rs
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Expand Up @@ -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(())
}
}
Expand Down Expand Up @@ -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)
}
}
Expand Down Expand Up @@ -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(())
}
}
Expand Down Expand Up @@ -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)
}
}
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2 changes: 1 addition & 1 deletion src/core/src/wasm.rs
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Expand Up @@ -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),
Expand Down
4 changes: 2 additions & 2 deletions src/core/tests/storage.rs
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Expand Up @@ -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(())
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