Replace serde_json with simd_json where supported

sourmash-bio · May 25, 2024 · 2d7b3e9 · 2d7b3e9
1 parent c192268
commit 2d7b3e9
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Showing 11 changed files with 247 additions and 71 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/flake.lock b/flake.lock
diff --git a/flake.nix b/flake.nix
@@ -43,11 +43,6 @@
             export MACOSX_DEPLOYMENT_TARGET=10.14
           '';
 
-          # Work around https://github.com/NixOS/nixpkgs/issues/166205.
-          env = lib.optionalAttrs stdenv.cc.isClang {
-            NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}";
-          };
-
           buildInputs = lib.optionals stdenv.isDarwin [ pkgs.libiconv pkgs.darwin.apple_sdk.frameworks.Security ];
 
           nativeBuildInputs = with rustPlatform; [ cargoSetupHook maturinBuildHook bindgenHook ];

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 = "0.10.4"
 roots = "0.0.8"
+simd-json = "0.13.10"
 serde = { version = "1.0.202", features = ["derive"] }
-serde_json = "1.0.117"
 statrs = "0.16.0"
 streaming-stats = "0.2.3"
 thiserror = "1.0"
@@ -98,6 +98,7 @@ skip_feature_sets = [
 js-sys = "0.3.68"
 web-sys = { version = "0.3.69", features = ["console", "File", "FileReaderSync"] }
 wasm-bindgen = { version = "0.2.89", features = ["serde-serialize"] }
+serde_json = { version = "1.0.117" }
 
 [target.'cfg(all(target_arch = "wasm32"))'.dependencies]
 chrono = { version = "0.4.32", features = ["wasmbind"] }

diff --git a/src/core/benches/minhash.rs b/src/core/benches/minhash.rs
@@ -16,7 +16,7 @@ fn intersection(c: &mut Criterion) {
     filename.push("../../tests/test-data/gather-abund/genome-s10.fa.gz.sig");
     let file = File::open(filename).unwrap();
     let reader = BufReader::new(file);
-    let mut sigs: Vec<Signature> = serde_json::from_reader(reader).expect("Loading error");
+    let mut sigs: Vec<Signature> = simd_json::from_reader(reader).expect("Loading error");
     let mh = if let Sketch::MinHash(mh) = &sigs.swap_remove(0).sketches()[0] {
         mh.clone()
     } else {
@@ -27,7 +27,7 @@ fn intersection(c: &mut Criterion) {
     filename.push("../../tests/test-data/gather-abund/genome-s11.fa.gz.sig");
     let file = File::open(filename).unwrap();
     let reader = BufReader::new(file);
-    let mut sigs: Vec<Signature> = serde_json::from_reader(reader).expect("Loading error");
+    let mut sigs: Vec<Signature> = simd_json::from_reader(reader).expect("Loading error");
     let mh2 = if let Sketch::MinHash(mh) = &sigs.swap_remove(0).sketches()[0] {
         mh.clone()
     } else {