Dev

Cargo.toml

@@ -3,13 +3,17 @@ members = ["crates/parser", "crates/cli", "crates/xtask"]
 resolver = "3"
 
 [workspace.package]
-version = "0.1.1"
+version = "0.1.2"
 license = "MIT"
 authors = [
     "Javier Osorio M <javier.osorio.mosquera@gmail.com>",
     "Julien Wist <julien.wist@correounivalle.edu.co>",
     "Jorge Osorio M <joheosmo@gmail.com>"
 ]
+edition = "2024"
+rust-version = "1.85"
+repository = "https://github.com/phenological/ionic"
+homepage = "https://github.com/phenological/ionic"
 
 [workspace.dependencies]
 base64 = "0.22.1"
@@ -19,8 +23,7 @@ quick-xml = "0.40.1"
 serde = { version = "1", features = ["derive"] }
 serde_json = "1.0"
 clap = "4.6.1"
-zstd = "0.13.3"
-ruzstd = "0.8.3"
+cosmoz = { version = "0.1.0", features = ["std"] }
 regex = "1.12.4"
 rayon = "1.12.0"
 itoa = "1.0"

README.md

@@ -122,7 +122,7 @@ output.flush()?;
 
 ```rust
 pub struct WriteOptions {
-    pub compression_level: u8,           // 0 = off, 1..=22 zstd; default 22
+    pub compression_level: u8,           // 0 = off, 1..=22 zstd; default 12
     pub force_f32: bool,                 // narrow f64 arrays to f32 (lossy); default false
     pub block_size: usize,               // target uncompressed block bytes; default 1 MiB
     pub parallel: bool,                  // default true
@@ -138,9 +138,10 @@ A fixed 1024-byte header stores the byte offset of every section. A reader uses
 ## Portability
 
 The library depends only on standard byte operations: no HDF5, no storage engine, nothing
-to install alongside a file. On `wasm32-unknown-unknown` the build swaps `zstd` for the
-pure-Rust `ruzstd` and drops `rayon` and `memmap2`, so the same reader compiles into a
-browser bundle. That is what [ion-beam](https://github.com/phenological/ion-beam) runs on.
+to install alongside a file. Compression uses the pure-Rust [cosmoz](https://crates.io/crates/cosmoz)
+on every target, so native and `wasm32-unknown-unknown` share the same zstd code. The wasm build
+drops `rayon` and `memmap2`, and browser conversions use compression level 1. That is what
+[ion-beam](https://github.com/phenological/ion-beam) runs on.
 
 ## Related projects
 

config.json

@@ -1,4 +1,12 @@
 [
+  {
+    "package": "0.1.2",
+    "format": {
+      "current": 1,
+      "min_supported": 0,
+      "max_supported": 1
+    }
+  },
   {
     "package": "0.1.1",
     "format": {

crates/cli/Cargo.toml

@@ -2,19 +2,20 @@
 name = "cli"
 version.workspace = true
 license.workspace = true
-edition = "2024"
+edition.workspace = true
+publish = false
 
 [dependencies]
 serde = { workspace = true }
 serde_json = { workspace = true }
 clap = { workspace = true, features = ["derive"] }
-ionic = { path = "../parser" }
+ionic = { package = "ionic-rs", path = "../parser", version = "0.1.2" }
 regex = { workspace = true }
 rayon = { workspace = true }
 mimalloc = { version = "0.1.48" }
 crc32fast = "1.5.0"
 memmap2 = "0.9"
-zstd = { workspace = true }
+cosmoz = { workspace = true }
 
 [[bin]]
 name = "ionic"

crates/cli/src/README.MD

@@ -67,7 +67,7 @@ the relative folder structure under `--output-path`.
 
 - `--level <0..22>`
   - zstd compression level for the data blocks. `0` disables compression.
-    Default: `22`.
+    Default: `12`.
 
 - `--mz-window <DA>`
   - Width, in Da (m/z units), of the windowed layout. A spectrum's m/z and intensity
@@ -153,7 +153,7 @@ You may pass **at most one** of the following:
 
 Defaults:
 
-- `--level 22`, `--mz-window 250`, `--block-size 8`, `--storage disk`
+- `--level 12`, `--mz-window 250`, `--block-size 8`, `--storage disk`
 
 Run (defaults):
 

crates/cli/src/main.rs

@@ -149,7 +149,7 @@ struct ConvertArgs {
     #[arg(
         long = "level",
         conflicts_with = "update",
-        default_value_t = 22,
+        default_value_t = 12,
         value_parser = clap::value_parser!(u8).range(0..=22),
         help = "Compression level 0–22 (0 = off)"
     )]
@@ -228,7 +228,6 @@ struct ConvertArgs {
     which: ConvertWhich,
 }
 
-
 #[derive(Args)]
 struct ConvertWhich {
     #[arg(long = "mzml-to-ion", help = "Convert mzML to ion (default)")]
@@ -973,8 +972,7 @@ fn convert(cmd: ConvertArgs) -> Result<(), String> {
 
     let t_all = Instant::now();
 
-    let default_mzml_to_ion =
-        !cmd.which.mzml_to_ion && !cmd.which.ion_to_mzml && !cmd.which.update;
+    let default_mzml_to_ion = !cmd.which.mzml_to_ion && !cmd.which.ion_to_mzml && !cmd.which.update;
 
     let mzml_to_ion = cmd.which.mzml_to_ion || default_mzml_to_ion;
     let ion_to_mzml = cmd.which.ion_to_mzml;