Updated dependecies and changed code to work for bincode 2.0

Author: douweschulte

Cargo.toml

@@ -28,18 +28,18 @@ codegen-units = 1
 [workspace.dependencies]
 afl = "0.15"
 base64 = "0.22"
-bincode = "1.3"
+bincode = { version = "2.0", features = ["serde"] }
 clap = { version = "4.5", features = ["derive", "cargo"] }
 directories = "6.0"
 flate2 = "1.0"
 iai-callgrind = "0.14"
 itertools = "0.14"
-mzdata = {version="0.49", default-features = false, features = ["miniz_oxide"]}
+mzdata = {version="0.52", default-features = false, features = ["miniz_oxide"]}
 ndarray = "0.16"
-ordered-float = { version = "4.6", features = ["serde"] }
+ordered-float = { version = "5.0", features = ["serde"] }
 png = "0.17"
 probability = "0.20"
-pyo3 = "0.23"
+pyo3 = "0.24"
 rand = "0.9"
 rayon = "1.10"
 regex = "1.11"

rustyms-generate-databases/src/atomic_masses.rs

@@ -1,5 +1,7 @@
 use std::{io::Write, path::Path};
 
+use bincode::config::Configuration;
+
 use crate::{system::f64::da, Element, ElementalData};
 
 use super::csv::parse_csv;
@@ -156,8 +158,14 @@ pub fn build_atomic_masses(out_dir: &Path) {
             )
         })
         .collect();
-    file.write_all(&bincode::serialize::<ElementalData>(&elements).unwrap())
-        .unwrap();
+    file.write_all(
+        &bincode::serde::encode_to_vec::<ElementalData, Configuration>(
+            elements,
+            Configuration::default(),
+        )
+        .unwrap(),
+    )
+    .unwrap();
 }
 
 fn get_ciaaw_number(text: &str) -> Result<f64, String> {

rustyms-generate-databases/src/gnome.rs

@@ -7,6 +7,7 @@ use super::{
     GnoSubsumption, ModificationId, SimpleModificationInner,
 };
 
+use bincode::config::Configuration;
 use thin_vec::ThinVec;
 
 pub fn build_gnome_ontology(out_dir: &Path) {
@@ -57,8 +58,14 @@ pub fn build_gnome_ontology(out_dir: &Path) {
         .map(|m| (None, m.id.name.clone(), m.into_mod()))
         .collect::<OntologyModificationList>();
     println!("Found {} GNOme modifications", final_mods.len());
-    file.write_all(&bincode::serialize::<OntologyModificationList>(&final_mods).unwrap())
-        .unwrap();
+    file.write_all(
+        &bincode::serde::encode_to_vec::<OntologyModificationList, Configuration>(
+            final_mods,
+            Configuration::default(),
+        )
+        .unwrap(),
+    )
+    .unwrap();
 }
 
 fn find_mass(mods: &HashMap<String, GNOmeModification>, mut name: String) -> Option<f64> {

rustyms-generate-databases/src/psi_mod.rs

@@ -1,5 +1,7 @@
 use std::{io::Write, path::Path};
 
+use bincode::config::Configuration;
+
 use crate::formula::MolecularFormula;
 
 use super::{
@@ -17,8 +19,14 @@ pub fn build_psi_mod_ontology(out_dir: &Path) {
     let mut file = std::fs::File::create(dest_path).unwrap();
     let final_mods = mods.into_iter().map(|m| m.into_mod()).collect::<Vec<_>>();
     println!("Found {} PSI-MOD modifications", final_mods.len());
-    file.write_all(&bincode::serialize::<OntologyModificationList>(&final_mods).unwrap())
-        .unwrap();
+    file.write_all(
+        &bincode::serde::encode_to_vec::<OntologyModificationList, Configuration>(
+            final_mods,
+            Configuration::default(),
+        )
+        .unwrap(),
+    )
+    .unwrap();
 }
 
 fn parse_psi_mod() -> Vec<OntologyModification> {

rustyms-generate-databases/src/resid.rs

@@ -10,6 +10,7 @@ use super::{
 };
 use crate::{formula::MultiChemical, MolecularFormula};
 
+use bincode::config::Configuration;
 use roxmltree::*;
 
 pub fn build_resid_ontology(out_dir: &Path) {
@@ -19,8 +20,14 @@ pub fn build_resid_ontology(out_dir: &Path) {
     let mut file = std::fs::File::create(dest_path).unwrap();
     let final_mods = mods.into_iter().map(|m| m.into_mod()).collect::<Vec<_>>();
     println!("Found {} RESID modifications", final_mods.len());
-    file.write_all(&bincode::serialize::<OntologyModificationList>(&final_mods).unwrap())
-        .unwrap();
+    file.write_all(
+        &bincode::serde::encode_to_vec::<OntologyModificationList, Configuration>(
+            final_mods,
+            Configuration::default(),
+        )
+        .unwrap(),
+    )
+    .unwrap();
 }
 
 fn parse_resid() -> Vec<OntologyModification> {

rustyms-generate-databases/src/unimod.rs

@@ -1,5 +1,6 @@
 use std::{io::Write, iter, path::Path, sync::LazyLock};
 
+use bincode::config::Configuration;
 use regex::Regex;
 
 use crate::{formula::MolecularFormula, NeutralLoss};
@@ -17,8 +18,14 @@ pub fn build_unimod_ontology(out_dir: &Path) {
     let mut file = std::fs::File::create(dest_path).unwrap();
     let final_mods = mods.into_iter().map(|m| m.into_mod()).collect::<Vec<_>>();
     println!("Found {} Unimod modifications", final_mods.len());
-    file.write_all(&bincode::serialize::<OntologyModificationList>(&final_mods).unwrap())
-        .unwrap();
+    file.write_all(
+        &bincode::serde::encode_to_vec::<OntologyModificationList, Configuration>(
+            final_mods,
+            Configuration::default(),
+        )
+        .unwrap(),
+    )
+    .unwrap();
 }
 
 static REGEX_POSITION: LazyLock<Regex> =

rustyms-generate-databases/src/xlmod.rs

@@ -1,5 +1,6 @@
 use std::{io::Write, path::Path};
 
+use bincode::config::Configuration;
 use itertools::Itertools;
 use thin_vec::ThinVec;
 
@@ -24,7 +25,13 @@ pub fn build_xlmod_ontology(out_dir: &Path) {
         .collect::<Vec<_>>();
     println!("Found {} XLMOD modifications", final_mods.len());
     mods_file
-        .write_all(&bincode::serialize::<OntologyModificationList>(&final_mods).unwrap())
+        .write_all(
+            &bincode::serde::encode_to_vec::<OntologyModificationList, Configuration>(
+                final_mods,
+                Configuration::default(),
+            )
+            .unwrap(),
+        )
         .unwrap();
 }
 

rustyms-generate-imgt/src/main.rs

@@ -16,6 +16,7 @@ mod structs;
 
 use crate::shared::*;
 
+use bincode::config::Configuration;
 use itertools::Itertools;
 use rustyms::{
     peptidoform::{Annotation, Region},
@@ -60,7 +61,7 @@ fn main() {
 
     writeln!(
         output,
-        "// @generated\n#![allow(non_snake_case,non_upper_case_globals)]\nuse std::sync::OnceLock;\nuse super::shared::{{Germlines, Species}};"
+        "// @generated\n#![allow(non_snake_case,non_upper_case_globals)]\nuse std::sync::LazyLock;\nuse bincode::config::Configuration;\nuse super::shared::{{Germlines, Species}};"
     )
     .unwrap();
     writeln!(output, "/// Get the germlines for any of the available species. See the main documentation for which species have which data available.").unwrap();
@@ -93,8 +94,14 @@ _Number of genes / number of alleles_
 
         let mut file =
             std::fs::File::create(format!("rustyms/src/imgt/germlines/{species}.bin")).unwrap();
-        file.write_all(&bincode::serialize::<Germlines>(&germlines).unwrap())
-            .unwrap();
+        file.write_all(
+            &bincode::serde::encode_to_vec::<Germlines, Configuration>(
+                germlines,
+                Configuration::default(),
+            )
+            .unwrap(),
+        )
+        .unwrap();
     }
     // germlines
     writeln!(
@@ -104,7 +111,13 @@ _Number of genes / number of alleles_
     .unwrap();
 
     for species in &found_species {
-        writeln!(output, "Species::{0} => Some(lock_{0}()),", species.ident()).unwrap();
+        writeln!(
+            output,
+            "Species::{} => Some(&{}),",
+            species.ident(),
+            species.ident().to_ascii_uppercase()
+        )
+        .unwrap();
     }
     writeln!(output, "_=>None}}}}").unwrap();
     // all_germlines
@@ -116,7 +129,7 @@ pub fn all_germlines() -> impl std::iter::Iterator<Item = &'static Germlines> {{
     .unwrap();
     writeln!(output, "[").unwrap();
     for species in &found_species {
-        writeln!(output, "lock_{}(),", species.ident()).unwrap();
+        writeln!(output, "&*{},", species.ident().to_ascii_uppercase()).unwrap();
     }
     writeln!(output, "].into_iter()\n}}").unwrap();
     // par_germlines
@@ -131,16 +144,15 @@ pub fn par_germlines() -> impl rayon::prelude::ParallelIterator<Item = &'static
     .unwrap();
     writeln!(output, "[").unwrap();
     for species in &found_species {
-        writeln!(output, "lock_{}(),", species.ident()).unwrap();
+        writeln!(output, "&*{},", species.ident().to_ascii_uppercase()).unwrap();
     }
     writeln!(output, "].into_par_iter()\n}}").unwrap();
 
     for species in &found_species {
         writeln!(
             output,
-"static LOCK_{0}: OnceLock<Germlines> = OnceLock::new();
-fn lock_{0}()->&'static Germlines{{LOCK_{0}.get_or_init(|| {{bincode::deserialize(include_bytes!(\"{species}.bin\")).unwrap()}})}}",
-            species.ident(),
+"static {0}: LazyLock<Germlines> = LazyLock::new(|| {{bincode::serde::decode_from_slice::<Germlines, Configuration>(include_bytes!(\"{species}.bin\"),Configuration::default(),).unwrap().0}});",
+            species.ident().to_ascii_uppercase(),
         )
         .unwrap();
     }

rustyms/Cargo.toml

@@ -13,6 +13,7 @@ repository = "https://github.com/snijderlab/rustyms"
 readme = "README.md"
 include = [
     "src/**/*",
+    "images/**/*",
     "README.md",
     "build.rs",
     "benches/**/*",