dependency upgrade

Author: kaizhang

Cargo.toml

@@ -26,7 +26,7 @@ anndata-hdf5 = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "cf0b
 #pyanndata = "0.6"
 pyanndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "cf0b312f2834884bd708595a63f12f34f1905b7b"}
 anyhow = "1.0"
-bed-utils = "0.10.2"
+bed-utils = "0.11"
 flate2 = "1.0"
 itertools = "0.14"
 indicatif = "0.18"

docs/_static/versions.json

@@ -5,9 +5,14 @@
         "url": "https://scverse.org/SnapATAC2/version/dev/"
     },
     {
-        "name": "2.8 (stable)",
-        "version": "2.8",
+        "name": "2.9 (stable)",
+        "version": "2.9",
         "preferred": true,
+        "url": "https://scverse.org/SnapATAC2/version/2.9/"
+    },
+    {
+        "name": "2.8",
+        "version": "2.8",
         "url": "https://scverse.org/SnapATAC2/version/2.8/"
     },
     {

docs/changelog.md

@@ -2,7 +2,7 @@
 
 ## Nightly (unreleased)
 
-## Release 2.9.0 (released March 05, 2026)
+## Release 2.9.0 (released March 13, 2026)
 
 ### Features:
 

snapatac2-core/Cargo.toml

@@ -15,9 +15,9 @@ anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "cf0b312f2
 anyhow = "1.0"
 bstr = "1.12"
 byteorder = "1.5"
-bincode-next = "3.0.0-rc.4"
 bigtools = { version = "0.5", features = ["read", "write"] }
-bed-utils = "0.10.2"
+bed-utils = "0.11"
+rkyv = "0.8"
 flate2 = "1.0"
 tokio = "1.34"
 hora = "0.1"

snapatac2-core/src/preprocessing/bam/flagstat.rs

@@ -1,5 +1,5 @@
-use bincode_next::{Decode, Encode};
 use noodles::{bam::Record, sam::alignment::record::{Cigar, Flags, cigar::op::Kind}};
+use rkyv::{Archive, Deserialize as RkyvDeserialize, Serialize as RkyvSerialize};
 use std::collections::{HashMap, HashSet};
 use anyhow::{Result, Context};
 use itertools::Itertools;
@@ -209,7 +209,7 @@ impl BamQC {
 }
 
 /// Minimal information about an alignment extracted from the BAM record.
-#[derive(Encode, Decode, Debug)]
+#[derive(Archive, RkyvSerialize, RkyvDeserialize, Debug)]
 pub struct AlignmentInfo {
     pub name: String,
     pub reference_sequence_id: u32,

snapatac2-core/src/preprocessing/qc.rs

@@ -1,7 +1,7 @@
 use anyhow::{Result, bail};
 use bed_utils::bed::{map::GIntervalMap, BEDLike, GenomicRange, ParseError, Strand};
-use bincode_next::{Decode, Encode};
 use ndarray::Array2;
+use rkyv::{Archive, Deserialize as RkyvDeserialize, Serialize as RkyvSerialize};
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
 use smallvec::{SmallVec, smallvec};
 use std::{
@@ -202,7 +202,7 @@ pub trait QualityControl: SnapData {
 impl<T: SnapData> QualityControl for T {}
 
 
-#[derive(Encode, Decode, Debug, Clone)]
+#[derive(Archive, RkyvSerialize, RkyvDeserialize, Debug, Clone)]
 pub enum Fragment {
     Single(SingleRead),
     Paired(PairRead),
@@ -361,7 +361,7 @@ impl BEDLike for Fragment {
 
 /// Fragments from single-cell ATAC-seq experiment. Each fragment is represented
 /// by a genomic coordinate, cell barcode and a integer value.
-#[derive(Encode, Decode, Debug, Clone)]
+#[derive(Archive, RkyvSerialize, RkyvDeserialize, Debug, Clone)]
 pub struct PairRead {
     pub chrom: String,
     pub start: u64,
@@ -489,7 +489,7 @@ impl std::str::FromStr for PairRead {
 }
 
 /// Single-ended reads from single-cell ATAC-seq experiment.
-#[derive(Encode, Decode, Debug, Clone)]
+#[derive(Archive, RkyvSerialize, RkyvDeserialize, Debug, Clone)]
 pub struct SingleRead {
     pub chrom: String,
     pub start: u64,
@@ -578,7 +578,7 @@ impl std::str::FromStr for SingleRead {
 }
 
 /// Chromatin interactions from single-cell Hi-C experiment.
-#[derive(Encode, Decode, Debug)]
+#[derive(Archive, RkyvSerialize, RkyvDeserialize, Debug)]
 pub struct Contact {
     pub chrom1: String,
     pub start1: u64,