From d18f87f862f89c306ebdcd0626d5c62dd95772c6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 4 Nov 2026 13:18:57 +0000
Subject: [PATCH] Bump zip from 2.4.2 to 9.0.5 in /rust

Bumps [zip](https://github.com/zip-rs/zip2) from 2.4.2 to 9.0.5.
- [Release notes](https://github.com/zip-rs/zip2/releases)
- [Changelog](https://github.com/zip-rs/zip2/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zip-rs/zip2/compare/v2.4.2...v9.0.5)

---
updated-dependencies:
- dependency-name: zip
  dependency-version: 9.0.5
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 rust/Cargo.lock                   | 54 ++++++++++++++++---------------
 rust/bioscript-cli/Cargo.toml     |  2 +-
 rust/bioscript-formats/Cargo.toml |  2 +-
 rust/bioscript-wasm/Cargo.toml    |  2 +-
 4 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/rust/Cargo.lock b/rust/Cargo.lock
index 588b636..960c6e8 100644
--- a/rust/Cargo.lock
+++ b/rust/Cargo.lock
@@ -102,15 +102,6 @@ version = "1.0.102"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7f202df86484c868dbad7eaa557ef785d5c66295e41b460ef922eca0723b842c"
 
-[[package]]
-name = "arbitrary"
-version = "1.4.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3d036a3c4ab069c7b410a2ce876bd74808d2d0888a82667669f8e783a898bf1"
-dependencies = [
- "derive_arbitrary",
-]
-
 [[package]]
 name = "atomic-polyfill"
 version = "1.0.3"
@@ -452,6 +443,12 @@ version = "1.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
 
+[[package]]
+name = "cfg_aliases"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f079e83a288787bcd14a6aea84cee5c87a67c5a3e660c30f557a3d24761b3527"
+
 [[package]]
 name = "chrono"
 version = "0.4.44"
@@ -652,17 +649,6 @@ dependencies = [
  "syn",
 ]
 
-[[package]]
-name = "derive_arbitrary"
-version = "1.4.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e567bd82dcff979e4b03460c307b3cdc9e96fde3d73bed1496d2bc75d9dd62a"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn",
-]
-
 [[package]]
 name = "digest"
 version = "0.10.7"
@@ -1606,6 +1592,18 @@ dependencies = [
  "strum",
 ]
 
+[[package]]
+name = "nix"
+version = "0.31.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf20d2fde8ff38632c426f1165ed7436270b44f199fc55284c38276f9db47c3d"
+dependencies = [
+ "bitflags",
+ "cfg-if",
+ "cfg_aliases",
+ "libc",
+]
+
 [[package]]
 name = "noodles"
 version = "0.110.0"
@@ -2808,6 +2806,12 @@ version = "0.2.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b"
 
+[[package]]
+name = "typed-path"
+version = "0.12.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "54ec2755506471f54baf5e4bb5499d8e510cc1caf271270e778a736bd2d7336c"
+
 [[package]]
 name = "typenum"
 version = "1.20.0"
@@ -3431,18 +3435,16 @@ dependencies = [
 
 [[package]]
 name = "zip"
-version = "2.4.2"
+version = "9.0.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fabe6324e908f85a1c52063ce7aa26b68dcb7eb6dbc83a2d148403c9bc3eba50"
+checksum = "6e04976da629d3b04204ba8105b396a193af8ad2583b2c79bfb3ab8af580a11e"
 dependencies = [
- "arbitrary",
  "crc32fast",
- "crossbeam-utils",
- "displaydoc",
  "flate2",
  "indexmap",
  "memchr",
- "thiserror 2.0.18",
+ "nix",
+ "typed-path",
  "zopfli",
 ]
 
diff --git a/rust/bioscript-cli/Cargo.toml b/rust/bioscript-cli/Cargo.toml
index f409206..a7114b6 100644
--- a/rust/bioscript-cli/Cargo.toml
+++ b/rust/bioscript-cli/Cargo.toml
@@ -17,7 +17,7 @@ monty = { path = "../../monty/crates/monty" }
 serde_json = { version = "1.0.133", features = ["preserve_order"] }
 serde_yaml = "0.9.34"
 sha2 = "0.10"
-zip = { version = "2.2.0", default-features = false, features = ["deflate"] }
+zip = { version = "9.0.5", default-features = false, features = ["deflate"] }
 
 [lints.clippy]
 pedantic = { level = "warn", priority = -1 }
diff --git a/rust/bioscript-formats/Cargo.toml b/rust/bioscript-formats/Cargo.toml
index 9e77c74..1f1ab1a 100644
--- a/rust/bioscript-formats/Cargo.toml
+++ b/rust/bioscript-formats/Cargo.toml
@@ -10,7 +10,7 @@ crate-type = ["rlib"]
 bioscript-core = { path = "../bioscript-core" }
 flate2 = "1.1.9"
 noodles = { version = "0.110.0", features = ["bam", "bcf", "bgzf", "core", "cram", "csi", "fasta", "sam", "tabix", "vcf"] }
-zip = { version = "2.2.0", default-features = false, features = ["deflate"] }
+zip = { version = "9.0.5", default-features = false, features = ["deflate"] }
 
 [lints.clippy]
 pedantic = { level = "warn", priority = -1 }
diff --git a/rust/bioscript-wasm/Cargo.toml b/rust/bioscript-wasm/Cargo.toml
index 087162b..5381575 100644
--- a/rust/bioscript-wasm/Cargo.toml
+++ b/rust/bioscript-wasm/Cargo.toml
@@ -26,7 +26,7 @@ serde = { version = "1", features = ["derive"] }
 serde_json = { version = "1", features = ["preserve_order"] }
 serde_yaml = "0.9"
 sha2 = "0.10"
-zip = { version = "2.2.0", default-features = false, features = ["deflate"] }
+zip = { version = "9.0.5", default-features = false, features = ["deflate"] }
 console_error_panic_hook = { version = "0.1", optional = true }
 
 [features]