From d781b22a9e00053eae9ff2caab9a68f877de4e72 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 12 Jun 2026 19:40:53 +0000
Subject: [PATCH] Bump pyo3 from 0.24.1 to 0.29.0

Bumps [pyo3](https://github.com/pyo3/pyo3) from 0.24.1 to 0.29.0.
- [Release notes](https://github.com/pyo3/pyo3/releases)
- [Changelog](https://github.com/PyO3/pyo3/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pyo3/pyo3/compare/v0.24.1...v0.29.0)

---
updated-dependencies:
- dependency-name: pyo3
  dependency-version: 0.29.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Cargo.lock | 68 ++++++++----------------------------------------------
 Cargo.toml |  2 +-
 2 files changed, 11 insertions(+), 59 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index bd8a79d..069652e 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2,18 +2,6 @@
 # It is not intended for manual editing.
 version = 4
 
-[[package]]
-name = "autocfg"
-version = "1.5.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f2032f911046de80f0a198e0901378627c33f59ea0ac00e363d481118bd70a53"
-
-[[package]]
-name = "cfg-if"
-version = "1.0.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
-
 [[package]]
 name = "crossbeam-deque"
 version = "0.8.6"
@@ -51,30 +39,12 @@ version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
-[[package]]
-name = "indoc"
-version = "2.0.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "79cf5c93f93228cf8efb3ba362535fb11199ac548a09ce117c9b1adc3030d706"
-dependencies = [
- "rustversion",
-]
-
 [[package]]
 name = "libc"
 version = "0.2.186"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "68ab91017fe16c622486840e4c83c9a37afeff978bd239b5293d61ece587de66"
 
-[[package]]
-name = "memoffset"
-version = "0.9.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
-dependencies = [
- "autocfg",
-]
-
 [[package]]
 name = "once_cell"
 version = "1.21.4"
@@ -98,37 +68,32 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.24.1"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "17da310086b068fbdcefbba30aeb3721d5bb9af8db4987d6735b2183ca567229"
+checksum = "cd274650b21d4bfc26a0a47587962c1edb425f69287324355cd040c3ea66071c"
 dependencies = [
- "cfg-if",
- "indoc",
  "libc",
- "memoffset",
  "once_cell",
  "portable-atomic",
  "pyo3-build-config",
  "pyo3-ffi",
  "pyo3-macros",
- "unindent",
 ]
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.24.1"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e27165889bd793000a098bb966adc4300c312497ea25cf7a690a9f0ac5aa5fc1"
+checksum = "c5e2a7d2f0d013342f295c048ad19237add5154a55b1c5a254c0ec93d4109078"
 dependencies = [
- "once_cell",
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.24.1"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "05280526e1dbf6b420062f3ef228b78c0c54ba94e157f5cb724a609d0f2faabc"
+checksum = "ca85c467da1bbc8d866eea5deff9cf29ea5f7785054a17da36e65bda9c05845b"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -136,9 +101,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.24.1"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c3ce5686aa4d3f63359a5100c62a127c9f15e8398e5fdeb5deef1fed5cd5f44"
+checksum = "9ac53762fd065daa3194dd09337a38bd793a188100fd1a9304c4ab312d901771"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -148,13 +113,12 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.24.1"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f4cf6faa0cbfb0ed08e89beb8103ae9724eb4750e3a78084ba4017cbe94f3855"
+checksum = "4ca3a1557399783172dc5bf39cfca835157732532cba56b71d2292161e53b362"
 dependencies = [
  "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
  "syn",
 ]
@@ -188,12 +152,6 @@ dependencies = [
  "crossbeam-utils",
 ]
 
-[[package]]
-name = "rustversion"
-version = "1.0.22"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
-
 [[package]]
 name = "seqfold"
 version = "0.10.1"
@@ -231,9 +189,3 @@ name = "unicode-ident"
 version = "1.0.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"
-
-[[package]]
-name = "unindent"
-version = "0.2.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7264e107f553ccae879d21fbea1d6724ac785e8c3bfc762137959b5802826ef3"
diff --git a/Cargo.toml b/Cargo.toml
index 822ccf8..12550b6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -21,7 +21,7 @@ python = ["dep:pyo3"]
 [dependencies]
 # abi3-py38: build a single stable-ABI wheel that works on CPython 3.8+,
 # instead of a separate wheel per Python minor version.
-pyo3 = { version = "0.24", features = ["extension-module", "abi3-py38"], optional = true }
+pyo3 = { version = "0.29", features = ["extension-module", "abi3-py38"], optional = true }
 # Data-parallel fill of the DP matrix (one task per cell on each anti-diagonal).
 rayon = "1.10"
 # Inline storage for the small per-cell basepair lists (no heap alloc for the