deps(python): upgrade pyo3 + rust-numpy to 0.29, clear 2 advisories (#295)

rust-numpy 0.29 lifted its pyo3 ^0.28 pin, so the resolver can now select
pyo3 0.29. Bump both (kept as a pair) and drop the temporary not-affected
exceptions for RUSTSEC-2026-0176 and RUSTSEC-2026-0177 from deny.toml and
osv-scanner.toml — pyo3 0.29 fixes both advisories.

No public API change; the Python test suite passes unchanged (957 tests).

CHANGELOG.md

@@ -15,6 +15,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   the language label, lists C and C++ separately, prefers `Node.js` and `WASM` in
   prose, and frames the C ABI as a hub (`C ABI hub → …`) rather than a
   language-list entry. Documentation only — no code or public API changes.
+- Python binding: upgraded `pyo3` and `rust-numpy` from 0.28 to 0.29. No public
+  API changes; the full test suite passes unchanged.
+
+### Security
+- Resolved the pyo3 advisories RUSTSEC-2026-0176 (out-of-bounds read in
+  `PyList`/`PyTuple` `nth`/`nth_back`) and RUSTSEC-2026-0177 (missing `Sync`
+  bound on `PyCFunction::new_closure`) by upgrading to pyo3 0.29, which fixes
+  both. The upgrade was previously blocked upstream by rust-numpy 0.28 pinning
+  pyo3 `^0.28`; rust-numpy 0.29 lifts that pin. The not-affected exceptions are
+  removed from `deny.toml` and `osv-scanner.toml`.
 
 ## [0.9.0] - 2026-06-13
 

Cargo.lock

@@ -945,9 +945,9 @@ dependencies = [
 
 [[package]]
 name = "numpy"
-version = "0.28.0"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "778da78c64ddc928ebf5ad9df5edf0789410ff3bdbf3619aed51cd789a6af1e2"
+checksum = "6a5b15d63a5ff39e378daed0e1340d3a5964703ea9712eb09a0dc66fade996f4"
 dependencies = [
  "libc",
  "ndarray",
@@ -1152,9 +1152,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91fd8e38a3b50ed1167fb981cd6fd60147e091784c427b8f7183a7ee32c31c12"
+checksum = "cd274650b21d4bfc26a0a47587962c1edb425f69287324355cd040c3ea66071c"
 dependencies = [
  "libc",
  "once_cell",
@@ -1166,18 +1166,18 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e368e7ddfdeb98c9bca7f8383be1648fd84ab466bf2bc015e94008db6d35611e"
+checksum = "c5e2a7d2f0d013342f295c048ad19237add5154a55b1c5a254c0ec93d4109078"
 dependencies = [
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f29e10af80b1f7ccaf7f69eace800a03ecd13e883acfacc1e5d0988605f651e"
+checksum = "ca85c467da1bbc8d866eea5deff9cf29ea5f7785054a17da36e65bda9c05845b"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -1185,9 +1185,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df6e520eff47c45997d2fc7dd8214b25dd1310918bbb2642156ef66a67f29813"
+checksum = "9ac53762fd065daa3194dd09337a38bd793a188100fd1a9304c4ab312d901771"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -1197,13 +1197,12 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4cdc218d835738f81c2338f822078af45b4afdf8b2e33cbb5916f108b813acb"
+checksum = "4ca3a1557399783172dc5bf39cfca835157732532cba56b71d2292161e53b362"
 dependencies = [
  "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
  "syn",
 ]

Cargo.toml

@@ -37,8 +37,8 @@ approx = "0.5"
 criterion = { version = "0.8", features = ["html_reports"] }
 
 # Python binding
-pyo3 = { version = "0.28", features = ["extension-module", "abi3-py39"] }
+pyo3 = { version = "0.29", features = ["extension-module", "abi3-py39"] }
-numpy = "0.28"
+numpy = "0.29"
 
 [workspace.lints.rust]
 unsafe_code = "forbid"

deny.toml

@@ -9,18 +9,6 @@ all-features = true
 # Fail on any security advisory or unmaintained/unsound crate in the tree.
 version = 2
 yanked = "deny"
-# Temporary, upstream-blocked exception. Both advisories are fixed in pyo3
-# 0.29.0, but rust-numpy 0.28 (latest release) hard-pins `pyo3 ^0.28.0`, so the
-# resolver cannot select 0.29 until rust-numpy ships a 0.29-compatible release
-# (PyO3/rust-numpy "Updated to PyO3 version 0.29.0" is open, not yet published).
-# Neither vulnerable code path is reachable from our binding: it never calls
-# `BoundListIterator::nth`/`nth_back` or the `PyTuple` equivalents (0176), nor
-# `PyCFunction::new_closure` (0177) — verified by grep over bindings/python/src.
-# Remove both once rust-numpy 0.29 lands and the pyo3 0.29 bump goes in.
-ignore = [
-    "RUSTSEC-2026-0176",
-    "RUSTSEC-2026-0177",
-]
 
 [bans]
 # Catch accidental duplicate versions and wildcard ("*") version requirements.

osv-scanner.toml

@@ -4,28 +4,6 @@
 # `ignore` list in deny.toml at the OSV layer. See the "Vulnerability
 # exploitability (VEX)" section of SECURITY.md.
 
-# pyo3 — both advisories are fixed in pyo3 0.29.0, but rust-numpy 0.28 (latest
-# release) hard-pins pyo3 ^0.28.0, so the bump is upstream-blocked. Neither
-# vulnerable code path is reachable from the binding: it never calls
-# BoundListIterator nth/nth_back, the PyTuple equivalents, or
-# PyCFunction::new_closure (verified by grep over bindings/python/src). Also
-# tracked in deny.toml; remove once rust-numpy 0.29 ships and pyo3 is bumped.
-[[IgnoredVulns]]
-id = "RUSTSEC-2026-0176"
-reason = "pyo3 OOB read in PyList/PyTuple nth/nth_back; vulnerable API unused; fix blocked upstream by rust-numpy. Tracked in deny.toml."
-
-[[IgnoredVulns]]
-id = "GHSA-36hh-v3qg-5jq4"
-reason = "Alias of RUSTSEC-2026-0176."
-
-[[IgnoredVulns]]
-id = "RUSTSEC-2026-0177"
-reason = "pyo3 missing Sync on PyCFunction::new_closure; vulnerable API unused; fix blocked upstream by rust-numpy. Tracked in deny.toml."
-
-[[IgnoredVulns]]
-id = "GHSA-chgr-c6px-7xpp"
-reason = "Alias of RUSTSEC-2026-0177."
-
 # jackson-core 3.x async-parser DoS — tools.jackson.core:jackson-core 3.x is not
 # a dependency of this project. No manifest, Maven plugin, or the GitHub
 # dependency-graph SBOM references jackson 3.x; the only jackson present is