From dcc3a81ef32d4f5843729b3cd30cde17117f5bf1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Oct 2024 11:35:44 -0700
Subject: [PATCH] Bump pyo3 from 0.22.3 to 0.22.5 (#122)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
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Bumps [pyo3](https://github.com/pyo3/pyo3) from 0.22.3 to 0.22.5.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/pyo3/pyo3/releases">pyo3's
releases</a>.</em></p>
<blockquote>
<h2>PyO3 0.22.5</h2>
<p>This release fixes a compile regression from 0.22.4 where
<code>#[pymethods]</code> with name <code>__clear__</code> and
<code>clear</code> would generate code with a naming conflict. Thanks <a
href="https://github.com/awolverp"><code>@​awolverp</code></a> for the
report and <a href="https://github.com/Icxolu"><code>@​Icxolu</code></a>
for the fix!</p>
<h2>PyO3 0.22.4</h2>
<p><em><strong>This release is a security fix for PyO3 0.22.0 through
0.22.3.</strong></em></p>
<p>The <code>PyWeakrefMethods</code> trait functions for reading
borrowed values from Python weak references have been identified as
unsound, because they did not account for the possibility the last
strong reference could be cleared at any time, leading the borrowed
value to be dangling and risk of use-after-free.</p>
<p>PyO3 0.22.4 protects against this issue by making these methods
permanently leak strong references. The methods are also marked
deprecated and will be removed in PyO3 0.23. Users should switch to use
the use <code>PyWeakrefMethods</code> functions which return owned
references (the deprecation messages indicate the appropriate upgrade
paths).</p>
<p>These functions were added in PyO3 0.22.0; all versions from 0.22.0
through 0.22.3 have been yanked.</p>
<p>Aside from the security fix, PyO3 0.22.4 contains a number of other
bugfixes, including:</p>
<ul>
<li>A fix for cases where <code>__traverse__</code> functions of base
types were not called when using <code>#[pyclass(extends =
...)]</code></li>
<li>A fix for a regression in 0.22.3 where PyO3 generated code would
trigger compile failures with crates using
<code>#![forbid(unsafe_code)]</code></li>
</ul>
<p>Thank you to the following contributors for the improvements:</p>
<p><a
href="https://github.com/davidhewitt"><code>@​davidhewitt</code></a>
<a href="https://github.com/ngoldbaum"><code>@​ngoldbaum</code></a>
<a href="https://github.com/exg"><code>@​exg</code></a>
<a href="https://github.com/Icxolu"><code>@​Icxolu</code></a></p>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/PyO3/pyo3/blob/main/CHANGELOG.md">pyo3's
changelog</a>.</em></p>
<blockquote>
<h2>[0.22.5] - 2024-10-15</h2>
<h3>Fixed</h3>
<ul>
<li>Fix regression in 0.22.4 of naming collision in
<code>__clear__</code> slot and <code>clear</code> method generated
code. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4619">#4619</a></li>
</ul>
<h2>[0.22.4] - 2024-10-12</h2>
<h3>Added</h3>
<ul>
<li>Add FFI definition <code>PyWeakref_GetRef</code> and
<code>compat::PyWeakref_GetRef</code>. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4528">#4528</a></li>
</ul>
<h3>Changed</h3>
<ul>
<li>Deprecate <code>_borrowed</code> methods on <code>PyWeakRef</code>
and <code>PyWeakrefProxy</code> (just use the owning forms). <a
href="https://redirect.github.com/PyO3/pyo3/pull/4590">#4590</a></li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Revert removal of private FFI function <code>_PyLong_NumBits</code>
on Python 3.13 and later. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4450">#4450</a></li>
<li>Fix <code>__traverse__</code> functions for base classes not being
called by subclasses created with <code>#[pyclass(extends =
...)]</code>. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4563">#4563</a></li>
<li>Fix regression in 0.22.3 failing compiles under
<code>#![forbid(unsafe_code)]</code>. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4574">#4574</a></li>
<li>Workaround possible use-after-free in <code>_borrowed</code> methods
on <code>PyWeakRef</code> and <code>PyWeakrefProxy</code> by leaking
their contents. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4590">#4590</a></li>
<li>Fix crash calling <code>PyType_GetSlot</code> on static types before
Python 3.10. <a
href="https://redirect.github.com/PyO3/pyo3/pull/4599">#4599</a></li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/PyO3/pyo3/commit/4c88e9afe8ece2b50af7e0dc0d7650c838f444ac"><code>4c88e9a</code></a>
release: 0.22.5</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/8f6464e5ee65c89b993307b23f01878045a1769c"><code>8f6464e</code></a>
fix <code>__clear__</code> slot naming collision with <code>clear</code>
method (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4619">#4619</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/dff972320287043777fd77063175d23879fef90f"><code>dff9723</code></a>
release: 0.22.4</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/3330bf2641144e2dc4d2730470af4d8623001c60"><code>3330bf2</code></a>
fix garbage collection in inheritance cases (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4563">#4563</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/8b23397c38a5ac7c3631d10ecdb60e249799d736"><code>8b23397</code></a>
ci: pypy 3.7 macos on x64 still</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/ce63713a9dda4a90ef2ab6ff7925751300561e11"><code>ce63713</code></a>
ci: run benchmarks on ubuntu 22.04 (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4609">#4609</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/b1173f5d434071300c48a93520732d9de1c81ddd"><code>b1173f5</code></a>
ci: fix more ubuntu-24.04 failures (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4610">#4610</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/7371028d3fe9bba440e683be8f8b3a4957ad166a"><code>7371028</code></a>
ci: move more jobs to macOS arm (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4600">#4600</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/8e3dc4524875b4b6b427373e7c42d7f0e22e9258"><code>8e3dc45</code></a>
avoid calling <code>PyType_GetSlot</code> on static types before Python
3.10 (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4599">#4599</a>)</li>
<li><a
href="https://github.com/PyO3/pyo3/commit/969300d73d9da10e74c311ba3454ce2df4583b31"><code>969300d</code></a>
leak references for safety in
<code>PyWeakRefMethods::upgrade_borrowed</code> (<a
href="https://redirect.github.com/pyo3/pyo3/issues/4590">#4590</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/pyo3/pyo3/compare/v0.22.3...v0.22.5">compare
view</a></li>
</ul>
</details>
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---
 Cargo.lock | 53 +++++++++++++++++++++++++++--------------------------
 Cargo.toml |  2 +-
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index a089546..d8a7a19 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -850,9 +850,9 @@ dependencies = [
 
 [[package]]
 name = "js-sys"
-version = "0.3.70"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a"
+checksum = "6a88f1bda2bd75b0452a14784937d796722fdebfe50df998aeb3f0b7603019a9"
 dependencies = [
  "wasm-bindgen",
 ]
@@ -1379,9 +1379,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.22.3"
+version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15ee168e30649f7f234c3d49ef5a7a6cbf5134289bc46c29ff3155fa3221c225"
+checksum = "3d922163ba1f79c04bc49073ba7b32fd5a8d3b76a87c955921234b8e77333c51"
 dependencies = [
  "anyhow",
  "cfg-if",
@@ -1398,9 +1398,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.22.3"
+version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e61cef80755fe9e46bb8a0b8f20752ca7676dcc07a5277d8b7768c6172e529b3"
+checksum = "bc38c5feeb496c8321091edf3d63e9a6829eab4b863b4a6a65f26f3e9cc6b179"
 dependencies = [
  "once_cell",
  "target-lexicon",
@@ -1408,9 +1408,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.22.3"
+version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "67ce096073ec5405f5ee2b8b31f03a68e02aa10d5d4f565eca04acc41931fa1c"
+checksum = "94845622d88ae274d2729fcefc850e63d7a3ddff5e3ce11bd88486db9f1d357d"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -1418,9 +1418,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.22.3"
+version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2440c6d12bc8f3ae39f1e775266fa5122fd0c8891ce7520fa6048e683ad3de28"
+checksum = "e655aad15e09b94ffdb3ce3d217acf652e26bbc37697ef012f5e5e348c716e5e"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -1430,9 +1430,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.22.3"
+version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1be962f0e06da8f8465729ea2cb71a416d2257dff56cbe40a70d3e62a93ae5d1"
+checksum = "ae1e3f09eecd94618f60a455a23def79f79eba4dc561a97324bf9ac8c6df30ce"
 dependencies = [
  "heck 0.5.0",
  "proc-macro2",
@@ -1853,8 +1853,9 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 
 [[package]]
 name = "sourmash"
-version = "0.15.2"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=latest#e1f88b114564f070dfbf9a9a1682e5e5e1c83a42"
+version = "0.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "596f20eac8896a06ca65889399ea6f408deeba375aa44c4a2efb3b46e31a02c0"
 dependencies = [
  "az",
  "byteorder",
@@ -2299,9 +2300,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5"
+checksum = "128d1e363af62632b8eb57219c8fd7877144af57558fb2ef0368d0087bddeb2e"
 dependencies = [
  "cfg-if",
  "once_cell",
@@ -2310,9 +2311,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b"
+checksum = "cb6dd4d3ca0ddffd1dd1c9c04f94b868c37ff5fac97c30b97cff2d74fce3a358"
 dependencies = [
  "bumpalo",
  "log",
@@ -2337,9 +2338,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf"
+checksum = "e79384be7f8f5a9dd5d7167216f022090cf1f9ec128e6e6a482a2cb5c5422c56"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -2347,9 +2348,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836"
+checksum = "26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -2360,9 +2361,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484"
+checksum = "65fc09f10666a9f147042251e0dda9c18f166ff7de300607007e96bdebc1068d"
 
 [[package]]
 name = "wasm-streams"
@@ -2379,9 +2380,9 @@ dependencies = [
 
 [[package]]
 name = "web-sys"
-version = "0.3.70"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0"
+checksum = "f6488b90108c040df0fe62fa815cbdee25124641df01814dd7282749234c6112"
 dependencies = [
  "js-sys",
  "wasm-bindgen",
diff --git a/Cargo.toml b/Cargo.toml
index da5fb8f..614ed2e 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,7 +9,7 @@ name = "sourmash_plugin_directsketch"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.22.3", features = ["extension-module", "anyhow"] }
+pyo3 = { version = "0.22.5", features = ["extension-module", "anyhow"] }
 rayon = "1.10.0"
 serde = { version = "1.0.204", features = ["derive"] }
 sourmash = { version = "0.16.0"}