I caught this while testing a dependent library with both rust-numpy and pyO3 installed from source
example logs

reprod:
cargo test with the following patch

diff --git a/Cargo.toml b/Cargo.toml
index c1d9b297..9b99fc9c 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -51,3 +51,6 @@ elided-lifetimes-in-paths = "deny"
 
 [lints.clippy]
 needless-lifetimes = "allow"
+
+[patch.crates-io]
+pyo3 = { git = "https://github.com/PyO3/pyo3.git" }

bisected to PyO3/pyo3@5226450 (PyO3/pyo3#4390), which lists 3 known breaking changes, so I don't assume this report comes as a surprise.
I don't know what's the expected way forward though, I assume rust-numpy is only expected to be compatible with its pinned pyO3 version, but I don't know when is most natural to upgrade ? does it need to wait for the next stable pyO3 ?