Update pybind11 requirement from >=2.10.0 to >=3.0.3

[dependabot]

Updates the requirements on pybind11 to permit the latest version.

Release notes

Sourced from pybind11's releases.

Version 3.0.3

Bug fixes:

• Fixed TSS key exhaustion in implicitly_convertible() when many implicit conversions are registered across large module sets. #6020

• Fixed heap-buffer-overflow in pythonbuf with undersized buffers by enforcing a minimum buffer size. #6019

• Fixed virtual-inheritance pointer offset crashes when dispatching inherited methods through virtual bases. #6017

• Fixed free(): invalid pointer crashes during interpreter shutdown with py::enum_<> by duplicating late-added def_property_static argument strings. #6015

• Fixed function_record heap-type deallocation to call PyObject_Free() and decref the type. #6010

• Hardened PYBIND11_MODULE_PYINIT and get_internals() against module-initialization crashes. #6018

• Fixed static_pointer_cast build failure with virtual inheritance in holder_caster_foreign_helpers.h. #6014

• Fixed ambiguous factory template specialization that caused compilation failures with nvcc + GCC 14. #6011

• Fixed crash in def_readwrite for non-smart-holder properties of smart-holder classes. #6008

• Fixed memory leak for py::dynamic_attr() objects on Python 3.13+ by clearing managed __dict__ contents during deallocation. #5999

• Fixed binding of noexcept and ref-qualified (&, &&) methods inherited from unregistered base classes. #5992

Internal:

• Moved tomlkit dependency to the dev dependency group. #5990

• Switched to newer public CPython APIs (PyType_GetFlags and public vectorcall APIs where available). #6005

Tests:

• Made an async callback test deterministic by replacing fixed sleep with bounded waiting. #5986

CI:

... (truncated)

Changelog

Sourced from pybind11's changelog.

Version 3.0.3 (March 31, 2026)

Bug fixes:

• Fixed TSS key exhaustion in implicitly_convertible() when many implicit conversions are registered across large module sets. #6020

• Fixed heap-buffer-overflow in pythonbuf with undersized buffers by enforcing a minimum buffer size. #6019

• Fixed virtual-inheritance pointer offset crashes when dispatching inherited methods through virtual bases. #6017

• Fixed free(): invalid pointer crashes during interpreter shutdown with py::enum_<> by duplicating late-added def_property_static argument strings. #6015

• Fixed function_record heap-type deallocation to call PyObject_Free() and decref the type. #6010

• Hardened PYBIND11_MODULE_PYINIT and get_internals() against module-initialization crashes. #6018

• Fixed static_pointer_cast build failure with virtual inheritance in holder_caster_foreign_helpers.h. #6014

• Fixed ambiguous factory template specialization that caused compilation failures with nvcc + GCC 14. #6011

• Fixed crash in def_readwrite for non-smart-holder properties of smart-holder classes. #6008

• Fixed memory leak for py::dynamic_attr() objects on Python 3.13+ by clearing managed __dict__ contents during deallocation. #5999

• Fixed binding of noexcept and ref-qualified (&, &&) methods inherited from unregistered base classes. #5992

Internal:

• Moved tomlkit dependency to the dev dependency group. #5990

• Switched to newer public CPython APIs (PyType_GetFlags and public vectorcall APIs where available). #6005

Tests:

• Made an async callback test deterministic by replacing fixed sleep with bounded waiting. #5986

... (truncated)

Commits

• 1b49908 docs: add v3.0.3 and v3.1.0 changelog updates. (#6023)
• c066c76 fix: add missing PYBIND11_ALWAYS_INLINE macro for v3.0.3 backports
• 76efcb3 Bump version from v3.0.2 → v3.0.3
• 0f41635 chore(deps): bump pygments from 2.17.2 to 2.20.0 in /docs (#6024)
• 54a4615 chore(deps): bump requests from 2.32.4 to 2.33.0 in /docs (#6013)
• d12037c chore(deps): update pre-commit hooks (#6002)
• 64eecc4 chore(deps): bump the actions group with 3 updates (#6000)
• c0ea8fc Fix heap-buffer-overflow in pythonbuf with undersized buffers (#6019)
• 8d621d6 fix: detect virtual inheritance in add_base to prevent pointer offset crash (...
• b6a616e fix: strdup "self" arg in def_property_static, partially revert #6010 (gh...
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

---

Note

Low Risk
Low risk change limited to build-time dependency constraints, but may surface compile/ABI incompatibilities in downstream extension builds if the project relied on older pybind11 behavior.

Overview
Updates pyproject.toml build-system requirements to raise the minimum pybind11 version from >=2.10.0 to >=3.0.3, allowing builds to use the latest pybind11 release.

^{Reviewed by Cursor Bugbot for commit 0da4501. Bugbot is set up for automated code reviews on this repo. Configure here.}

[github-actions]

🤖 Cursor Dependency Analysis

Supply-Chain Malware Review

Reviewing how pybind11 is declared in the repo and cross-checking the malware report.

Verdict: benign

Checklist

• Classic obfuscation / process spawning: The scanner’s shell_process_spawn hits are false positives: they match the C++ API name py::exec and comments containing “exec” in upstream pybind11 tests and docs, not execve, shells, or subprocess usage. No credible obfuscation or unexpected process-spawn patterns in the reported evidence.

• Invisible Unicode / GlassWorm: Scanner reports Unicode: 0; nothing to support hidden-character tampering.

• Dependency integrity: The update targets pybind11, the standard project at pybind/pybind11, not a typosquat. A 3.x line is consistent with real pybind11 releases; the PR body’s v3.0.3 changelog and fix list match a normal maintenance release. ghost_version_or_missing_tag on >=3.0.3 is almost certainly the tool not mapping a PEP 440 constraint to a git tag, not proof of a nonexistent PyPI version. maintainer_drift / npm-maintainers is misapplied to this PyPI package and is not evidence of publisher compromise.

• Dependabot context: Report shows 0 changed lockfiles and 0 changed node/vendor paths in the scan metadata you provided—consistent with a small manifest-only bump. The long list of changed paths (including upstream .github/workflows/) reflects diffing the upstream library between tags/commits, not an automatic claim that your app PR rewrites those files; for a normal Dependabot PR you should still confirm the actual PR diff is only pyproject.toml / requirements as expected.

Scanner vs interpretation: The warn status is driven by heuristic noise (exec substring, workflow path touch, version-spec “ghost” heuristics), not by IOCs or Unicode findings. Treat those as low signal unless the merged PR contains unexpected files or scripts.

Actionable follow-up (non-malware): Independently validate build/API compatibility with pybind11 3.x (major bump); that is a correctness concern, not a supply-chain malware signal from this review.

Compatibility Analysis

Exploring the repository for pybind11 usage and build integration to produce a compatibility analysis.

1) Where pybind11 is used

Location	Role
pyproject.toml ([build-system] requires)	Build-time dependency so PEP 517 builds get headers/CMake helpers.
src/CMakeLists.txt (lines ~220–247)	find_package(pybind11 CONFIG), optional FetchContent checkout if the package is missing.
src/python_bindings/fastvdf.cpp	Only C++ binding TU: PYBIND11_MODULE, m.def(...), py::bytes, py::tuple, py::gil_scoped_release, py::make_tuple.

There is no py::class_, py::enum_, iostream integration, smart holders, or custom type casters in project src/. Vendored headers under .upstream-dependency/ are for reference/scanning, not normal app code.

---

2) Overlap with 3.0.3 / changed internals

Release notes emphasize fixes in implicitly_convertible, pythonbuf / iostream, virtual inheritance / add_base, py::enum_ / def_property_static, smart-holder def_readwrite, py::dynamic_attr, etc.

fastvdf.cpp does not use those APIs—only free functions and primitive/pytypes. So there is little direct API surface overlap with the listed behavioral fixes.

---

3) Risks / unknowns

• Major 2 → 3: In general, consumers should rebuild the extension and run tests; this tree’s bindings are small, so compile break risk is low, but not zero until CI passes.
• CMake vs. pyproject drift: If find_package(pybind11) fails, CMake FetchContent uses GIT_TAG v2.13.6 (src/CMakeLists.txt), which is not aligned with a declared >=3.0.3 build requirement. That path is a consistency and supportability risk (and matches the “maintainer drift” style hints in your scan artifacts).
• Runtime: No evidence this module relies on the buggy subsystems above; remaining risk is generic (init/internals paths used by every module).

---

4) Recommendation

Merge-with-caveats: Merge after green CI on the PR branch; caveat: plan a small follow-up to bump FetchContent’s GIT_TAG to a 3.x tag (e.g. v3.0.3) so offline / no-pip fallbacks match the declared requirement, unless you explicitly intend 2.13.6 only for legacy environments (then document and reconsider the >=3.0.3 pin).

---

Malware Scan Summary

• Status: warn
• Warn only mode: true
• Changed upstream files scanned: 21
• Resolution strategy: commit_list
• Changed node/vendor paths: 0
• Changed lockfiles: 0
• Resolved refs: from=n/a to=n/a
• Unicode findings (post-allowlist): 0
• Confusable findings (post-allowlist): 0
• IOC findings (post-allowlist): 0
• Heuristic findings (post-allowlist): 12

Top findings

• tests/test_with_catch/test_interpreter.cpp:117 shell_process_spawn :: py::exec(R"(
• tests/test_with_catch/test_interpreter.cpp:167 shell_process_spawn :: py::exec(R"(
• tests/test_with_catch/test_interpreter.cpp:375 shell_process_spawn :: // When the interpreter is embedded, there is no execution frame, but py::exec
• tests/test_with_catch/test_interpreter.cpp:377 shell_process_spawn :: py::exec("var = dict(number=42)");
• include/pybind11/pybind11.h:1578 shell_process_spawn :: /// Initialize an array of slots based on the supplied exec slot and options.
• docs/changelog.md:2058 shell_process_spawn :: - py::exec, py::eval, and py::eval_file now add the builtins
• docs/changelog.md:2060 shell_process_spawn :: matching exec and eval in pure Python.
• docs/changelog.md:2746 shell_process_spawn :: - Added py::exec() as a shortcut for py::eval<py::eval_statements>()
• .github/workflows/nightlies.yml:0 workflow_path_touch :: path-touch
• .github/workflows/pip.yml:0 workflow_path_touch :: path-touch
• pybind11:0 ghost_version_or_missing_tag :: >=3.0.3
• pybind11:0 maintainer_drift :: >=2.10.0->>=3.0.3

[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

^{❌ Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

^{Reviewed by Cursor Bugbot for commit 0da4501. Configure here.}

[cursor]

CMake fallback fetches outdated pybind11 v2.13.6 version

Medium Severity

The pyproject.toml build requirement now mandates pybind11>=3.0.3, but src/CMakeLists.txt line 244 has a FetchContent_Declare fallback pinned to GIT_TAG v2.13.6. If CMake can't find the pip-installed pybind11 (e.g., in certain CI or from-source builds), the fallback fetches a 2.x version that's incompatible with the 3.x minimum. This version mismatch can lead to build failures or subtle ABI incompatibilities since pybind11 3.0 is a major version with breaking changes.

 

^{Reviewed by Cursor Bugbot for commit 0da4501. Configure here.}