pybind updates for latest master #1090

PhilipDeegan · 2025-10-15T11:19:35Z

seeing compile errors since pybind/pybind11#5866

should be resolved with the additional requires

also updated to smart_holders instead of shared_ptrs as noted here https://pybind11.readthedocs.io/en/stable/advanced/smart_ptrs.html#py-smart-holder

coderabbitai · 2025-10-15T11:20:00Z

📝 Walkthrough

Walkthrough

Replace std::shared_ptr holder policies with py::smart_holder in multiple pybind11 class bindings, adjust Span and PyWrapper bindings, move PatchDataVectorDouble registrations earlier in module init, and add a requires clause to PatchData’s templated constructor to restrict constructibility.

Changes

Cohort / File(s)	Summary
Smart holder migration `src/python3/cpp_simulator.hpp`, `src/python3/cpp_etc.cpp`	Replace `std::shared_ptr<T>` holder policies with `py::smart_holder` for multiple `py::class_` bindings (e.g., `PatchData` variants, `ContiguousParticles`, `DataWrangler`, `PatchLevel`, `Splitter`, `Simulator`, `SamraiLifeCycle`, `PHARE::amr::Hierarchy`, `Span`, `PyWrapper`).
Span / PyWrapper binding adjustments `src/python3/cpp_etc.cpp`	Change `py::class_<core::Span<double>, std::shared_ptr<...>>` → `py::class_<core::Span<double>, py::smart_holder>`. Change `PyArrayWrapper<double>` binding to use `py::smart_holder` and declare `core::Span<double>` as a base.
PatchDataVectorDouble registration move `src/python3/cpp_simulator.cpp`	Add `declarePatchData<std::vector<double>, N>(...)` for N=1,2,3 earlier in module init and remove the later duplicate registrations.
Constructor constraint addition `src/python3/patch_data.hpp`	Add `requires std::is_constructible_v<Data, Args&&...>` to `PatchData(Args&&...)` and fix forwarding to `data(std::forward<Args>(args)...)`.

Sequence Diagram(s)

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related PRs

pybind visbility werrors #1054 — Modifies Python-binding types (PyArrayWrapper/PyWrapper and PatchData) and overlaps on binding declarations.
Simulator template struct #1056 — Adjusts pybind11 class instantiations in src/python3, overlapping holder-policy changes.

Suggested labels

refactoring

Suggested reviewers

nicolasaunai
UCaromel

Pre-merge checks and finishing touches

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.
Title Check	❓ Inconclusive	The title broadly indicates pybind related updates but fails to specify the key changes such as switching to pybind11 smart_holder and pinning the pybind11 version to resolve compile errors, making it too generic to clearly convey the main purpose of the PR.	Please rename the PR to explicitly mention using smart_holder and pinning the pybind11 version to address compile errors, for example “Use pybind11 smart_holder and pin version to fix compile errors.”

✅ Passed checks (1 passed)

Check name	Status	Explanation
Description Check	✅ Passed	The description clearly states the compile errors introduced by a recent pybind11 pull request, references the need for an additional `requires` clause, and notes the switch to smart_holder usage, directly correlating to the changes made in the code.

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Actionable comments posted: 1

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Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

src/python3/cpp_simulator.hpp (1)

35-41: Add pybind11 smart_holder include and type-casters for shared_ptr interop

Add #include <pybind11/smart_holder.h> in src/python3/cpp_simulator.hpp (or a common binding header).

Define PYBIND11_SMART_HOLDER_TYPE_CASTERS for your shared_ptr-backed types (e.g. Sim, PHARE::amr::Hierarchy, and any other smart_holder types) alongside your type aliases.

🧹 Nitpick comments (1)

src/python3/cpp_etc.cpp (1)

44-46: Switch to smart_holder: ensure header and casters are available.

Verify that pybind11/smart_holder.h is included (likely via python3/pybind_def.hpp). If not, include it explicitly here or in a common header.

If Span/PyArrayWrapper (or any related APIs) pass/return std::shared_ptr across the Python boundary, add the required smart‑holder type‑casters for those types.

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📥 Commits

Reviewing files that changed from the base of the PR and between 238185f and 8d5c772.

📒 Files selected for processing (4)

res/cmake/dep/pybind.cmake (1 hunks)
src/python3/cpp_etc.cpp (1 hunks)
src/python3/cpp_simulator.cpp (1 hunks)
src/python3/cpp_simulator.hpp (7 hunks)

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**/*.hpp

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Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.

Files:

src/python3/cpp_simulator.hpp

🧠 Learnings (1)

📓 Common learnings

Learnt from: PhilipDeegan
PR: PHAREHUB/PHARE#784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.

Learnt from: PhilipDeegan
PR: PHAREHUB/PHARE#784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.

🧬 Code graph analysis (1)

src/python3/cpp_simulator.cpp (1)

src/python3/cpp_simulator.hpp (8)

declarePatchData (32-42)

declarePatchData (32-32)

declare_essential (182-194)

declare_essential (182-182)

declareDim (45-60)

declareDim (45-45)

declare_all (168-179)

declare_all (168-168)

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GitHub Check: Analyze (cpp)
GitHub Check: build (ubuntu-latest, clang)
GitHub Check: build (ubuntu-latest, gcc)
GitHub Check: build (macos-14)
GitHub Check: build (macos-latest)
GitHub Check: build (macos-13)

🔇 Additional comments (1)

src/python3/cpp_simulator.cpp (1)

15-17: OK to register PatchDataVectorDouble_ earlier.*

Reordering looks fine. Please confirm the later duplicate registrations were removed to avoid multiple-definition/overwrite at import.

res/cmake/dep/pybind.cmake

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Actionable comments posted: 1

📜 Review details

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Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 8d5c772 and e4601bb.

📒 Files selected for processing (1)

src/python3/patch_data.hpp (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

**/*.hpp

⚙️ CodeRabbit configuration file

Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.

Files:

src/python3/patch_data.hpp

🧠 Learnings (1)

📓 Common learnings

Learnt from: PhilipDeegan
PR: PHAREHUB/PHARE#784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.

Learnt from: PhilipDeegan
PR: PHAREHUB/PHARE#784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.

src/python3/patch_data.hpp

PhilipDeegan · 2025-10-17T13:59:07Z

this is unnecessary strictly since pybind was fixed, but maybe we want it regardless

pin pybind version and use smart_holder

8d5c772

coderabbitai bot reviewed Oct 15, 2025

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res/cmake/dep/pybind.cmake Outdated Show resolved Hide resolved

PhilipDeegan changed the title ~~pin pybind version and use smart_holder~~ pybind updates for latest master Oct 15, 2025

coderabbitai bot reviewed Oct 15, 2025

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src/python3/patch_data.hpp Show resolved Hide resolved

block non-constructible arguments due to catch-all Args...

0c7a120

PhilipDeegan force-pushed the pyb branch from e4601bb to 0c7a120 Compare October 15, 2025 11:49

nicolasaunai approved these changes Nov 7, 2025

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nicolasaunai merged commit 45128ed into PHAREHUB:master Nov 7, 2025
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pybind updates for latest master #1090

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