build: :package: use nanobind 3 in split mode by robertodr · Pull Request #243 · Algorithmiq/monoprop

robertodr · 2026-08-19T08:55:31Z

Summary

New split mode in the upcoming nanobind 3 release series promises to reduce compile times by a lot and produce more efficient wheels. This PR is to keep track of its development and flag any issues early.

Note

We might want to drop the microbenchmark on binding overhead entirely from the repo.

Changes

Use latest nanobind and build the Python package in split mode.

Checklist

Tests added or updated to cover the changes
Documentation updated (docstrings, docs/, CONTRIBUTING.md) if needed
CHANGELOG / release notes updated if applicable

AI/LLM disclosure

I did not use LLM tooling, or used it only privately for ideation
I used the following tool to help write this PR description:
I used the following tool to generate or modify code:

Important

By opening this PR I confirm that I have read CONTRIBUTING.md and I agree to the terms of the Contributor License Agreement.

Warning

If you're contributing on behalf of your employer, contact cla@algorithmiq.fi to arrange a Corporate CLA.

github-actions · 2026-08-19T09:02:06Z

Docs preview: https://pr-243.monoprop-docs.pages.dev

3.10 is not supported

codecov · 2026-08-19T09:19:04Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.70%. Comparing base (ca69496) to head (121dd0e).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files

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Flag	Coverage Δ
cpp	`97.70% <ø> (ø)`

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robertodr · 2026-08-19T10:18:48Z

🤖 AI text below 🤖

nanobind 3 benchmark results

Benchmarked using Python 3.12.14 and Release builds on the same host. Results are the median of five interleaved runs; lower is better.

Benchmark	nanobind 2	nanobind 3	With `tuple_builder`	Total improvement
Positional dispatch	72.1 ns	47.0 ns	47.2 ns	34.6%
Keyword dispatch	113.9 ns	84.6 ns	86.2 ns	24.4%
Bound `size()`	41.3 ns	48.4 ns	44.6 ns	-8.1%
Expectation-value functional	10.92 µs	10.45 µs	10.49 µs	4.0%
One-term conversion	9.05 µs	8.89 µs	8.82 µs	2.5%
1,024-term conversion	169.0 µs	126.4 µs	110.2 µs	34.8%

Conclusions

nanobind 3 reduces positional dispatch latency by 34.8% and keyword dispatch latency by 25.8% without source changes.
Replacing list-based tuple construction with nb::tuple_builder reduces 1,024-term conversion latency by a further 12.8%.
The combined improvement for 1,024-term conversion is 34.8%.
Functional and one-term conversion performance improve slightly.
The size() difference is only a few nanoseconds and is considered inconclusive due to measurement noise.

Assisted-by: GitHubCopilot:gpt-5.6.sol

robertodr · 2026-08-19T10:23:53Z

Ready to go when nanobind 3 is officially stable.

robertodr · 2026-08-19T10:24:44Z

PS: I don't think commit 43d61b9 adds much to our benchmarks, I'm ok with tossing it

Signed-off-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>

matteoacrossi · 2026-08-23T18:08:19Z

PS: I don't think commit 43d61b9 adds much to our benchmarks, I'm ok with tossing it

I would toss it but I can leave with it.

Assisted-by: GitHubCopilot:gpt-5.6

sonarqubecloud · 2026-08-24T07:47:42Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

🤖 _AI text below_ 🤖 Adds a Nix flake so Nix/NixOS users can build and hack on monoprop without installing the C++ toolchain, hwloc, Boost or MPI by hand. Stacked on #314 — this branch is rebased onto `chore-mpi4py-build-req-dynamically` and should merge after it. ## Outputs | Command | What it gives you | | --- | --- | | `nix develop` | dev shell: GCC 15, CMake, Ninja, Boost, hwloc, Open MPI, `uv`, `just`, Node.js, clang-tools, gdb, lcov, doxygen | | `nix build .#monoprop` | the Python package, without MPI | | `nix build .#monoprop-mpi` | the same package with `monoprop_ENABLE_MPI=ON` | | `nix run` | a Python interpreter with `monoprop` importable | Inside `nix develop`, the existing `uv sync` and `just` workflows apply unchanged. The shell sets `UV_PYTHON_PREFERENCE=only-system` (uv's managed interpreters expect a loader NixOS does not provide, and `[tool.uv]` pins `only-managed`) and `LD_LIBRARY_PATH` so manylinux wheels resolve `libstdc++`. ## Blocker: the packages do not currently build `nix build .#monoprop` and `.#monoprop-mpi` both fail in `pypaBuildPhase` with `Unmet dependencies`: #243 pinned `nanobind==3.0.0` and added `nanobind-backend>=1.0.0` to `[build-system] requires`, but nixpkgs ships nanobind 2.13.0 and has no `nanobind-backend` at all. This predates the rebase — it arrived in this branch through its last `Merge branch 'main'` and the validation below was never re-run against it. The flake needs the same kind of override it already applies to scikit-build-core before this can merge. The dev shell is unaffected. ## Deviations from the `uv` build All in `nix/monoprop.nix` and documented in the building guide: - C++ unit tests are off — they resolve msgpack-cxx through a CPM git fetch that the build sandbox denies. Build them from the dev shell instead. - `monoprop_ENABLE_ARCH_FLAGS` is off, since a store path may be substituted onto a machine other than the one that built it. `.override { enableArchFlags = true; }` restores `-march=native`. - The version is pinned, because setuptools-scm cannot read git metadata inside the sandbox. **It needs bumping alongside the release tag.** - MPI is enabled by setting the CMake option directly rather than through #314's `monoprop_ENABLE_MPI` environment switch, because that switch also appends mpi4py to `build.requires` — a PyPI resolution the sandbox denies. The store copy of mpi4py is supplied as a build input of `monoprop-mpi` only. ## Notes for reviewers - nixpkgs ships scikit-build-core 1.0.2 while `[build-system] requires` asks for `>=1.0.3`, so the flake overrides it with the 1.0.3 PyPI sdist. That override should be dropped once nixpkgs catches up. - `tools/generate-dispatch.py` reads `.github/license-header.txt` during `cmake --install`, but `.github` is in `sdist.exclude`. The flake works around it by including that one file in the source set; an sdist-based install would presumably hit the same failure. ## Validation On `x86_64-linux`, **before #243 landed**: `nix build .#monoprop` and `.#monoprop-mpi` both compiled and passed the import check, `nix flake check` passed, `nix run` evaluated a `MajoranaOperator`, and `uv sync` inside `nix develop` built the bindings against the Nix toolchain. All of that needs re-running once the nanobind override is in. Darwin and `aarch64-linux` are exposed via `flake-utils.lib.eachDefaultSystem` but untested. --------- Signed-off-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>

build: use latest nanobind in split mode

eb80b18

robertodr added the test-in-draft Run CI even in Draft mode label Aug 19, 2026

github-actions Bot added dependencies Pull requests that update a dependency file python labels Aug 19, 2026

robertodr added 3 commits August 19, 2026 09:02

build(python): ⚡ prune cibuildwheel build matrix

231bf14

build: set wheel.py-api to cp311

ac9fc21

3.10 is not supported

fix(cibuildwheel): build selector needs wildcard

189dfec

fix(cibuildwheel): recover testing against all supported python versions

9c45aad

robertodr added 2 commits August 19, 2026 10:20

perf: use improved nanobind tuple creation methods

b9b9bec

feat(benches): 📈 add microbenchmarks to measure binding overhead

43d61b9

Assisted-by: GitHubCopilot:gpt-5.6.sol

github-actions Bot added the documentation Improvements or additions to documentation label Aug 19, 2026

matteoacrossi changed the title ~~build: use latest nanobind in split mode~~ build: use nanobind 3 in split mode Aug 20, 2026

build: 📦 update nanobind/nanobind-backend versions

427a415

Signed-off-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>

robertodr changed the title ~~build: use nanobind 3 in split mode~~ build: 📦 use nanobind 3 in split mode Aug 20, 2026

robertodr and others added 3 commits August 20, 2026 14:39

Merge branch 'main' into chore-deps-update-nanobind

e78d776

Signed-off-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>

chore(deps): nanobind 3 is stable!

d62a4cd

Merge branch 'main' into chore-deps-update-nanobind

09015c3

Signed-off-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>

robertodr marked this pull request as ready for review August 22, 2026 07:45

robertodr requested review from adamglos92, diagonal-hamiltonian, fpietra and ludmilaasb as code owners August 22, 2026 07:45

matteoacrossi previously approved these changes Aug 23, 2026

View reviewed changes

chore(benches): 🗑️ remove binding microbenchmarks

121dd0e

Assisted-by: GitHubCopilot:gpt-5.6

robertodr dismissed matteoacrossi’s stale review via 121dd0e August 24, 2026 07:37

robertodr enabled auto-merge (squash) August 24, 2026 07:37

matteoacrossi approved these changes Aug 24, 2026

View reviewed changes

robertodr merged commit 8ba1554 into main Aug 24, 2026
30 checks passed

robertodr deleted the chore-deps-update-nanobind branch August 24, 2026 07:45

robertodr mentioned this pull request Aug 31, 2026

feat(nix): ❄️ add a flake with package, app and dev shell #241

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build: 📦 use nanobind 3 in split mode - #243

build: 📦 use nanobind 3 in split mode#243
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Summary

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nanobind 3 benchmark results

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