Nanobind migration discussion

[vincefn]

@sbillinge this is to discuss the (possible) migration to nanobind instead of boost.python, e.g. as implemented in the nanobind_migration test branch

Please really consider this as a tentative organisation - I did this as a summer job and as a large vibe-coding exercise, so no worries if it does not match what you would like, it can be redone with different principles.

The main points are:

• switch to nanobind
• objcryst++ as submodule and cctbx/newmat code directly embedded, so no more need of libobjcryst
• pyproject.toml and cmake for compilation (I don't know if you want to stick with scons
• so far only tested on mac and linux

Also see the extended migration notes (rationale for various implementation decisions, issues with inheritance, etc..)

[sbillinge]

Thanks @vincefn this is super-helpful. We haven't formulated specific standards for this migration and so lessons learned and recommendations from you are super helpful. As a general issue, moving to pyproject.toml/cmake builds seems like it is taking us in the right direction. I don't think there is any downside for us to drop scons, but as I said, I don't have tons of experience with that. Also, getting rid of the extra layer of libobjcryst seems like a win, so I don't object to that at all.

I will read the notes in detail with my c++ enabled folks and see if they have any feedback.

[vincefn]

nanobind branch update (September 2026)

The nanobind_migration_test branch has been updated and is now based on the current main HEAD.

What was done

Submodule update

• extern/objcryst updated from bfdcfda → 30fc8df (8 new upstream commits), adding GetRwHistory, minRwpVar, ReflectionProfilePseudoVoigtTCH, PowderPatternBackgroundHist, aniso PV constructor fix, etc.

Translated from main branch commits (boost.python → nanobind):

• PR makeNdArray: return pyarray directly instead of bp::incref  #108: makeNdArray memory fix — N/A for nanobind (no bp::incref)
• PR Add lsq.GetVarianceCovarianceMap() #109: lsq.GetVarianceCovarianceMap() → dict keyed by (param_name, param_name) tuples
• PR Fix EraseAllParamSet binding for compiled RefinableObj #110: EraseAllParamSet fix on compiled RefinableObj — already correct in nanobind via lambda; added test
• PR Expose objcryst's anisotropic Pseudo-Voigt reflection profile #112: Expose ReflectionProfilePseudoVoigt and ReflectionProfilePseudoVoigtAnisotropic as constructible classes; add IsAnisotropic() to base
• PR Expose PowderPatternDiffraction.X2XCorrPhase #114: PowderPatternDiffraction.X2XCorrPhase()

Translated from open PRs (#107, #113, #115, #116):

• PR Add method GetRwHistory to lsq #107: lsq.GetRwHistory() → list[float] of per-cycle Rw values
• PR Add Rwp threshold minRwpVar for lsq.Refine() #113: minRwpVar argument added to lsq.Refine() and lsq.SafeRefine()
• PR Add profile ReflectionProfilePseudoVoigtTCH with TCH instead of explicit Eta mixing #115: ReflectionProfilePseudoVoigtTCH (TCH implicit-eta profile) with 8-parameter SetProfilePar()
• PR Make LSQ.PrepareRefParList silent by default via new verbose argument #116: verbose overload for LSQ.PrepareRefParList()

Bug fixes in nanobind bindings:

• Fixed pre-existing build error in nb_crystal.cpp: replaced non-existent nb::detail::keep_alive() free function (nanobind 3.x) with nb::keep_alive<1,2>() annotation
• CMakeLists.txt: added homebrew include paths for Boost headers on macOS
• Added SetProfile() to PowderPatternDiffraction (needed to install concrete profile objects)

Tests: 171 tests, all passing.