PR - [9] Bind 3-center 2-electron integrals, add cartesian support via macro type parameter

[San1357]

Changes

3-center 2-electron integrals

• Bound int3c2e_sph in libcint_wrap.c using 3 nested shell loops with shls[3] = 0
• Added three_center_two_electron() to CBasis with transform support
• Generated PySCF reference .npy files for He, C, H+He, Be+C systems (STO-6G)
• Added 4 tests against PySCF reference values (atol=1e-10)

Macro refactor

• Updated DEFINE_INT1E_ARRAY_FN, DEFINE_INT1E_LOOP_FN, and DEFINE_INT1E_LOOP_FN_OPT to accept a type parameter via token pasting
• Both _sph and _cart variants now generated from the same macro call
• e.g. DEFINE_INT1E_ARRAY_FN(overlap, sph, int1e_ovlp) → generates overlap_sph

coord_type aware C bindings

• All CBasis C-loop methods now dynamically select _sph or _cart based on coord_type at runtime

Tests

572 passed, 4 skipped

Still in progress

• int3c2e_cart binding and cartesian reference tests
• Cartesian tests for test_c_shellloop_integral
• Code cleanup (removing make_int1e, make_int2e, old *_integral() wrappers)

[msricher]

Great, thanks for also adding the automatic selection of (cart|sph) at runtime.

[Copilot]

Pull request overview

This PR introduces a Python C-extension (libcint_bindings) to accelerate/extend libcint-backed integral evaluation (including new 3-center 2-electron integrals), refactors macro-based generation for spherical/cartesian variants, and updates packaging/build tooling to use a CMake/scikit-build-core workflow.

Changes:

• Added a new C-extension wrapper (gbasis/integrals/src/libcint_wrap.c) exposing shell-loop integral array builders (plus int3c2e_sph).
• Extended gbasis.integrals.libcint.CBasis with new C-backed shell-loop methods (and three_center_two_electron()), including runtime _sph/_cart selection via a suffix.
• Updated tests and build configuration (pyproject + CI) to support the new build and validate new bindings.

Reviewed changes

Copilot reviewed 6 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/test_libcint.py	Expands libcint test coverage to include new C shell-loop bindings and 3c2e reference comparisons.
pyproject.toml	Switches build backend to scikit-build-core and updates dependency minimums.
gbasis/integrals/src/libcint_wrap.c	Adds the C-extension module implementing array builders and new integral bindings.
gbasis/integrals/libcint.py	Wires the new extension into CBasis and adds higher-level Python methods for new bindings.
CMakeLists.txt	Defines the CMake build for the extension and fetches/builds libcint/qcint.
.github/workflows/pytest.yaml	Updates minimal dependency pins used in CI (numpy/scipy).

Comments suppressed due to low confidence (3)

gbasis/integrals/libcint.py:234

• The ctypes loader hard-codes a platform-specific libcint filename under gbasis/integrals/lib (e.g. libcint.so on Linux). With this PR switching to a CMake/scikit-build-core build that installs libcint_bindings into gbasis/integrals/lib, it’s easy to end up with the extension present but no libcint.* shared library at the expected path (and/or a different SONAME like libcint.so.6). That will make gbasis.integrals.libcint fail to import when _LibCInt is used (since LIBCINT is instantiated at import time). Please ensure the build/install step also installs a compatible libcint shared library and the expected filename/symlink into gbasis/integrals/lib, or refactor so the ctypes path is optional/lazy when libcint.* is absent.

    elif _system == "Windows":
        _lib_name = "libcint.dll"
    else:
        _lib_name = "libcint.so"
    _libcint: CDLL = cdll.LoadLibrary(str(_lib_dir / _lib_name))

CMakeLists.txt:55

• INSTALL_RPATH is set to @loader_path unconditionally. @loader_path is a macOS-specific placeholder; on Linux this value is not meaningful and can lead to runtime loader issues (especially if cint is built/linked as a shared library). Consider setting RPATH conditionally (Darwin: @loader_path, Linux: $ORIGIN).

    # Set RPATH so libcint.dylib is found at runtime.
    INSTALL_RPATH "@loader_path"
    BUILD_WITH_INSTALL_RPATH TRUE)

CMakeLists.txt:67

• Only the Python extension module is installed into gbasis/integrals/lib, but the Python ctypes path (_LibCInt) still expects a loadable libcint.* shared library under the same directory. If cint is built as a shared library, it should also be installed next to the extension so runtime loading works; if it’s built statically, the ctypes path likely needs to be removed/disabled (since there won’t be a libcint.* to load).

# Install C extension module.
set(GBASIS_WHEEL_DIRECTORY "${SKBUILD_PLATLIB_DIR}/gbasis/integrals/lib")
install(TARGETS gbasis_ext LIBRARY DESTINATION ${GBASIS_WHEEL_DIRECTORY})

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[msricher]

@San1357 verify this, and possibly implement?

[San1357]

Done

[msricher]

@San1357 this one too

[San1357]

Implemented.

[msricher]

You shouldn't have to do this! Last time we edited the CMakeLists.txt, we made libcint a static library that is compiled directly into the extension module.

[San1357]

Got it