PR[1]: build: migrate from setuptools to scikit-build-core by San1357 · Pull Request #252 · theochem/gbasis

San1357 · 2026-06-04T19:58:38Z

Summary

I migrated the build system from setuptools to scikit-build-core.
In the existing pyproject.toml, setuptools was being used — but setuptools cannot compile C code. So I replaced it with
scikit-build-core — because scikit-build-core can call CMake, and CMake will compile libcint.
I referred to the repo matrix-permanent project for this — it already had the same
scikit-build-core setup. so I followed the same structure.
Added CMakeLists.txt with FetchContent for automatic libcint/qcint download
Platform detection: x86+AVX2 → qcint (optimized), ARM/non-AVX → libcint (generic)
Referenced matrix-permanent repo and Libcint 6 paper (Section IV) for structure and compile flags
Part of Issue GSoC 2026: Better linking between Libcint and GBasis #229 (PR-1)[Week-1]

Description:

Migrated build backend from setuptools to scikit-build-core
Updated numpy dependency to >=2.0
Removed setuptools specific configurations
Added scikit-build configuration
This enables CMake integration for libcint compilation
Added root level CMakeLists.txt
FetchContent automatically downloads and compiles libcint or qcint based on platform
x86 + AVX2 → qcint (SIMD optimized)
ARM/non-AVX → libcint (generic, works on all platforms)
Compile flags: WITH_FORTRAN=OFF, WITH_RANGE_COULOMB=ON
Added placeholder gbasis/integrals/src/libcint_wrap.c (actual C wrapper will be in next PR)
Updated numpy version in .github/workflows/pytest.yaml for consistency with pyproject.toml

How To Test

Tested locally on Mac M5 (ARM):

Prerequisites:

pip install scikit-build-core==0.9.0

Build locally:

pip install -e . --no-build-isolation -v

... ... ... ...

Expected output during build:

-- Architecture: ARM/non-AVX detected — use libcint   (on ARM/Mac M-series)
-- Architecture: x86 + AVX2 detected — use qcint      (on Intel/AMD x86)
-- Configuring done
-- Build files have been written to: ...
Successfully installed qc-gbasis

Verify installation:

python -c "import gbasis; print('gbasis import successful')"

Expected output:

gbasis import successful

IMPORTANT NOTES:

Note: CMakeLists.txt has been included in this PR.
Note: CMakeLists.txt has been included in this PR.
Note: pytest CI checks are expected to fail — CI/CD will be configured in a later PR.
Note: C wrapper (libcint_wrap.c) is a placeholder — actual implementation will follow in next PR.

msricher

Please also upload the CMakeLists.txt. Thanks

msricher · 2026-06-05T14:15:40Z

-# E is pycodestyle
-# F is pyflakes
-# UP is pyupgrade - automatically updates syntax
-# B is flake8-bugbear
-# I is sort imports alphabetically
-# PGH is pygrep-hooks
-# PL is pylint
-# RUF is Ruff-specific rules


Why remove someone's comments? Keep them

msricher

Thank you, this seems fine. Can you create a new branch, san1357:dev, from theochem:master? We should merge these PRs into your dev branch, and then at the end, merge that into theochem:master.

PaulWAyers · 2026-06-08T15:01:31Z

I'm going to run a copilot review. I usually do that automatically (we should add it to the GitHub actions workflow). It's not perfect but it often helps a bit.

Copilot

Pull request overview

This PR migrates the Python packaging/build backend from setuptools to scikit-build-core in order to integrate a CMake-based build that can fetch and compile libcint/qcint as part of building GBasis wheels.

Changes:

Switch pyproject.toml build backend to scikit_build_core.build, add scikit-build configuration, and raise NumPy baseline to >=2.0.
Add a top-level CMakeLists.txt that uses FetchContent to pull/build libcint or qcint based on platform/AVX2 detection.
Add a placeholder C source for future Python/C bindings and update the pytest workflow’s NumPy pin.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 13 comments.

File	Description
`pyproject.toml`	Migrates build backend to scikit-build-core, adjusts dependencies, and adds scikit-build metadata/version config.
`CMakeLists.txt`	Introduces CMake build logic to fetch/build libcint/qcint and build/install a Python extension module.
`gbasis/integrals/src/libcint_wrap.c`	Adds a placeholder C file intended for future libcint Python/C bindings.
`.github/workflows/pytest.yaml`	Updates CI dependency pinning for NumPy in the Py3.9 “old deps” step.

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San1357 · 2026-06-08T21:40:39Z

 [build-system]
-requires = ["setuptools>=64", "setuptools-scm>=8"]
-build-backend = "setuptools.build_meta"
+requires = ["numpy>=2.0", "scikit-build-core>=0.9"]
+build-backend = "scikit_build_core.build"


Fixed — added setuptools-scm to [build-system].requires.

San1357 · 2026-06-08T21:45:59Z

 dependencies = [
-    # Ensure the minimal versions are kept consistent with those in .github/workflows/pytest.yaml
-    "numpy >=1.22, <2.0.0; platform_system=='Windows'",
-    "numpy >=1.22; platform_system=='Linux'",
+    # Updated to numpy>=2.0 required for scikit-build-core C extension support
+    # Note: Keep consistent with .github/workflows/pytest.yaml
+    "numpy>=2.0",
    "scipy>=1.11.1",
    "importlib_resources",
    "sympy",


Raised scipy minimum to 1.13.0 which added NumPy 2.x support.

San1357 · 2026-06-08T21:59:51Z

 [project.optional-dependencies]
+
+# Install with: pip install gbasis[dev]
+


fixed - updated package name from gbasis to qc-gbasis in install comment

San1357 · 2026-06-08T22:00:13Z

+# Install with: pip install gbasis[doc]
+


San1357 · 2026-06-08T22:07:16Z

+include(CheckCCompilerFlag)
+check_c_compiler_flag("-mavx2" HAS_AVX2)
+


Added Windows-specific AVX2 detection using /arch:AVX2 for MSVC compilers.

San1357 · 2026-06-08T22:16:10Z

+if(HAS_AVX2 AND NOT CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+    set(USE_QCINT ON)
+    message(STATUS "Architecture: x86 + AVX2 detected → use qcint")
+else()
+    set(USE_QCINT OFF)
+    message(STATUS "Architecture: ARM/non-AVX detected → use libcint")
+endif()


Added user override support — if USE_QCINT is explicitly set by the user, auto-detection is skipped.

San1357 · 2026-06-08T22:20:28Z

+# Link C extension with libcint
+target_link_libraries(libcint_bindings PRIVATE cint)
+
+# Prevent libcint from installing to system directories
+set(CINT_INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/cint_install CACHE PATH "" FORCE)
+
+# Install only the Python extension into the wheel
+install(TARGETS libcint_bindings
+    LIBRARY DESTINATION ${SKBUILD_PLATLIB_DIR}/gbasis/integrals/lib
+)


This will be addressed in the next PR which adds the platform-aware libcint shared library copying alongside the extension.

San1357 · 2026-06-08T22:28:56Z

+
+/* libcint Python/C API bindings
+ * PR 3 mein implement hoga
+ */


This is just a placeholder file in PR 1. The full implementation including PyInit_libcint_bindings will be added in the follow-up PR.

San1357 · 2026-06-08T22:37:29Z

@@ -33,7 +33,7 @@ jobs:
        if: ${{ matrix.py == '3.9'}}
        # Ensure these versions are consistent with the minimal version requirements
        # in pyproject.toml
-        run: pip install numpy==1.22 scipy==1.11.1
+        run: pip install numpy==2.0 scipy==1.11.1


Fixed — bumped scipy to 1.13.0 in pytest.yaml to match pyproject.toml minimum.

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

San1357 · 2026-06-09T02:00:34Z

Thank you, this seems fine. Can you create a new branch, san1357:dev, from theochem:master? We should merge these PRs into your dev branch, and then at the end, merge that into theochem:master.

@msricher Created san1357:dev branch from theochem:master.
Here is the branch: https://github.com/San1357/gbasis/tree/dev

msricher · 2026-06-09T11:31:48Z

OK, fixes look good. Please merge this into your dev branch and we'll continue from there with the next PR.

PaulWAyers

I'd like @msricher or @marco-2023 to do a detailed review and final approval but it is OK for me.

msricher · 2026-06-09T18:43:16Z

I'd like @msricher or @marco-2023 to do a detailed review and final approval but it is OK for me.

I'm fine with it, it's just boilerplate he's going to merge into his dev branch,.

PaulWAyers

@San1357 you can merge it now, then.

marco-2023 · 2026-06-09T18:58:00Z

@msricher, @PaulWAyers, @San1357 if it is going to be merged in dev, it would need to be another PR. This one is trying to merge on main.

San1357 · 2026-06-09T23:38:56Z

As suggested by @marco-2023, I've created a new PR targeting san1357:dev: San1357#1

The changes have been successfully merged into the dev branch.

San1357 · 2026-06-10T00:03:19Z

@msricher @marco-2023 @PaulWAyers For the next PR, I'll create them targeting san1357:dev on my fork. I can add you as collaborators so you can review them there. Would that work, or do you prefer a different approach?

msricher · 2026-06-10T14:33:03Z

Sure, that works for me.

build: migrate from setuptools to scikit-build-core

0fb4fce

San1357 requested a review from msricher June 4, 2026 19:58

msricher requested changes Jun 5, 2026

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Aayush Gupta added 3 commits June 7, 2026 22:32

build: restore comments and fix numpy version consistency

8a37c73

build: add CMakeLists.txt with FetchContent and platform detection

b7c0938

style: fix comments

4b3ac64

msricher reviewed Jun 8, 2026

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PaulWAyers requested a review from Copilot June 8, 2026 15:01

Copilot started reviewing on behalf of PaulWAyers June 8, 2026 15:02 View session

Copilot AI reviewed Jun 8, 2026

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San1357 and others added 2 commits June 9, 2026 03:21

build: fix misleading comment about setuptools in pyproject.toml

467ae73

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

build: address Copilot review comments

334ecc4

PaulWAyers reviewed Jun 9, 2026

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PaulWAyers approved these changes Jun 9, 2026

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		[project.optional-dependencies]

		# Install with: pip install gbasis[dev]

		include(CheckCCompilerFlag)
		check_c_compiler_flag("-mavx2" HAS_AVX2)

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San1357 commented Jun 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Summary

Description:

How To Test

IMPORTANT NOTES:

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San1357 commented Jun 9, 2026

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San1357 commented Jun 4, 2026 •

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