Migrate from setuptools to Scikit-build-core

.github/workflows/build-wheels.yml

@@ -84,6 +84,9 @@ jobs:
           # Set LD_LIBRARY_PATH so auditwheel can find shared libs to bundle
           CIBW_ENVIRONMENT_LINUX: >
             LD_LIBRARY_PATH=/usr/local/deps/lib:/usr/local/deps/lib64:$LD_LIBRARY_PATH
+            CMAKE_PREFIX_PATH=/usr/local/deps
+            OMEGA_H_ROOT=/usr/local/deps
+            KOKKOS_ROOT=/usr/local/deps
 
           # auditwheel repair is run automatically by cibuildwheel
 

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         build_type: ["Release", "Debug"]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.13"]
 
     name: "Python ${{ matrix.python-version }} - ${{ matrix.build_type }}"
 
@@ -117,6 +117,9 @@ jobs:
         shell: bash
         run: |
           cd ${GITHUB_WORKSPACE}
+          export CMAKE_PREFIX_PATH="${{ runner.temp }}/build-omega_h/install:${{ runner.temp }}/build-kokkos/install:$CMAKE_PREFIX_PATH"
+          export OMEGA_H_ROOT="${{ runner.temp }}/build-omega_h/install/"
+          export KOKKOS_ROOT="${{ runner.temp }}/build-kokkos/install"
           python -m build
           pip install .[test]
 
@@ -129,61 +132,15 @@ jobs:
           export OMP_NUM_THREADS=2
           pytest -vv -s
 
-      - name: Create and repair wheel
+      # Creating the wheel is enough now since it will be repaired by cibuildwheel
+      - name: Create wheel
         shell: bash
         run: |
           cd ${GITHUB_WORKSPACE}
-          pip install auditwheel patchelf
           # Build the wheel
+          export CMAKE_PREFIX_PATH="${{ runner.temp }}/build-omega_h/install:${{ runner.temp }}/build-kokkos/install:$CMAKE_PREFIX_PATH"
+          export OMEGA_H_ROOT="${{ runner.temp }}/build-omega_h/install/"
+          export KOKKOS_ROOT="${{ runner.temp }}/build-kokkos/install"
           python -m build --wheel --outdir dist/
           echo "---- Built wheels ----"
           ls -la dist/
-          # Repair the wheel — bundle shared libs (omega_h, kokkos, etc.)
-          export LD_LIBRARY_PATH="${{ runner.temp }}/build-omega_h/install/lib:${{ runner.temp }}/build-kokkos/install/lib:${LD_LIBRARY_PATH}"
-          auditwheel show dist/*.whl
-          auditwheel repair dist/*.whl --wheel-dir repaired_wheels/
-          echo "---- Repaired wheels ----"
-          ls -la repaired_wheels/
-
-      - name: Upload repaired wheel
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheel-py${{ matrix.python-version }}-${{ matrix.build_type }}
-          path: repaired_wheels/*.whl
-
-  test-wheel:
-    needs: main
-    runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        python-version: ["3.11"]
-
-    name: "Test Wheel - Python ${{ matrix.python-version }}"
-
-    steps:
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Download repaired wheel
-        uses: actions/download-artifact@v4
-        with:
-          name: wheel-py${{ matrix.python-version }}-Release
-          path: wheel/
-
-      - name: Install wheel
-        shell: bash
-        run: |
-          ls -la wheel/
-          pip install --extra-index-url https://shimwell.github.io/wheels openmc
-          pip install netCDF4==1.7.2
-          pip install wheel/*.whl
-
-      - name: Test convert2degas2 --help
-        shell: bash
-        run: convert2degas2 --help
-
-      - name: Test convert2openmc --help
-        shell: bash
-        run: convert2openmc --help

README.md

@@ -1,8 +1,7 @@
 # Convert `Omega_h` Mesh to CSG Format
 [![License](https://img.shields.io/badge/license-BSD--3--Clause-02B36C)](https://github.com/Fuad-HH/readOH2csg/blob/parallel/LICENSE)
 [![GitHub Actions build status (Linux)](https://github.com/Fuad-HH/readOH2csg/actions/workflows/ci.yml/badge.svg?branch=parallel)](https://github.com/Fuad-HH/readOH2csg/actions/workflows/ci.yml)
-[![Release](https://img.shields.io/github/v/release/Fuad-HH/readOH2csg?include_prereleases
-)](https://github.com/Fuad-HH/readOH2csg/releases)
+[![Release](https://img.shields.io/github/v/release/Fuad-HH/readOH2csg?include_prereleases)](https://github.com/Fuad-HH/readOH2csg/releases)
 
 Efficiently convert Tokamak mesh of `Omega_h` (`.osh`) format
 to Constructive Solid Geometry (CSG). It supports creating
@@ -16,6 +15,8 @@ CSG representation in
 ### 1. Pre-built Wheel
 This is the recommended way to install this package. We provide a pre-built wheel (`Kokkos` with `OpenMP` backend) for Python. Follow these steps to install the latest version of `readOH2csg` using pip:
 
+Wheels are built in CI and uploaded as workflow artifacts for each Python version and build type.
+
 1. On any Linux system, make sure you have Python (Version ≥ 3.11) installed. Go to the terminal
 and `cd` to the directory where you want to install the Python virtual environment.
 ```bash
@@ -31,13 +32,17 @@ pip install --extra-index-url https://shimwell.github.io/wheels openmc
 pip install netCDF4==1.7.2
 ```
 3. Install `readOH2csg`:
+
 ```bash
-pip install https://github.com/Fuad-HH/readOH2csg/releases/download/v0.0.1-alpha/omegah2csg-0.0.1-py3-none-any.whl omegah2csg
+pip install omegah2csg
 ```
-or
+Or if you want to install the latest release from GitHub:
 ```bash
-pip install -i https://test.pypi.org/simple/ omegah2csg
+pip install <link-to-release-wheel-file> omegah2csg
 ```
+>[!TIP]
+> Find the latest release on the [Releases Page](https://github.com/Fuad-HH/readOH2csg/releases/)
+> and copy the link to the wheel file for your Python version and system architecture.
 
 4. Try running the CLI tool, and it should print the help message:
 ```bash
@@ -51,7 +56,7 @@ with [`Kokkos`](https://github.com/kokkos/kokkos) and it supports any [`Kokkos`]
 
 Follow these steps to build and install `readOH2csg` from source:
 1. Make sure you have compilers (at least `g++` or some alternative), `Python` (Version ≥ 3.11), and `CMake` available.
-1. Install [`Kokkos`](https://github.com/kokkos/kokkos) following the instructions in
+2. Install [`Kokkos`](https://github.com/kokkos/kokkos) following the instructions in
 [Kokkos Build Documentation](https://kokkos.org/kokkos-core-wiki/get-started/building-from-source.html#configuring-and-building-kokkos). You can choose any backend supported. Here's an example for building with the `OpenMP` backend:
 ```bash
 git clone --depth=2 --branch 4.7.02 https://github.com/kokkos/kokkos.git
@@ -98,10 +103,13 @@ cmake --build build -j4 --target install
 >[!WARNING]
 > For now, only the Python API and CLI work. Please do not turn off the option for Python bindings. It is
 > enabled by default.
+
 5. Create Python virtual environment and install dependencies as described in the [Pre-built Wheel](#1-pre-built-wheel) section.
 6. Install `readOH2csg` and run the CLI tool, and it should print the help message:
 ```bash
 # from the source directory
+export KOKKOS_ROOT=<Kokkos_install_dir>
+export OMEGA_H_ROOT=<Omega_h_install_dir>
 python -m pip install .
 convert2degas2 --help
 ```

doc/DEVELOPERS_GUIDE.md

@@ -4,13 +4,14 @@ It describes the packaging strategy and choices of tools.
 To get started with Python packaging, check out the [Python Packaging User Guide](https://packaging.python.org/en/latest/).
 
 ## Formatting Style
-All codes in this project are formatted with formatting tools. All these formattings are enforced in the CI pipeline.
-
->[!TIP] If formatting is passing locally but failing in CI, make sure you are using the same version of the formatting tools as specified in the CI pipeline.
+Formatting tools are used to maintain a consistent code style across the project. They are also enforced in CI to ensure that all contributions adhere to the same style guidelines. The formatting tools used in this project are:
 
 - C++ uses `clang-format` with the configuration specified in the [.clang-format](../.clang-format) file.
 - CMake files use `cmake-format` with the configuration specified in the [.cmake-format](../.cmake-format.yaml) file.
-- Python files uses [`ruff`](https://docs.astral.sh/ruff/formatter/) to format the code with the configuration specified in the [pyproject.toml](../pyproject.toml) file.
+- Python files use [`ruff`](https://docs.astral.sh/ruff/formatter/) to format the code with the configuration specified in the [pyproject.toml](../pyproject.toml) file.
+
+>[!TIP]
+> If formatting is passing locally but failing in CI, make sure you are using the same version of the formatting tools as specified in the CI pipeline.
 
 ### C++ and CMake Formatting
 The C++ codes use the [.clang-format](../.clang-format) file and to format the code, you can use `clang-format` tool
@@ -296,47 +297,51 @@ pytest
 ```
 
 ## Packaging
-### Create Distribution Files
-After development and testing, to create the archive and wheel for distribution, install `build` using `pip` and run:
+### Overview
+This project uses `scikit-build-core` to build a Python wheel that includes the native
+`libomegah2csg.so` shared library. You can build locally or use the CI workflow to
+produce manylinux wheels.
+
+### Local build (developer machine)
+You must have Omega_h and Kokkos installed and discoverable by CMake before building.
 
+1. Install build tooling:
 ```bash
-python -m build
+python -m pip install -U build
 ```
-which will create the distribution files in the `dist/` directory.
-
-### Repair the Wheel with `auditwheel`
-The built wheel contains a shared library (`omegah2csg.so`) that links against external shared
-libraries (Omega\_h, Kokkos, etc.). To make the wheel portable and self-contained, use
-[`auditwheel`](https://github.com/pypa/auditwheel) to bundle those shared libraries into the wheel.
 
-First, install `auditwheel` and `patchelf`:
+2. Provide CMake hints (use your install prefixes):
 ```bash
-pip install auditwheel patchelf
+export CMAKE_PREFIX_PATH="<Omega_h_install_dir>:<Kokkos_install_dir>:${CMAKE_PREFIX_PATH}"
 ```
 
-Make sure the shared libraries that the wheel depends on are discoverable via `LD_LIBRARY_PATH`.
-For example, if Omega\_h and Kokkos are installed under `/path/to/omega_h` and `/path/to/kokkos`:
+3. Build sdist + wheel:
 ```bash
-export LD_LIBRARY_PATH="/path/to/omega_h/lib64:/path/to/kokkos/lib64:${LD_LIBRARY_PATH}"
+python -m build
 ```
 
-Then inspect and repair the wheel:
+Artifacts are written to `dist/`.
+
+### CI build (manylinux wheels)
+The `Build Manylinux Wheels` workflow builds Omega_h and Kokkos in the container and
+then builds wheels with `cibuildwheel`. The resulting wheels are uploaded as workflow
+artifacts named `manylinux-wheels`.
+
+To download wheels from CI with GitHub CLI:
 ```bash
-# Show external shared library dependencies
-auditwheel show dist/*.whl
+# Find the workflow run you want
+gh run list --workflow "Build Manylinux Wheels"
 
-# Repair the wheel — bundles shared libs into the wheel
-auditwheel repair dist/*.whl --wheel-dir repaired_wheels/
+# Download the wheels from a specific run
+gh run download <jobid> --name manylinux-wheels
 ```
 
-The repaired wheel will be in the `repaired_wheels/` directory and can be installed on any
-compatible Linux system without needing Omega\_h or Kokkos installed separately.
-
 ### Upload to PyPI/TestPyPI
-To upload the distribution files to PyPI or TestPyPI, install `twine` using `pip` and run:
+To upload the distribution files to PyPI or TestPyPI, install `twine` and run:
 ```bash
+python -m pip install -U twine
 python -m twine upload --repository testpypi dist/*
 ```
 
-It will require a `testpypi` `index-server` entry in your `~/.pypirc` file. See PyPI documentation
-for more details.
+This requires a `testpypi` `index-server` entry in your `~/.pypirc`. See the PyPI
+documentation for details.

doc/top_bottom_flag.md

@@ -1,6 +1,6 @@
 # Top or Bottom of a Cone
 
 This figure illustrates that both on the line segments here create two different cones. But for
-our case, we only want to half cone that touches the line.
+our case, we only want the half cone that touches the line.
 
-![Figure shows two different cones generated by two lines](images/compute_coefficients.svg)
+![Figure shows two different cones generated by two lines](images/compute_coefficients.svg)

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools >= 77.0.3", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core>=0.12.2"]
+build-backend = "scikit_build_core.build"
 
 [project]
 name = "omegah2csg"
@@ -9,7 +9,7 @@ authors = [
 ]
 description = "Convert Omega_h mesh files generated using TOMMS for TOKAMAKs to CSG format for OpenMC and Degas2."
 readme = "README.md"
-version = "0.0.1"
+dynamic = ["version"]
 requires-python = ">=3.11"
 classifiers = [
     "Intended Audience :: Developers",
@@ -39,21 +39,38 @@ test = [
 Homepage = "https://github.com/Fuad-HH/readOH2csg"
 Issues = "https://github.com/Fuad-HH/readOH2csg/issues"
 
-[tool.setuptools.packages.find]
-where = ["pythonAPI"]
-include = ["omegah2csg*"]
-exclude = ["tests*"]
-namespaces = true
-
-
-[tool.setuptools.package-data]
-"omegah2csg" = ["*.txt", "*.dat", "*.osh", "*.so"]
-
 [project.scripts]
 convert2openmc = "omegah2csg.convert2openmc.convert2openmc_cli:app"
 convert2degas2 = "omegah2csg.convert2degas2.convert2degas2_cli:app"
 
 
+[tool.scikit-build]
+minimum-version = "build-system.requires"
+wheel.packages = ["pythonAPI/omegah2csg"]
+metadata.version.provider = "scikit_build_core.metadata.regex"
+metadata.version.input = "CMakeLists.txt"
+metadata.version.regex = "project\\([^)]*?\\bVERSION\\s+(?P<value>[0-9]+\\.[0-9]+\\.[0-9]+)[^)]*\\)"
+sdist.include = [
+    "CMakeLists.txt",
+    "cmake/**",
+    "src/**",
+    "pythonAPI/**",
+    "tests/**",
+    "README.md",
+    "LICENSE",
+    "pyproject.toml",
+    "pytest.toml",
+]
+
+[tool.scikit-build.cmake.define]
+CMAKE_PREFIX_PATH = { env = "CMAKE_PREFIX_PATH", default = "" }
+Omega_h_ROOT = { env = "OMEGA_H_ROOT", default = "" }
+Kokkos_ROOT = { env = "KOKKOS_ROOT", default = "" }
+CMAKE_C_COMPILER = { env = "CC", default = "" }
+CMAKE_CXX_COMPILER = { env = "CXX", default = "" }
+CMAKE_BUILD_TYPE = { env = "CMAKE_BUILD_TYPE", default = "RelWithDebInfo" }
+
+
 [tool.ruff]
 include = ["pyproject.toml", "pythonAPI/omegah2csg/**/*.py", "tests/**/*.py"]
 line-length = 88

pythonAPI/omegah2csg/__init__.py

@@ -1,3 +1,7 @@
+from importlib import metadata
+from pathlib import Path
+import re
+
 from .config import KokkosRuntime, kokkos_runtime
 from .OmegaHMesh import (
     OmegaHMesh,
@@ -9,6 +13,29 @@
 )
 from .convert2degas2 import convert2degas2
 
+
+def _read_cmake_version() -> str | None:
+    cmake_path = Path(__file__).resolve().parents[2] / "CMakeLists.txt"
+    if not cmake_path.is_file():
+        return None
+    content = cmake_path.read_text(encoding="utf-8")
+    match = re.search(
+        r"project\([^)]*?\bVERSION\s+([0-9]+\.[0-9]+\.[0-9]+)[^)]*\)",
+        content,
+        re.DOTALL,
+    )
+    return match.group(1) if match else None
+
+
+def _get_version() -> str:
+    try:
+        return metadata.version("omegah2csg")
+    except metadata.PackageNotFoundError:
+        return _read_cmake_version() or "0.0.0"
+
+
+__version__ = _get_version()
+
 __all__ = [
     # runtime
     "KokkosRuntime",
@@ -21,4 +48,6 @@
     "convert2openmcXML",
     # degas2
     "convert2degas2",
+    # version
+    "__version__",
 ]