Build limited-API (abi3) wheels: mark CFFI extension py_limited_api and remove wrong bdist_wheel hack

.github/windows_arm64_steps/action.yml

@@ -0,0 +1,22 @@
+name: Build Dependencies(Win-ARM64)
+description: "Setup LLVM for Win-ARM64 builds"
+# https://github.com/numpy/numpy-release/blob/295d6a70a867972774ff05ae98d7a560a659e2b4/.github/windows_arm64_steps/action.yml
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install LLVM with checksum verification
+      shell: pwsh
+      run: |
+        Invoke-WebRequest https://github.com/llvm/llvm-project/releases/download/llvmorg-20.1.6/LLVM-20.1.6-woa64.exe -UseBasicParsing -OutFile LLVM-woa64.exe
+        $expectedHash = "92f69a1134e32e54b07d51c6e24d9594852f6476f32c3d70471ae00fffc2d462"
+        $fileHash = (Get-FileHash -Path "LLVM-woa64.exe" -Algorithm SHA256).Hash
+        if ($fileHash -ne $expectedHash) {
+            Write-Error "Checksum verification failed. The downloaded file may be corrupted or tampered with."
+            exit 1
+        }
+        Start-Process -FilePath ".\LLVM-woa64.exe" -ArgumentList "/S" -Wait
+        echo "C:\Program Files\LLVM\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+        echo "CC=clang-cl" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        echo "CXX=clang-cl" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        echo "FC=flang-new" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append

.github/workflows/python.yml

@@ -95,10 +95,11 @@ jobs:
         run: python3 -m build
         working-directory: python
 
+        # This is needed for publishing to PyPI
       - name: Publish artifacts
         uses: actions/upload-artifact@v4
         with:
-          name: moocore-wheels-${{ matrix.os }}-${{ matrix.python-version }}
+          name: moocore-wheels-sdist-${{ matrix.os }}-${{ matrix.python-version }}
           path: python/dist/*.tar.gz
 
   build-doc:
@@ -120,7 +121,6 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
-          cache-dependency-path: '**/requirements_dev.txt'
 
       - name: Ensure Pip and Build
         run: |
@@ -131,13 +131,8 @@ jobs:
         run: python3 -m build
         working-directory: python
 
-      - name: install the package
-        run: python3 -m pip install .
-        working-directory: python
-
-      - name: install the doc build requirements
-        run: |
-          python3 -m pip install -r requirements_dev.txt
+      - name: Install the package and the doc build requirements
+        run: python3 -m pip install .[docs]
         working-directory: python
 
       - name: Build the docs 🔧
@@ -161,7 +156,6 @@ jobs:
     name: Coverage ${{ matrix.os }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     strategy:
-      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
       matrix:
         os: [ubuntu-latest]
         python-version: ['3.10']
@@ -203,10 +197,15 @@ jobs:
       matrix:
         # FIXME: add windows-11-arm and ubuntu-24.04-arm
         # https://github.com/scipy/scipy/blob/6b79a4dec1f9ca2db4e49c328d04d293880991c6/.github/workflows/wheels.yml#L78
-        # macos-14 is apple silicon
-        os: [ubuntu-22.04, windows-2025, macos-14]
+        # https://github.com/numpy/numpy-release/blob/main/.github/workflows/wheels.yml
+        # macos-14 is Apple Silicon (arm64), but we build an universal2 wheel.
+        # The configuration of cibuildwheel can be found in pyproject.toml
+        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, macos-14]
         python-version: ['3.10']
-        CIBW_ARCHS_MACOS: ['universal2']
+        include:
+          # 3.11 is the earliest version on windows-arm
+          - os: windows-11-arm
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v5
@@ -215,18 +214,14 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
-      - name: Set up QEMU
-        if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v3
-        with:
-          platforms: arm64
+      - name: Setup LLVM for Windows ARM64 (NOT WORKING/FIXME)
+        if: ${{ matrix.os == 'windows-11-arm' }}
+        uses: ./.github/windows_arm64_steps
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.3
-        env:
-          CIBW_ARCHS_MACOS: ${{ matrix.CIBW_ARCHS_MACOS }}
-          CIBW_TEST_SKIP: ${{ matrix.CIBW_TEST_SKIP }}
+        uses: pypa/cibuildwheel@v3.2.1
         with:
           package-dir: python
           output-dir: wheelhouse

.pre-commit-config.yaml

@@ -14,10 +14,13 @@ repos:
       - id: no-print-statement
       - id: no-debug-statement
       - id: deps-in-desc
-        args: [--root=r/]
+        args: [--root=./r/]
         exclude: '(do\.R|vignettes/articles/.+\.Rmd)'
       - id: roxygenize
-        args: [--root=<R package root>]
+        args: [--root=./r/]
+        additional_dependencies:
+          - doctest
+          - Rdpack
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

python/Makefile

@@ -20,7 +20,7 @@ pre-commit:
 	pre-commit run -a
 
 docdeps:
-	python3 -m pip install -r requirements_dev.txt --disable-pip-version-check --quiet
+	python3 -m pip install .[docs] --disable-pip-version-check --quiet
 
 show:
 	$(MAKE) -C doc show

python/benchmarks/bench_ndom.py

@@ -65,7 +65,7 @@ def get_dataset(name):
                 z, maximise=True, keep_weakly=False
             ),
             "botorch": lambda z: botorch_is_nondominated(z, deduplicate=True),
-            "paretoset": lambda z: paretoset(
+            "paretoset (numba)": lambda z: paretoset(
                 z, sense=z.shape[1] * ["max"], distinct=True, use_numba=True
             ),
         },
@@ -116,7 +116,7 @@ def get_dataset(name):
             "botorch": lambda z: bool2pos(
                 botorch_is_nondominated(z, deduplicate=False)
             ),
-            "paretoset": lambda z: bool2pos(
+            "paretoset (numba)": lambda z: bool2pos(
                 paretoset(
                     z,
                     sense=z.shape[1] * ["max"],

python/benchmarks/python-requirements.txt

@@ -1,10 +1,11 @@
+botorch
 cpuinfo
+desdeo
+jmetal
+matplotlib
+nevergrad
+numba
 numpy
 pandas
-matplotlib
-botorch
-pymoo
-jmetal
-desdeo
 paretoset
-nevergrad
+pymoo

python/doc/source/REFERENCES.bib

@@ -200,8 +200,7 @@ @article{DiaLop2020ejor
 
 @article{DubLopStu2011amai,
   author = { J{\'e}r{\'e}mie Dubois-Lacoste  and  Manuel L{\'o}pez-Ib{\'a}{\~n}ez  and  Thomas St{\"u}tzle },
-  title = {Improving the Anytime Behavior of Two-Phase Local
-                  Search},
+  title = {Improving the Anytime Behavior of Two-Phase Local Search},
   journal = {Annals of Mathematics and Artificial Intelligence},
   year = 2011,
   volume = 61,
@@ -233,7 +232,8 @@ @article{GueFonPaq2021hv
   year = 2021,
   volume = 54,
   number = 6,
-  pages = {1--42}
+  pages = {1--42},
+  doi = {10.1145/3453474}
 }
 
 @article{HerWer1987tabucol,
@@ -296,6 +296,9 @@ @article{LopVerDreDoe2025
                   Single-objective Black-box Optimization Algorithms},
   journal = {IEEE Transactions on Evolutionary Computation},
   year = 2025,
+  volume = 29,
+  number = 5,
+  pages = {1774--1782},
   annote = {Pre-print: \url{https://doi.org/10.48550/arXiv.2404.02031}},
   doi = {10.1109/TEVC.2024.3462758},
   abstract = {A widely accepted way to assess the performance of iterative
@@ -366,10 +369,11 @@ @article{ZitThiLauFon2003:tec
   year = 2003,
   volume = 7,
   number = 2,
-  amonth = apr,
   pages = {117--132},
-  doi = {10.1109/TEVC.2003.810758},
-  annote = {Proposed the combination of quality indicators; proposed epsilon-indicator}
+  annote = {Proposed the combination of quality indicators; proposed
+                  epsilon-indicator},
+  amonth = apr,
+  doi = {10.1109/TEVC.2003.810758}
 }
 
 @incollection{AugBadBroZit2009gecco,

python/doc/source/whatsnew/index.rst

@@ -7,15 +7,20 @@ What's new
 Version 0.1.9 (dev)
 -------------------
 
-- :func:`~moocore.hv_contributions` ignores dominated points by default.  Set ``ignore_dominated=False`` to restore the previous behavior.  The 3D case uses the HVC3D algorithm.
+- :func:`~moocore.hv_contributions` ignores dominated points by default.
+  Set ``ignore_dominated=False`` to restore the previous behavior.
+  The 3D case uses the HVC3D algorithm.
 - New function :func:`~moocore.any_dominated` to quickly detect if a set is
   nondominated.
 - New function :func:`~moocore.generate_ndset` to generate random nondominated
   sets with different shapes.
 - New example :ref:`sphx_glr_auto_examples_plot_generate.py`.
-- :func:`~moocore.is_nondominated`, :func:`~moocore.any_dominated`, :func:`~moocore.pareto_rank` now handle single-objective inputs correctly (:issue:`27`, :issue:`29`).
+- :func:`~moocore.is_nondominated`, :func:`~moocore.any_dominated`,
+  :func:`~moocore.pareto_rank` now handle single-objective inputs correctly (:issue:`27`, :issue:`29`).
 - Ranks returned by :func:`~moocore.pareto_rank` are 0-based.
 - :func:`~moocore.is_nondominated` and :func:`~moocore.filter_dominated` are faster for dimensions larger than 3.
+- ``moocore`` wheels are now built for ``aarch64`` (ARM64) in Linux and Windows.
+  See the `installation instructions <https://github.com/multi-objective/moocore/tree/main/python#install>`_.
 
 Version 0.1.8 (15/07/2025)
 --------------------------

python/pyproject.toml

@@ -86,45 +86,45 @@ skip = [
   "*_ppc64le",
   "*_s390x",
   "*_i686",    # Skip 32-bit builds
+  "cp313t-*",
+  "cp314t-*",  # Skip free-threaded builds
 ]
 build-verbosity = 2
-# Will cause the wheel to be installed with these groups of dependencies
-test-groups = [ "test" ]
+# Will cause the wheel to be installed with these optional-dependencies
+test-extras = [ "test" ]
 test-command = [
   "pytest --doctest-modules --doctest-continue-on-failure {package}/tests {package}/src/moocore/_moocore.py",
 ]
-test-skip = "*-*linux_{aarch64,ppc64le,s390x}"
+#test-skip = "*-*linux_{aarch64,ppc64le,s390x}"
 
 [tool.cibuildwheel.linux]
-archs = [
-  "x86_64",
-  #  "aarch64", FAILS doctests
-]
+archs = [ "native" ]
 manylinux-x86_64-image = "manylinux_2_28"
+manylinux-aarch64-image = "manylinux_2_28"
+musllinux-x86_64-image = "musllinux_1_2"
+musllinux-aarch64-image = "musllinux_1_2"
 # Use abi3audit to catch issues with Limited API wheels
+before-build = "pip install abi3audit"
 repair-wheel-command = [
   "auditwheel repair -w {dest_dir} {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.windows]
-archs = [
-  "AMD64",
-]
+archs = [ "native" ]
 # Use delvewheel on windows
-before-build = "pip install delvewheel"
+before-build = "pip install delvewheel abi3audit"
 repair-wheel-command = [
   "delvewheel repair -w {dest_dir} {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.macos]
-archs = [
-  "universal2",
-]
+archs = [ "universal2" ]
+before-build = "pip install abi3audit"
 repair-wheel-command = [
   "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.ruff]

python/setup.py

@@ -3,17 +3,19 @@
 from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
 
 
-class bdist_wheel_abi_none(_bdist_wheel):
+class bdist_wheel_abi3(_bdist_wheel):
     def finalize_options(self):
         _bdist_wheel.finalize_options(self)
-        self.root_is_pure = False
-
-    def get_tag(self):
-        _python, _abi, plat = _bdist_wheel.get_tag(self)
-        return "py3", "none", plat
+        # Automatically detect py_limited_api from extension modules
+        if not self.py_limited_api:
+            for ext in self.distribution.ext_modules or []:
+                if getattr(ext, "py_limited_api", False):
+                    # Use cp310 as the minimum Python version for abi3
+                    self.py_limited_api = "cp310"
+                    break
 
 
 setup(
     cffi_modules=["src/moocore/_ffi_build.py:ffibuilder"],
-    cmdclass={"bdist_wheel": bdist_wheel_abi_none},
+    cmdclass={"bdist_wheel": bdist_wheel_abi3},
 )