Modernize build system

- replace setup.py with pyproject.toml + scikit-build-core
- add install step for python bindings to CMakeLists.txt
- scikit-build-core requires Python >= 3.7
- skip tests for Python 3.12 until numpy 1.26 is released with Python 3.12 support
- bump deps
  - cibuildwheel to 2.15 - this now builds Python 3.12 wheels
  - pybind11 to v2.11.1
  - cpu_features to v0.8.0
  - catch2 to v2.13.10
  - benchmark to 1.8.2
- bump version to 0.20.0
- resolves #91

.github/workflows/ci.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
   workflow_dispatch:
 
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   BUILD_TYPE: Release
   HAMMING_WITH_AVX2: OFF
@@ -20,24 +24,30 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+          - os: ubuntu-latest
+            open-mp: "ON"
+          - os: macos-latest
+            open-mp: "OFF"
+          - os: windows-latest
+            open-mp: "OFF"
 
     steps:
       - uses: actions/checkout@v3
         with:
           submodules: "recursive"
 
-      - name: enable openmp on linux
-        run: echo "HAMMING_WITH_OPENMP=ON" >> $GITHUB_ENV
-        if: runner.os == 'Linux'
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
 
       - name: make build directory
         run: cmake -E make_directory ${{runner.workspace}}/build
 
       - name: configure cmake
         shell: bash
         working-directory: ${{runner.workspace}}/build
-        run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBUILD_TESTING=ON -DHAMMING_BUILD_BENCHMARKS=ON -DHAMMING_WITH_SSE2=ON -DHAMMING_WITH_AVX2=$HAMMING_WITH_AVX2 -DHAMMING_WITH_AVX512=$HAMMING_WITH_AVX512 -DHAMMING_BUILD_PYTHON=ON -DHAMMING_WITH_OPENMP=$HAMMING_WITH_OPENMP
+        run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBUILD_TESTING=ON -DHAMMING_BUILD_BENCHMARKS=ON -DHAMMING_WITH_SSE2=ON -DHAMMING_WITH_AVX2=$HAMMING_WITH_AVX2 -DHAMMING_WITH_AVX512=$HAMMING_WITH_AVX512 -DHAMMING_BUILD_PYTHON=ON -DHAMMING_WITH_OPENMP=${{ matrix.open-mp }}
 
       - name: build
         shell: bash

.github/workflows/wheels.yml

@@ -9,17 +9,14 @@ on:
   release:
     types: [published]
 
+concurrency:
+  group: wheels-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
-    env:
-      CIBW_TEST_REQUIRES: "pytest numpy"
-      CIBW_TEST_COMMAND: "pytest {project}/python/tests -v"
-      CIBW_TEST_SKIP: "pp* *-musllinux*"
-      CIBW_ENVIRONMENT: "BLAS=None LAPACK=None ATLAS=None"
-      CIBW_SKIP: "*-manylinux_i686"
-      CIBW_BUILD_VERBOSITY: 3
 
     strategy:
       matrix:
@@ -30,11 +27,7 @@ jobs:
         with:
           submodules: "recursive"
 
-      - name: enable openmp on linux
-        run: echo 'CIBW_ENVIRONMENT=HAMMING_WITH_OPENMP=ON' >> $GITHUB_ENV
-        if: runner.os == 'Linux'
-
-      - uses: pypa/[email protected]
+      - uses: pypa/[email protected]
 
       - uses: actions/upload-artifact@v3
         with:

.pre-commit-config.yaml

@@ -12,28 +12,24 @@ repos:
     hooks:
       - id: black
 
-  - repo: https://github.com/dfm/black_nbconvert
-    rev: v0.4.0
-    hooks:
-      - id: black_nbconvert
-
   - repo: https://github.com/cheshirekow/cmake-format-precommit
     rev: v0.6.13
     hooks:
       - id: cmake-format
-        additional_dependencies: [pyyaml==5.4.1]
-
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
-    hooks:
-      - id: nbstripout
+        additional_dependencies: [pyyaml]
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
     rev: v16.0.6
     hooks:
       - id: clang-format
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0
+    rev: v3.0.1
     hooks:
       - id: prettier
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.22.0
+    hooks:
+      - id: check-github-workflows
+      - id: check-readthedocs

CMakeLists.txt

@@ -1,8 +1,8 @@
-cmake_minimum_required(VERSION 3.11)
+cmake_minimum_required(VERSION 3.11..3.26)
 
 project(
   hammingdist
-  VERSION 0.19.0
+  VERSION 0.20.0
   LANGUAGES CXX)
 
 include(CTest)

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["scikit-build-core"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "hammingdist"
+version = "0.20.0"
+description = "A fast tool to calculate Hamming distances"
+readme = "README.md"
+license = {text = "MIT"}
+authors=[{name="Liam Keegan", email="[email protected]"}, {name="Dominic Kempf", email="[email protected]"}]
+requires-python = ">=3.7"
+classifiers=[
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "Programming Language :: C++",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+]
+
+[project.urls]
+Github = "https://github.com/ssciwr/hammingdist"
+Issues = "https://github.com/ssciwr/hammingdist/issues"
+
+[project.optional-dependencies]
+test = ["pytest", "numpy"]
+
+[tool.scikit-build.cmake.define]
+BUILD_TESTING = "OFF"
+HAMMING_BUILD_BENCHMARKS = "OFF"
+HAMMING_BUILD_PYTHON = "ON"
+
+[tool.cibuildwheel]
+skip = "*-manylinux_i686"
+# skip tests for python 3.12 until numpy 1.26 is available
+test-skip = "pp* *-musllinux* cp312-*"
+test-extras = "test"
+test-command = "pytest {project}/python/tests -v"
+environment = { BLAS="None", LAPACK="None", ATLAS="None" }
+build-verbosity = 3
+
+[tool.cibuildwheel.linux]
+environment = { CMAKE_ARGS="-DHAMMING_WITH_OPENMP=ON" }

python/CMakeLists.txt

@@ -1,2 +1,3 @@
 pybind11_add_module(hammingdist hammingdist.cc)
 target_link_libraries(hammingdist PUBLIC hamming)
+install(TARGETS hammingdist DESTINATION .)