BLD: Vendor OpenMP binary in wheel

.clangd

@@ -1,2 +1,3 @@
 CompileFlags:
   Add: [-Wall -Wextra -Wunused-variable -Wunused-const-variable]
+  Remove: [-fopenmp]

.github/workflows/nonvendored_wheels.yml

@@ -0,0 +1,78 @@
+name: Non-vendored Wheels
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - stable
+  release:
+    types:
+      - published
+
+jobs:
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install deps
+      run: python -m pip install twine build
+
+    - name: Build SDist
+      run: python -m build -s
+
+    - name: Check metadata
+      run: twine check dist/*
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: artifact-sdist
+        path: dist/*.tar.gz
+
+
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install cibuildwheel
+      run: python -m pip install cibuildwheel
+
+    - name: Build wheel
+      run: python -m cibuildwheel --output-dir wheelhouse
+      env:
+        CIBW_ENVIRONMENT: CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF -DDIPTEST_ENABLE_OPENMP=OFF"
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="10.13" CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF -DDIPTEST_ENABLE_OPENMP=OFF"
+
+    - name: Show files
+      run: ls -lh wheelhouse
+      shell: bash
+
+    - name: Verify clean directory
+      run: git diff --exit-code
+      shell: bash
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        name: artifact-${{ matrix.os }}
+        path: wheelhouse/*.whl

.github/workflows/wheels.yml

@@ -1,10 +1,11 @@
-name: Wheels
+name: Build and Publish
 
 on:
   workflow_dispatch:
   pull_request:
+  push:
     branches:
-      - stable
+     - main
   release:
     types:
       - published
@@ -18,18 +19,11 @@ jobs:
       with:
         submodules: true
 
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.10'
-
-    - name: Install deps
-      run: python -m pip install twine build
-
     - name: Build SDist
-      run: python -m build -s
+      run: pipx run build --sdist
 
     - name: Check metadata
-      run: twine check dist/*
+      run: pipx run twine check dist/*
 
     - uses: actions/upload-artifact@v4
       with:
@@ -43,35 +37,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: true
 
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.10'
+    - uses: actions/setup-python@v3
 
     - name: Install cibuildwheel
-      run: python -m pip install cibuildwheel
+      run: python -m pip install cibuildwheel==2.16.5
 
-    - name: Build wheel
+    - name: Build wheels
       run: python -m cibuildwheel --output-dir wheelhouse
       env:
-        CIBW_ENVIRONMENT: MACOSX_DEPLOYMENT_TARGET="10.13" SKBUILD_CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF"
-        CIBW_BUILD: 'cp38-* cp39-* cp310-* cp311-* cp312-*'
-        CIBW_TEST_EXTRAS: test
-        CIBW_TEST_COMMAND: python -m pytest {project}/tests/test_diptest.py
-        CIBW_ARCHS: "auto64"
-        CIBW_ARCHS_MACOS: "x86_64 arm64"
-        # Skip 32-bit builds
-        CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux_x86_64"
-
-    - name: Show files
-      run: ls -lh wheelhouse
-      shell: bash
+        CIBW_ENVIRONMENT: CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF -DDIPTEST_ENABLE_OPENMP=ON"
+        CIBW_TEST_COMMAND: pytest {project}/tests && python -c "from diptest import _has_openmp_support; assert _has_openmp_support"
+        # only build for x86_64; ARM wheels are build seperately
+        CIBW_ARCHS_MACOS: "x86_64"
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="10.13" CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF -DDIPTEST_ENABLE_OPENMP=ON"
 
     - name: Verify clean directory
       run: git diff --exit-code
@@ -83,16 +68,69 @@ jobs:
         name: artifact-${{ matrix.os }}
         path: wheelhouse/*.whl
 
+  build_arm_wheels:
+    name: MacOS ARM wheels
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - name: Cache OpenMP repo
+      id: clone-openmp
+      uses: actions/cache@v4
+      with:
+        path: llvm-project
+        key: macos-arm-openmp
+
+    - name: Clone OpenMP repo
+      if: steps.clone-openmp.outputs.cache-hit != 'true'
+      run: |
+        git clone --depth 1 --branch llvmorg-17.0.6 https://github.com/llvm/llvm-project
+
+    - name: Build OpenMP
+      shell: bash
+      run: |
+        mv llvm-project/openmp ./openmp
+        mv llvm-project/cmake ./cmake
+        rm -rf llvm-project
+        mkdir openmp_build
+        cmake -S openmp -B openmp_build \
+            -DCMAKE_OSX_ARCHITECTURES="arm64" \
+            -DCMAKE_OSX_DEPLOYMENT_TARGET="10.13" \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_C_COMPILER=clang \
+            -DCMAKE_CXX_COMPILER=clang++ \
+            -DCMAKE_INSTALL_PREFIX="/usr/local"
+        cmake --build openmp_build --target install --config Release
+
+    - uses: pypa/cibuildwheel@v2.16.2
+      env:
+        # only build for ARM; x86_64 wheels are build seperately
+        CIBW_ARCHS: "arm64"
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="10.13" CMAKE_ARGS="-DDIPTEST_ENABLE_ARCH_FLAGS=OFF -DDIPTEST_ENABLE_OPENMP=ON -DOpenMP_ROOT=/usr/local"
+
+    - name: Verify clean directory
+      run: git diff --exit-code
+      shell: bash
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        name: artifact-macos-arm
+        path: wheelhouse/*.whl
+
   upload_all:
     name: Upload if release
-    needs: [build_wheels, build_sdist]
+    needs: [build_sdist, build_wheels, build_arm_wheels]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.10'
+    - uses: actions/setup-python@v4
 
     - uses: actions/download-artifact@v4
       with:

CMakeLists.txt

@@ -46,7 +46,24 @@ target_compile_options(
 
 if(DIPTEST_ENABLE_OPENMP)
   message(STATUS "diptest: Building with OpenMP support")
-  find_package(OpenMP REQUIRED)
+  if (APPLE)
+    find_package(OpenMP)
+    if (NOT OpenMP_FOUND)
+      if(NOT DEFINED ${HOMEBREW_PREFIX})
+        if(DEFINED ENV{HOMEBREW_PREFIX} AND IS_DIRECTORY ENV{HOMEBREW_PREFIX})
+          set(HOMEBREW_PREFIX ENV{HOMEBREW_PREFIX})
+        elseif(IS_DIRECTORY /opt/homebrew)
+          set(HOMEBREW_PREFIX /opt/homebrew)
+        else()
+          set(HOMEBREW_PREFIX /usr/local)
+        endif()
+      endif()
+      set(OpenMP_ROOT ${HOMEBREW_PREFIX}/opt/libomp)
+      find_package(OpenMP REQUIRED)
+    endif()
+  else()
+    find_package(OpenMP REQUIRED)
+  endif()
   target_compile_definitions(_diptest_core
                              PUBLIC DIPTEST_HAS_OPENMP_SUPPORT=TRUE)
   target_link_libraries(_diptest_core PRIVATE OpenMP::OpenMP_CXX)

README.md

@@ -13,6 +13,35 @@ unimodal distribution function that minimizes that maximum difference. Other
 than unimodality, it makes no further assumptions about the form of the null
 distribution.
 
+## Usage
+
+This library provides two functions:
+* `dipstat`
+* `diptest`
+
+The first only computes Hartigan's dip statistic. `diptest` computes both the
+statistic and the p-value. The p-value can be computed using interpolation of a
+critical value table (default) or by bootstrapping the null hypothesis.
+Note that for larger samples (N > 1e5) this is quite compute and memory intensive.
+
+```python3
+    import numpy as np
+    import diptest
+
+    # generate some bimodal random draws
+    N = 1000
+    hN = N // 2
+    x = np.empty(N, dtype=np.float64)
+    x[:hN] = np.random.normal(0.4, 1.0, hN)
+    x[hN:] = np.random.normal(-0.4, 1.0, hN)
+
+    # only the dip statistic
+    dip = diptest.dipstat(x)
+
+    # both the dip statistic and p-value
+    dip, pval = diptest.diptest(x)
+```
+
 ## Dependencies
 * `numpy`
 * [Optional] `OpenMP`
@@ -33,11 +62,26 @@ diptest can be installed from PyPi using:
 
 Wheels containing the pre-compiled extension are available for:
 
-- Windows x84-64 - CPython 3.7 - 3.12
-- Linux x84-64 - CPython 3.7 - 3.12
-- MacOS x84-64 - CPython 3.7 - 3.12
+- Windows x84-64 - CPython 3.8 - 3.12
+- Linux x84-64 - CPython 3.8 - 3.12
+- MacOS x84-64 - CPython 3.8 - 3.12
 - MacOS ARM-64 - CPython 3.8 - 3.12
 
+Note that the wheels vendor/ships OpenMP with the extension to provide parallelisation out-of-the-box.
+If you run into issue with multiple versions of OpenMP being loaded you have two options: build from source or install a non-bundled wheel.
+
+### Non-bundled wheels
+
+We provide the same wheels without OpenMP bundled here: https://github.com/RUrlus/diptest/releases 
+You than install the wheel that corresponds to your Python and OS.
+For example, for CPython 3.11 and MacOS ARM:
+
+```shell
+pip install diptest-0.8.0-cp311-cp311-macosx_11_0_arm64.whl
+```
+
+### Building from source
+
 If you have a C/C++ compiler available it is advised to install without
 the wheel as this enables architecture specific optimisations.
 
@@ -55,11 +99,12 @@ Compatible compilers through Pybind11:
 - NVCC (CUDA 11.0 tested in CI)
 - NVIDIA PGI (20.9 tested in CI)
 
-#### Enable OpenMP
+#### Disable OpenMP
+
+To disable OpenMP use:
 
-To enable OpenMP use:
 ```bash
-    SKBUILD_CMAKE_ARGS="-DDIPTEST_ENABLE_OPENMP=ON" pip install diptest --no-binary diptest
+    SKBUILD_CMAKE_ARGS="-DDIPTEST_ENABLE_OPENMP=OFF" pip install diptest --no-binary diptest
 ```
 
 #### Debug installation
@@ -80,35 +125,6 @@ then call the function with debug argument set to a value greater than zero:
     diptest(x, debug=1)
 ```
 
-## Usage
-
-This library provides two functions:
-* `dipstat`
-* `diptest`
-
-The first only computes Hartigan's dip statistic. `diptest` computes both the
-statistic and the p-value. The p-value can be computed using interpolation of a
-critical value table (default) or by bootstrapping the null hypothesis.
-Note that for larger samples (N > 1e5) this is quite compute and memory intensive.
-
-```python3
-    import numpy as np
-    import diptest
-
-    # generate some bimodal random draws
-    N = 1000
-    hN = N // 2
-    x = np.empty(N, dtype=np.float64)
-    x[:hN] = np.random.normal(0.4, 1.0, hN)
-    x[hN:] = np.random.normal(-0.4, 1.0, hN)
-
-    # only the dip statistic
-    dip = diptest.dipstat(x)
-
-    # both the dip statistic and p-value
-    dip, pval = diptest.diptest(x)
-```
-
 ## References
 
 Hartigan, J. A., & Hartigan, P. M. (1985). The Dip Test of Unimodality. The

mbuild.sh

@@ -0,0 +1,16 @@
+cmake -S . -G Ninja -B build \
+    -DSKBUILD_PROJECT_NAME="diptest" \
+    -DSKBUILD_PROJECT_VERSION="0.8.0" \
+    -DDIPTEST_MBUILD=ON \
+    -DDIPTEST_CPP_STANDARD="11" \
+    -DDIPTEST_ENABLE_DEVMODE=ON \
+    -DDIPTEST_ENABLE_DEBUG=OFF \
+    -DDIPTEST_ENABLE_OPENMP=ON \
+    -DDIPTEST_ENABLE_EXT_TESTS=OFF \
+    -DDIPTEST_ENABLE_ARCH_FLAGS=ON \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DOpenMP_ROOT=$(brew --prefix)/opt/libomp \
+    -Dpybind11_DIR=$(python3 -c "import pybind11; print(pybind11.get_cmake_dir())") \
+    -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+
+cmake --build build --target install --config Release --parallel 4