Convert build system to scikit-build-core (#22)

* Convert build system to scikit-build-core

- Replace meson files with cmake

- Build a stand-alone compiled library and header which are
  installed to python environment lib / include dirs

- Update test and wheel matrix to include python-3.14 and
  drop support for python-3.9

* Restore workaround for Python.h include of crypt.h

* Bump manylinux docker version

* Fix wheel builds

* create compiled test

* Move verify function into tests

* generate version with setuptools_scm.  Propagate that to python and C.

* Fix sdist exclusion

* Add flacarray_config script

* Add external C link test.  Update generation of the flacarray_config script

* Update docs.  Fix flacarray_config and cmake tests.

* Revert tweak to conditional thread use

* Small tweaks to the compiled test program

* Fix message typo

* Enable rebuild on import for editable installs

* Add new unit tests for arbitrary custom MPI distribution on load in conjunction with a keep array.  Fix corner case typo that caused these to fail.

* Clean up flacarray_config and Findflacarray.cmake macro

* Add sdist to wheel upload.  Bump artifact action versions.

Author: tskisner

.github/workflows/docs.yml

@@ -55,21 +55,10 @@ jobs:
             && popd >/dev/null 2>&1
 
       - name: Install Docs Dependencies
-        # AttributeError: 'MathBlockParser' object has no attribute 'parse_axt_heading'
-        # https://github.com/jupyter/nbconvert/issues/2198
-        # mistune = "<3.1"
         run: |
           source ~/conda/etc/profile.d/conda.sh \
             && conda activate docs \
-            && conda install --yes \
-              mkdocs \
-              mkdocstrings \
-              mkdocstrings-python \
-              mkdocs-material \
-              mkdocs-material-extensions \
-              mkdocs-jupyter \
-              "mistune<3.1" \
-            && pip install mkdocs-print-site-plugin \
+            && ./docs/install_requirements.sh \
             && git config user.name 'github-actions[bot]' \
             && git config user.email 'github-actions[bot]@users.noreply.github.com'
 

.github/workflows/test.yml

@@ -29,30 +29,30 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: "3.9"
+            python: "3.10"
             arch: Linux-x86_64
             ompdisable: 0
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
             arch: Linux-x86_64
             ompdisable: 0
           - os: ubuntu-latest
-            python: "3.13"
+            python: "3.14"
             arch: Linux-x86_64
             ompdisable: 0
-          - os: macos-latest
+          - os: macos-15-intel
             python: "3.10"
             arch: MacOSX-x86_64
             ompdisable: 1
-          - os: macos-latest
+          - os: macos-15-intel
             python: "3.13"
             arch: MacOSX-x86_64
             ompdisable: 1
-          - os: macos-latest
+          - os: macos-15
             python: "3.10"
             arch: MacOSX-arm64
             ompdisable: 1
-          - os: macos-latest
+          - os: macos-15
             python: "3.13"
             arch: MacOSX-arm64
             ompdisable: 1
@@ -85,7 +85,7 @@ jobs:
             && conda create --yes -n test python==${{ matrix.python }} \
             && conda activate test \
             && conda install --yes --file packaging/conda_build_requirements.txt
-          if test ${{ matrix.python }} = "3.9"; then conda install libxcrypt; fi
+          if test ${{ matrix.python }} = "3.10"; then conda install libxcrypt; fi
 
       - name: Install
         run: |
@@ -123,3 +123,21 @@ jobs:
             && pushd test >/dev/null 2>&1 \
             && mpirun -np 2 python -m mpi4py -c 'import flacarray.tests; flacarray.tests.run()' \
             && popd >/dev/null 2>&1
+
+      - name: External C Link Tests (Dynamic)
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate test \
+            && export OMP_NUM_THREADS=2 \
+            && cmake -S packaging/test_c_link -B build_c_link \
+            && cmake --build build_c_link \
+            && ctest --test-dir build_c_link
+
+      - name: External C Link Tests (Static)
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate test \
+            && export OMP_NUM_THREADS=2 \
+            && cmake -S packaging/test_c_link -B build_c_link_static \
+            && cmake --build build_c_link_static \
+            && ctest --test-dir build_c_link_static

.github/workflows/wheels.yml

@@ -11,6 +11,22 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
   build_wheels:
     name: Build wheel for cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
@@ -21,10 +37,6 @@ jobs:
       matrix:
         include:
           # Linux 64 bit manylinux
-          - os: ubuntu-latest
-            arch: x86_64
-            python: 39
-            builder: manylinux
           - os: ubuntu-latest
             arch: x86_64
             python: 310
@@ -41,48 +53,54 @@ jobs:
             arch: x86_64
             python: 313
             builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 314
+            builder: manylinux
 
-          # MacOS x86_64.  The macos-13 runner is the last
-          # Intel-based runner version.  At some point we'll
-          # need to switch to macos-latest and test cross compiling.
-          - os: macos-13
+          # MacOS x86_64.
+          - os: macos-15-intel
             arch: x86_64
             python: 310
             builder: macosx
-          - os: macos-13
+          - os: macos-15-intel
             arch: x86_64
             python: 311
             builder: macosx
-          - os: macos-13
+          - os: macos-15-intel
             arch: x86_64
             python: 312
             builder: macosx
-          - os: macos-13
+          - os: macos-15-intel
             arch: x86_64
             python: 313
             builder: macosx
 
           # MacOS arm64
-          - os: macos-latest
+          - os: macos-15
             arch: arm64
             python: 310
             builder: macosx
-          - os: macos-latest
+          - os: macos-15
             arch: arm64
             python: 311
             builder: macosx
-          - os: macos-latest
+          - os: macos-15
             arch: arm64
             python: 312
             builder: macosx
-          - os: macos-latest
+          - os: macos-15
             arch: arm64
             python: 313
             builder: macosx
+          - os: macos-15
+            arch: arm64
+            python: 314
+            builder: macosx
     env:
       CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
-      CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
-      CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.builder }}2014
+      CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}_2_28
+      CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.builder }}_2_28
       CIBW_BUILD_VERBOSITY: 3
       CIBW_ENVIRONMENT_LINUX: >
         CC=gcc
@@ -100,19 +118,19 @@ jobs:
       - uses: actions/setup-python@v6
         name: Install Python
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.22.0
+          python -m pip install cibuildwheel==3.3.1
 
       - name: Build wheel
         run: |
           python -m cibuildwheel --output-dir wheelhouse
 
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         with:
-          name: flacarray-cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+          name: cibw-wheels_cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
           path: ./wheelhouse/flacarray*cp${{ matrix.python }}-${{ matrix.builder }}*${{ matrix.arch }}*.whl
 
   upload_pypi:
@@ -122,10 +140,10 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v7
+      - uses: actions/download-artifact@v8
         with:
           # Unpacks all artifacts into dist/
-          pattern: flacarray-*
+          pattern: cibw-*
           path: dist
           merge-multiple: true
 

.gitignore

@@ -1,3 +1,7 @@
+# Generated files
+src/flacarray/_version.py
+src/flacarray/libflacarray/version.c
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CMakeLists.txt

@@ -0,0 +1,73 @@
+cmake_minimum_required(VERSION 3.21)
+
+# Warn if the user invokes CMake directly
+if (NOT SKBUILD)
+    message(WARNING "\
+    This CMake file is meant to be executed using 'scikit-build-core'.
+    Running it directly will almost certainly not produce the desired
+    result. If you are a user trying to install this package, use the
+    command below, which will install all necessary build dependencies,
+    compile the package in an isolated environment, and then install it.
+
+    $ pip install .
+
+    ")
+endif()
+
+message(STATUS "CMAKE_BUILD_TYPE set to '${CMAKE_BUILD_TYPE}'")
+
+# Auxiliary files
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+
+# Define the project with name and version from pyproject.toml
+project(${SKBUILD_PROJECT_NAME} LANGUAGES C VERSION ${SKBUILD_PROJECT_VERSION})
+
+# We are building libraries that will eventually be linked into shared
+# modules.  All code should be built with PIC.
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# Use modern C
+set(CMAKE_C_STANDARD 11)
+
+# For installing the stand-alone library and header
+include(GNUInstallDirs)
+
+# OpenMP
+if(NOT DISABLE_OPENMP)
+    find_package(OpenMP)
+endif()
+
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+include(UseCython)
+
+execute_process(
+    COMMAND "${Python_EXECUTABLE}" -c "import numpy; print(numpy.get_include(), end='')"
+    OUTPUT_VARIABLE NUMPY_INCLUDE_DIR
+)
+
+find_package(FLAC REQUIRED)
+
+if(DEFINED FLAC_VERSION)
+    if(FLAC_VERSION STREQUAL "")
+        message(STATUS "Cannot determine FLAC version- assuming it is >= 1.4.0")
+    else()
+        string(REGEX REPLACE "^([0-9]+)\\.[0-9]+\\..*" "\\1"
+            FLAC_MAJ_VERSION "${FLAC_VERSION}")
+        string(REGEX REPLACE "^[0-9]+\\.([0-9]+)\\..*" "\\1"
+            FLAC_MIN_VERSION "${FLAC_VERSION}")
+        if(FLAC_MAJ_VERSION GREATER 1)
+            # Future proofing
+            message(STATUS "Found FLAC version ${FLAC_VERSION}")
+        else()
+            if(FLAC_MIN_VERSION GREATER_EQUAL 4)
+                message(STATUS "Found FLAC version ${FLAC_VERSION}")
+            else()
+                message(FATAL_ERROR "FLAC version ${FLAC_VERSION} is not >= 1.4.0")
+            endif()
+        endif()
+    endif()
+else()
+    message(STATUS "Cannot determine FLAC version- assuming it is >= 1.4.0")
+endif()
+
+add_subdirectory(src)