Build against NumPy 2.x and harden the meson/CI build

.github/workflows/CI.yml

@@ -2,38 +2,63 @@ name: Run tests
 
 on:
   push:
+  pull_request:
   release:
   workflow_dispatch:
 
+# Cancel superseded runs on the same ref so stale jobs don't pile up.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
 
   test_ubuntu:
+    name: py${{ matrix.python-version }} / ${{ matrix.numpy-spec }}
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
+      # This workflow's unique job is to prove a NumPy-2-built package runs on
+      # NumPy 1.x (the gh-114 ABI path) from a source install. Per-OS / per-Python
+      # coverage with NumPy 2.x is already provided by the wheel build+test in
+      # pypi.yml, so we only need a small representative matrix here:
+      #   - NumPy 1.x runtime on the oldest and a recent Python (the ABI path)
+      #   - one NumPy 2.x source-build smoke test on the newest Python
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-
+        include:
+          - python-version: "3.9"
+            numpy-spec: "numpy>=1.19,<2"
+          - python-version: "3.12"
+            numpy-spec: "numpy>=1.19,<2"
+          - python-version: "3.13"
+            numpy-spec: "numpy>=2"
+
     steps:
-      - uses: actions/checkout@v2
-      
+      - uses: actions/checkout@v4
+
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-          pip install numpy
-          pip install scipy
-          pip install Cython
-
-      - name: Install
-        run: |
-          pip install .
-
+      - name: Set up build environment (Fortran + ninja)
+        uses: ./.github/workflows/setup-build-env
+
+      - name: Build and install stripy
+        # Built with PEP 517 isolation -> compiled against NumPy 2.x
+        run: pip install .
+
+      - name: Pin runtime NumPy and install test deps
+        # Resolve together so the NumPy pin is honoured (a separate scipy/pytest
+        # resolve could otherwise pull NumPy back up).
+        run: pip install "${{ matrix.numpy-spec }}" pytest scipy
+
+      - name: Show resolved versions
+        run: pip list | grep -iE "numpy|stripy" || true
+
       - name: Run tests
+        # Run from a neutral directory so the *installed* package (with its
+        # compiled extensions) is imported, not the ./stripy source-tree shadow.
         run: |
-          pip install pytest
-          pytest -v
+          cd "${{ runner.temp }}"
+          python -m pytest -v "${{ github.workspace }}/stripy/tests"

.github/workflows/build_deploy_jbdoc.yml

@@ -1,51 +1,48 @@
 name: API docs / jupyterbook
 
-# We should trigger this from an upload event 
+# We should trigger this from an upload event
 
 on:
   push:   # We publish the beta docs as well
-    branches: 
-      - master 
+    branches:
+      - master
       - dev
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
+
+      - name: Set up build environment (Fortran + ninja)
+        uses: ./.github/workflows/setup-build-env
 
-      - name: Install dependencies
+      - name: Install stripy and doc dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-          pip install numpy
-          pip install scipy
-          pip install Cython
-          pip install jupyter-book
-
-      - name: Install latest stripy
-        run: |
+          pip install scipy jupyter-book
           pip install .
 
       - name: Build docs with jupyterbook
         shell: bash -l {0}
         run: |
-          VERSION=`python setup.py --version`
+          VERSION=`python -c "from importlib.metadata import version; print(version('stripy'))"`
           echo "VERSION=$(echo $VERSION)" >> $GITHUB_ENV
           cd jupyterbook
-          ./build-book.sh 
+          ./build-book.sh
 
       # Note deploy key needs the ----BEGIN ... KEY---- lines too
 
       ## Always deploy to version directory
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
-        
+
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           destination_dir: ${{ env.VERSION }}
           publish_dir: jupyterbook/_build/html
-
-

.github/workflows/build_deploy_pdoc.yml

@@ -1,32 +1,30 @@
-name: API docs / pdoc3 
+name: API docs / pdoc3
 
-# We should trigger this from an upload event 
+# We should trigger this from an upload event
 
 on:
-  push:       # This is not really a great idea 
+  push:       # This is not really a great idea
     branches:
       - master
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - name: Install dependencies
+      - name: Set up build environment (Fortran + ninja)
+        uses: ./.github/workflows/setup-build-env
+
+      - name: Install stripy and doc dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-          pip install numpy
-          pip install scipy
-          pip install Cython
-          pip install pdoc3
-          pip install pytest
-
-      - name: Install latest stripy
-        run: |
+          pip install scipy pdoc3
           pip install .
 
       - name: Build docs with pdoc
@@ -38,15 +36,15 @@ jobs:
           cd docs
           pdoc --config latex_math=True --html -o api --force stripy
 
-      # Here we can add an action to build the jupyter book to a different directory 
+      # Here we can add an action to build the jupyter book to a different directory
       # and then they can be uploaded together. The jupyter book can contain a link to the
       # API docs.
 
       # Note deploy key needs the ----BEGIN ... KEY---- lines too
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
-        
+
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           destination_dir: docs/
-          publish_dir: docs/api/stripy
+          publish_dir: docs/api/stripy

.github/workflows/pypi.yml

@@ -1,34 +1,77 @@
 name: Build wheels
 
-on: [push,pull_request,release,workflow_dispatch]
+on:
+  push:
+    branches: [master]   # feature branches are covered by the pull_request event
+  pull_request:
+  release:
+  workflow_dispatch:
+
+# Cancel superseded runs on the same ref so stale wheel builds don't pile up in
+# the (slow) macOS runner queue.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
+      # Don't let one OS failing cancel (and mask) the others.
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        include:
+          - os: ubuntu-latest
+          - os: windows-latest
+          # Apple-silicon (arm64) only; Intel-mac (x86_64) users are served by conda.
+          - os: macos-14
+            macos_target: "14.0"
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.x
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           # Disable building PyPy wheels on all platforms
           CIBW_SKIP: 'pp*'
-          CIBW_ENVIRONMENT_WINDOWS: "CFLAGS='-lquadmath'"
+          # PIP_ONLY_BINARY=scipy: install the test-time scipy from a wheel only.
+          # Otherwise pip may pick a scipy version with no wheel for the target
+          # interpreter and try to build it from source, which fails in the
+          # manylinux container (no OpenBLAS/build tooling). Forcing wheels makes
+          # pip fall back to the newest scipy that ships one.
+          CIBW_ENVIRONMENT_LINUX: "PIP_ONLY_BINARY=scipy"
+          CIBW_ENVIRONMENT_WINDOWS: "CFLAGS='-lquadmath' PIP_ONLY_BINARY=scipy"
+          # Homebrew's gfortran on the macos-14 runner targets the runner's
+          # macOS version, so the libgfortran/libquadmath that delocate bundles
+          # require that minimum. Match MACOSX_DEPLOYMENT_TARGET to the runner or
+          # delocate rejects the wheel ("Library dependencies do not satisfy
+          # target MacOS version"). (This does raise the wheel's minimum macOS;
+          # a portable gfortran targeting an older macOS could lower it later.)
+          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.macos_target }} PIP_ONLY_BINARY=scipy"
           CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
           CIBW_ARCHS: 'auto64'
+          # Use the modern manylinux/musllinux images (GCC 12). The default
+          # manylinux2014 image ships GCC 10.2, but recent NumPy only publishes
+          # manylinux_2_28 wheels and its source build requires GCC >= 10.3, so
+          # the build-isolation NumPy install would fail there. manylinux_2_28
+          # has wheels available and a new enough compiler.
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+          CIBW_MUSLLINUX_X86_64_IMAGE: musllinux_1_2
           CIBW_BEFORE_BUILD_WINDOWS: "choco install ninja"
           CIBW_BEFORE_BUILD_MACOS: "brew install ninja gcc && brew reinstall gcc"
           # CIBW_BEFORE_BUILD_LINUX: "apt-get install -y ninja-build"
-          CIBW_BEFORE_BUILD: "pip install numpy meson-python ninja setuptools build"
-          CIBW_TEST_REQUIRES: pytest
+          # NumPy is NOT installed here on purpose: cibuildwheel builds with PEP 517
+          # isolation, so the compile-time NumPy comes from `build-system.requires`
+          # in pyproject.toml (numpy>=2.0), giving wheels that run on NumPy 1.x and 2.x.
+          # A system ninja just lets meson find one without a per-build pip install.
+          CIBW_BEFORE_BUILD: "pip install ninja"
+          # scipy is needed by the mesh tests (stripy uses scipy.optimize/spatial lazily)
+          CIBW_TEST_REQUIRES: pytest scipy
           CIBW_TEST_COMMAND: "pytest {project}/stripy/tests"
         #    ...
         # with:
@@ -38,6 +81,9 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          # Unique name per matrix job: upload-artifact@v4 rejects duplicate
+          # artifact names within a run, so a shared default name would fail the build.
+          name: cibw-wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
@@ -51,6 +97,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   upload_pypi:
@@ -63,11 +110,11 @@ jobs:
     # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
     # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v4.1.7
+      - uses: actions/download-artifact@v4
         with:
-          # unpacks default artifact into dist/
-          # if `name: artifact` is omitted, the action will create extra parent dir
-          name: artifact
+          # Gather every wheel/sdist artifact from the build jobs into dist/
+          pattern: cibw-*
+          merge-multiple: true
           path: dist
 
       - uses: pypa/gh-action-pypi-publish@release/v1