Include 3.13 and numpy 2 support in binaries (#210)

Updating to np 2 and 3.13. Should close issues #205, #207. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
impy-project · Nov 11, 2024 · b7d7035 · b7d7035
1 parent 3adc6b7
commit b7d7035
Show file tree

Hide file tree

Showing 29 changed files with 835 additions and 546 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -22,10 +22,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        arch: [native]
-        py: [cp310]
+        arch: [auto]
+        py: [cp313]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -37,19 +37,20 @@ jobs:
         id: setup-fortran
         with:
           compiler: gcc
-          version: 11
+          version: 13
 
       - name: cibuildwheel on Linux
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_PASS_LINUX: CI
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
+          name: wheel-${{ matrix.py }}-${{ matrix.os }}-${{ matrix.arch }}
 
 
 
@@ -60,36 +61,39 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        arch: [native, arm64]
-        py: [cp39, cp310, cp311, cp312]
+        os: [ubuntu-latest, macos-13, macos-14] # windows-latest: Disable windows for now
+        arch: [auto, aarch64]
+        py: [cp39, cp310, cp311, cp312, cp313]
         exclude:
-            - os: ubuntu-latest
-              arch: arm64
-            - os: windows-latest
-              arch: arm64
+          - os: windows-latest
+            arch: aarch64
+          - os: macos-13
+            arch: aarch64
+          - os: macos-14
+            arch: aarch64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
+          fetch-depth: 0
+
+      - if: ${{ matrix.arch == 'aarch64' }}
+        uses: docker/setup-qemu-action@v3
 
       - name: Get latest CMake and Ninja
         uses: lukka/get-cmake@latest
 
-      - if: ${{ matrix.arch == 'aarch64' }}
-        uses: docker/setup-qemu-action@v2
+      # Set deployment target env var on macos 13
+      - if: ${{ matrix.os == 'macos-13' }}
+        name: Set deployment target for MacOS-13
+        run: export MACOSX_DEPLOYMENT_TARGET=13.0
 
-      # Remove after January 16th 2023 when GA switches to 14.2 by default
-      # Remove someday when migration for all nodes will be finished
-      - if: ${{ matrix.os == 'macos-latest' }}
+      - if: ${{ matrix.os == 'macos-13'}}
+        name: Use a more legacy version of Xcode tools on MacOS-13
         run: sudo xcode-select -s "/Applications/Xcode_14.2.app"
 
-      - if: ${{ matrix.os == 'macos-latest' &&  matrix.arch == 'native'}}
-        name: Install graphviz for tests on MacOS native
-        uses: tlylt/install-graphviz@v1
-
-      - if: ${{ matrix.os == 'macos-latest' &&  matrix.arch == 'native'}}
-        name: Setup gfortran for MacOS native
+      - if: ${{ matrix.os == 'macos-13'}}
+        name: Setup gfortran for MacOS 13
         run: |
           # Taken from https://github.com/numpy/numpy/tree/main/tools/wheels
           set -xe
@@ -99,17 +103,22 @@ jobs:
           gfortran --version
           which gfortran
 
-      - if: ${{ matrix.os == 'ubuntu-latest' ||  matrix.os == 'windows-latest' }}
-        name: Setup gfortran for Linux or Windows
-        uses: awvwgk/setup-fortran@main
+      - if: ${{ matrix.os != 'macos-13'}}
+        name: Setup gfortran
+        uses: awvwgk/setup-fortran@v1.6.1
         id: setup-fortran
         with:
           compiler: gcc
-          version: 11
+          version: 13
+
+      - if: ${{ matrix.os != 'macos-13' }}
+        uses: ts-graphviz/setup-graphviz@v2
+        name: Install Graphviz
+
 
       - if: ${{ matrix.os == 'windows-latest' }}
         name: cibuildwheel on Windows
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
@@ -118,52 +127,44 @@ jobs:
 
       - if: ${{ matrix.os == 'ubuntu-latest' }}
         name: cibuildwheel on Linux
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_PASS_LINUX: CI
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          # Will avoid testing on emulated architectures
+          CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x,armv7l}"
+
 
-      - if: ${{ matrix.os == 'macos-latest' &&  matrix.arch == 'native' }}
-        name: cibuildwheel on MacOS native
-        uses: pypa/cibuildwheel@v2.16.5
+      - if: ${{ matrix.os == 'macos-13'}}
+        name: cibuildwheel on MacOS-13
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
           no_proxy: '*'
+          CHROMO_SKIP_GRAPHVIZ: 1
 
-      - if: ${{ matrix.os == 'macos-latest' &&  matrix.arch == 'arm64' }}
-        name: cibuildwheel on MacOS arm64
-        id: cibw_step
-        uses: pypa/cibuildwheel@v2.16.5
+      - if: ${{ matrix.os == 'macos-14' }}
+        name: cibuildwheel on MacOS-14
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
-          CIBW_ARCHS_MACOS: arm64
-          CIBW_BEFORE_BUILD: |
-            # Taken from https://github.com/numpy/numpy/tree/main/tools/wheels
-            set -xe
-            export PLAT="arm64"
-            chmod +x .github/workflows/gfortran_utils.sh
-            source .github/workflows/gfortran_utils.sh
-            install_arm64_cross_gfortran
-          # Although FC is set in the CIBW_BEFORE_BUILD script above,
-          # it is not found by pip and cmake. So here FC is set by hand!!!
-          # It can be a problem if gfortran will be installed in different place.
-          FC: "/opt/gfortran-darwin-arm64-cross/bin/arm64-apple-darwin20.0.0-gfortran"
-          MACOSX_DEPLOYMENT_TARGET: "11.0"
           no_proxy: '*'
+          MACOSX_DEPLOYMENT_TARGET: 14.0
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheel-${{ matrix.py }}-${{ matrix.os }}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
 
   sdist:
     name: source package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -173,17 +174,17 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: '3.12'
 
       - uses: tlylt/install-graphviz@v1
+        name: Install Graphviz
 
-      - run: python -m pip install --upgrade pip wheel
-      - run: python -m pip install numpy packaging
-      - run: python setup.py sdist
+      - run: python -m pip install --upgrade pip wheel setuptools
+      - run: pipx run build --sdist
       - run: python -m pip install --prefer-binary -v `echo dist/chromo-*`[test]
-      - run: python -m pytest -vv
+      - run: python -m pytest -v
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -194,13 +195,13 @@ jobs:
     if: ${{ startsWith(github.ref, 'refs/tags/v') }}
     steps:
       - name: Download files in artifact to "dist/" directory
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4.1.7
         with:
           name: artifact
           path: dist
 
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.6.4
+        uses: pypa/gh-action-pypi-publish@release/v1.8
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -18,37 +18,48 @@ jobs:
       matrix:
         include:
           # Python version number must be string, otherwise 3.10 becomes 3.1
-          - os: windows-latest
-            python-version: "3.12"
+          # Disable Windows for now, as long as numpy is buggy on Windows
+          # - os: windows-latest
+          #   python-version: "3.12"
+          #   installs: "numpy==1.26.4"
 
-          - os: macos-latest
+          - os: macos-14
             python-version: "3.12"
+            installs: "numpy>=2"
 
           - os: ubuntu-latest
-            python-version: "3.12"
-
+            python-version: "3.13"
+            installs: "numpy>=2"
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
-
-    - uses: actions/setup-python@v4
+        fetch-depth: 3
+    - name: Get latest CMake and Ninja
+      uses: lukka/get-cmake@latest
+    # must come after checkout
+    - uses: hendrikmuhs/ccache-action@v1.2
+      with:
+        key: ${{ github.job }}-${{ matrix.os }}-${{ matrix.python-version }}
+    - uses: astral-sh/setup-uv@v3
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        allow-prereleases: true
     - uses: awvwgk/setup-fortran@main
       id: setup-fortran
       with:
         compiler: gcc
-        version: 11
+        version: 13
 
     - run: python -m pip install --upgrade pip
 
     - if: ${{ matrix.os != 'windows-latest' }}
-      run: python -m pip install --prefer-binary -v .[test]
+      run: uv pip install --system -v .[test] ${{ matrix.installs }}
 
     - if: ${{ matrix.os == 'windows-latest' }}
-      run: python -m pip install --prefer-binary -v .[test]
+      run: python -m pip install --prefer-binary -v .[test] ${{ matrix.installs }}
       env:
         CMAKE_GENERATOR: "MinGW Makefiles"
         FC: ${{ steps.setup-fortran.outputs.fc }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@
 repos:
 # Standard hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-case-conflict
   - id: check-docstring-first
@@ -32,18 +32,26 @@ repos:
 
 # Python formatting
 - repo: https://github.com/psf/black
-  rev: 24.8.0
+  rev: 24.10.0
   hooks:
   - id: black
 
-# Python linter (Flake8)
-- repo: https://github.com/pycqa/flake8
-  rev: 7.1.1
+# Ruff linter, replacement for flake8, pydocstyle, isort
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: 'v0.6.9'
   hooks:
-  - id: flake8
-    files: chromo/[^_].*\.py
-    args: [--config, setup.cfg]
+    - id: ruff
+      args: [--fix, --show-fixes]
 
+# # CMake formatting
+# - repo: https://github.com/cheshirekow/cmake-format-precommit
+#   rev: v0.6.13
+#   hooks:
+#   - id: cmake-format
+#     additional_dependencies: [pyyaml]
+#     types: [file]
+#     files: (\.cmake|CMakeLists.txt)(.in)?$
+
 # # Enable the following later
 # # Python docstring formatting
 # - repo: https://github.com/pycqa/pydocstyle