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Fix wheels for macOS #3371

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Merged
jeromekelleher merged 4 commits into from
Jan 23, 2026
Merged

Fix wheels for macOS #3371

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c7c8afd
Bump GitHub Actions
hugovk Jan 21, 2026
5db113c
Add colour to GitHub Actions logs for readability
hugovk Jan 21, 2026
31102c5
macos-14 is ARM-only
hugovk Jan 21, 2026
4e29cd3
Fix deprecation warning in GHA
hugovk Jan 21, 2026
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4 changes: 4 additions & 0 deletions .github/workflows/docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,10 @@ on:
branches: [main]
tags:
- '*'

env:
FORCE_COLOR: 1

jobs:
Docs:
uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
Expand Down
14 changes: 8 additions & 6 deletions .github/workflows/release.yml
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Expand Up @@ -5,14 +5,17 @@ on:
branches: [main, test]
tags: ['*']

env:
FORCE_COLOR: 1

jobs:
build:
runs-on: ubuntu-24.04
steps:
- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2
- name: Set up Python
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: '3.12'
- name: Install dependencies and set up venv
Expand All @@ -36,10 +39,9 @@ jobs:
python docs/convert_changelog.py python/CHANGELOG.rst > PYTHON-CHANGELOG.txt
- name: Get the version
id: get_version
run:
echo ::set-output name=VERSION::$(echo $GITHUB_REF | cut -d / -f 3)
run: echo "VERSION=$(echo $GITHUB_REF | cut -d / -f 3)" >> $GITHUB_OUTPUT
- name: C Release
uses: softprops/action-gh-release@v2.2.1
uses: softprops/action-gh-release@v2.5.0
if: startsWith(github.ref, 'refs/tags/') && contains(github.event.ref, 'C_')
with:
name: C API ${{ steps.get_version.outputs.VERSION }}
Expand All @@ -48,7 +50,7 @@ jobs:
fail_on_unmatched_files: True
files: build-gcc/meson-dist/*
- name: Python Release
uses: softprops/action-gh-release@v2.2.1
uses: softprops/action-gh-release@v2.5.0
if: startsWith(github.ref, 'refs/tags/') && !contains(github.event.ref, 'C_')
with:
name: Python ${{ steps.get_version.outputs.VERSION }}
Expand Down
26 changes: 14 additions & 12 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ on:
push:
branches: [main, test]

env:
FORCE_COLOR: 1
jobs:
pre-commit:
name: Lint
Expand All @@ -24,12 +26,12 @@ jobs:
shell: bash
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.12.1
uses: styfle/cancel-workflow-action@0.13.0
with:
access_token: ${{ github.token }}

- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2

- name: Install OSX libs
if: matrix.os == 'macos-latest'
Expand All @@ -47,7 +49,7 @@ jobs:
cp ../c/tskit.h lib/.

- name: Install uv and set the python version
uses: astral-sh/setup-uv@v6
uses: astral-sh/setup-uv@v7
with:
python-version: ${{ matrix.python }}
version: "0.8.15"
Expand Down Expand Up @@ -78,7 +80,7 @@ jobs:
NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v5.4.0
uses: codecov/codecov-action@v5.5.2
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
Expand All @@ -96,7 +98,7 @@ jobs:
fi

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v5.4.0
uses: codecov/codecov-action@v5.5.2
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
Expand All @@ -114,20 +116,20 @@ jobs:
shell: bash
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.12.1
uses: styfle/cancel-workflow-action@0.13.0
with:
access_token: ${{ github.token }}

- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2

- name: Setup Python
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: '3.12'

- name: Install uv
uses: astral-sh/setup-uv@v6
uses: astral-sh/setup-uv@v7
with:
version: "0.8.15"

Expand All @@ -150,7 +152,7 @@ jobs:
uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py tests/test_highlevel.py

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v5.4.0
uses: codecov/codecov-action@v5.5.2
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
Expand All @@ -172,12 +174,12 @@ jobs:
shell: msys2 {0}
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.12.1
uses: styfle/cancel-workflow-action@0.13.0
with:
access_token: ${{ github.token }}

- name: 'Checkout'
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2

- name: Setup MSYS2 ${{matrix.sys}}
uses: msys2/setup-msys2@v2.27.0
Expand Down
51 changes: 30 additions & 21 deletions .github/workflows/wheels.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,17 +10,22 @@ on:
release:
types: [published]


env:
FORCE_COLOR: 1

jobs:
OSX:
runs-on: macos-latest
strategy:
fail-fast: false
matrix:
python: ["3.10", 3.11, 3.12, 3.13]
steps:
- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: ${{ matrix.python }}
- name: Install deps
Expand All @@ -36,20 +41,21 @@ jobs:
pip install delocate
delocate-wheel -v dist/*.whl
- name: Upload Wheels
uses: actions/upload-artifact@v4.6.1
uses: actions/upload-artifact@v6.0.0
with:
name: osx-wheel-${{ matrix.python }}
path: python/dist

windows:
runs-on: windows-latest
strategy:
fail-fast: false
matrix:
python: ["3.10", 3.11, 3.12, 3.13]
wordsize: [64]
steps:
- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2
- name: Install deps
env:
PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
Expand All @@ -74,7 +80,7 @@ jobs:
cp ../c/tskit.h lib/.
${PYTHON} -m build --wheel
- name: Upload Wheels
uses: actions/upload-artifact@v4.6.1
uses: actions/upload-artifact@v6.0.0
with:
name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
path: python/dist
Expand All @@ -83,10 +89,10 @@ jobs:
runs-on: ubuntu-24.04
steps:
- name: Checkout
uses: actions/checkout@v4.2.2
uses: actions/checkout@v6.0.2

- name: Set up Python 3.10
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: "3.10"

Expand All @@ -98,7 +104,7 @@ jobs:
python -m build --sdist

- name: Upload sdist
uses: actions/upload-artifact@v4.6.1
uses: actions/upload-artifact@v6.0.0
with:
name: sdist
path: python/dist
Expand All @@ -109,30 +115,31 @@ jobs:
docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh

- name: Upload Wheels
uses: actions/upload-artifact@v4.6.1
uses: actions/upload-artifact@v6.0.0
with:
name: linux-wheels
path: python/dist/wheelhouse

OSX-test:
needs: ['OSX']
strategy:
fail-fast: false
matrix:
python: ["3.10", 3.11, 3.12, 3.13]
runner: [macos-14, macos-15]
runner: [macos-15, macos-15-intel]
include:
- runner: macos-14
arch: x86_64
- runner: macos-15
arch: arm64
- runner: macos-15-intel
arch: x86_64
runs-on: ${{ matrix.runner }}
steps:
- name: Download wheels
uses: actions/download-artifact@v4.2.0
uses: actions/download-artifact@v7.0.0
with:
name: osx-wheel-${{ matrix.python }}
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: ${{ matrix.python }}
- name: Verify architecture
Expand All @@ -154,16 +161,17 @@ jobs:
needs: ['windows']
runs-on: windows-latest
strategy:
fail-fast: false
matrix:
python: ["3.10", 3.11, 3.12, 3.13]
wordsize: [64]
steps:
- name: Download wheels
uses: actions/download-artifact@v4.2.0
uses: actions/download-artifact@v7.0.0
with:
name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: ${{ matrix.python }}
- name: Install wheel and test
Expand All @@ -178,6 +186,7 @@ jobs:
runs-on: ubuntu-24.04
needs: ['manylinux']
strategy:
fail-fast: false
matrix:
python: ["3.10", 3.11, 3.12, 3.13]
include:
Expand All @@ -191,11 +200,11 @@ jobs:
wheel: cp313
steps:
- name: Download wheels
uses: actions/download-artifact@v4.2.0
uses: actions/download-artifact@v7.0.0
with:
name: linux-wheels
- name: Set up Python
uses: actions/setup-python@v5.4.0
uses: actions/setup-python@v6.1.0
with:
python-version: ${{ matrix.python }}
- name: Install wheel and test
Expand All @@ -213,16 +222,16 @@ jobs:
id-token: write
steps:
- name: Download all
uses: actions/download-artifact@v4.2.0
uses: actions/download-artifact@v7.0.0
- name: Move to dist
run: |
mkdir dist
cp */*.{whl,gz} dist/.
- name: Publish distribution to Test PyPI
if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && !contains(github.event.ref, 'C_')
uses: pypa/gh-action-pypi-publish@v1.12.4
uses: pypa/gh-action-pypi-publish@v1.13.0
with:
repository_url: https://test.pypi.org/legacy/
- name: Publish distribution to PRODUCTION PyPI
if: github.event_name == 'release' && !startsWith(github.event.release.tag_name, 'C_')
uses: pypa/gh-action-pypi-publish@v1.12.4
uses: pypa/gh-action-pypi-publish@v1.13.0