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Fix tests for lshmm 0.0.8 #7

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Fix tests for lshmm 0.0.8

Fix tests for lshmm 0.0.8 #7

Workflow file for this run

.github/workflows/wheels.yml at c818a6c
name: Build and test wheels
on:
push:
branches:
- main
- test
tags:
- '*'
release:
types: [published]
jobs:
OSX:
runs-on: macos-latest
strategy:
matrix:
python: [3.8, 3.9, "3.10", 3.11]
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
- name: Install deps
run: |
# Upgrade pip to get bdist_wheel
pip install --upgrade pip
pip install setuptools wheel
# Instead of letting setup.py install a newer numpy we install it here
# using the oldest supported version for ABI compatibility
pip install oldest-supported-numpy
- name: Build C extension
run: |
cd python
python -VV
python setup.py build_ext --inplace
- name: Build Wheel
run: |
cd python
python setup.py bdist_wheel
- name: Delocate to bundle dynamic libs
run: |
cd python
pip install delocate
delocate-wheel -v dist/*.whl
- name: Upload Wheels
uses: actions/upload-artifact@v4
with:
name: osx-wheel-${{ matrix.python }}
path: python/dist
windows:
runs-on: windows-latest
strategy:
matrix:
python: [3.8, 3.9, "3.10", 3.11]
wordsize: [64]
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install deps
env:
PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
shell: bash
run: |
set -ex
${PYTHON} -m pip install --upgrade pip
${PYTHON} -m pip install setuptools wheel
# Instead of letting setup.py install a newer numpy we install it here
# using the oldest supported version for ABI compatibility
${PYTHON} -m pip install oldest-supported-numpy
- name: Build C Extension
env:
PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
shell: bash
run: |
set -ex
git reset --hard
cd python
${PYTHON} -VV
# For some reason I can't work out the C compiler is not following symlinks
rm -r lib
mkdir lib
cp -r --dereference ../c/subprojects lib/.
cp -r --dereference ../c/tskit lib/.
cp ../c/tskit.h lib/.
${PYTHON} setup.py build_ext --inplace
- name: Build Wheel
env:
PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
shell: bash
run: |
set -ex
cd python
${PYTHON} setup.py bdist_wheel
- name: Upload Wheels
uses: actions/upload-artifact@v4
with:
name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
path: python/dist
manylinux:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python 3.8
uses: actions/setup-python@v5
with:
python-version: 3.8
- name: Build sdist
shell: bash
run: |
cd python
python setup.py sdist
- name: Upload sdist
uses: actions/upload-artifact@v4
with:
name: sdist
path: python/dist
- name: Build wheels in docker
shell: bash
run: |
docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh
- name: Upload Wheels
uses: actions/upload-artifact@v4
with:
name: linux-wheels
path: python/dist/wheelhouse
OSX-test:
needs: ['OSX']
runs-on: macos-latest
strategy:
matrix:
python: [3.8, 3.9, "3.10", 3.11]
steps:
- name: Download wheels
uses: actions/download-artifact@v4
with:
name: osx-wheel-${{ matrix.python }}
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
- name: Install wheel and test
run: |
python -VV
# Install the local wheel
pip install ./tskit-*.whl
python -c "import tskit"
windows-test:
needs: ['windows']
runs-on: windows-latest
strategy:
matrix:
python: [3.8, 3.9, "3.10", 3.11]
wordsize: [64]
steps:
- name: Download wheels
uses: actions/download-artifact@v4
with:
name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
- name: Install wheel and test
shell: bash
run: |
python -VV
# Install the local wheel
python -m pip install *.whl
python -c "import tskit"
manylinux-test:
runs-on: ubuntu-latest
needs: ['manylinux']
strategy:
matrix:
python: [3.8, 3.9, "3.10", 3.11]
include:
- python: 3.8
wheel: cp38
- python: 3.9
wheel: cp39
- python: "3.10"
wheel: cp310
- python: 3.11
wheel: cp311
steps:
- name: Download wheels
uses: actions/download-artifact@v4
with:
name: linux-wheels
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python }}
- name: Install wheel and test
run: |
python -VV
# Install the local wheel
pip install ./tskit-*-${{ matrix.wheel }}-*.whl
python -c "import tskit"
PyPI_Upload:
runs-on: ubuntu-latest
environment: release
needs: ['windows-test', 'OSX-test', 'manylinux-test']
permissions:
id-token: write
steps:
- name: Download all
uses: actions/download-artifact@v4
- 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@release/v1
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@release/v1