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test.yml
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name: Test
on:
- push
- pull_request
jobs:
test_linux_x86:
name: Test (Linux)
runs-on: ubuntu-latest
env:
OS: Linux
strategy:
matrix:
include:
- python-version: 3.7
python-release: v3.7
python-impl: CPython
- python-version: 3.8
python-release: v3.8
python-impl: CPython
- python-version: 3.9
python-release: v3.9
python-impl: CPython
- python-version: '3.10'
python-release: 'v3.10'
python-impl: CPython
- python-version: '3.11'
python-release: 'v3.11'
python-impl: CPython
- python-version: '3.12'
python-release: 'v3.12'
python-impl: CPython
- python-version: pypy-3.7
python-release: v3.7
python-impl: PyPy
- python-version: pypy-3.8
python-release: v3.8
python-impl: PyPy
- python-version: pypy-3.9
python-release: v3.9
python-impl: PyPy
- python-version: pypy-3.10
python-release: v3.10
python-impl: PyPy
steps:
- name: Checkout code
uses: actions/checkout@v4
with:
submodules: true
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Show Python build environment
run: python -m sysconfig
- name: Update pip
run: python -m pip install -U pip wheel setuptools
- name: Install Python requirements
run: python -m pip install -r .github/workflows/requirements.txt
- name: Build C extension
run: pip install -e . --no-build-isolation
- name: Install test requirements
run: python -m pip install -r pyhmmer/tests/requirements.txt
- name: Test with coverage
run: python -m coverage run -m unittest pyhmmer.tests -vv
- name: Upload to Codecov
if: matrix.python-impl == 'CPython'
uses: codecov/codecov-action@v3
with:
flags: ${{ matrix.python-release }}
env_vars: OS
name: test-python-${{ matrix.python-version }}
fail_ci_if_error: false
token: ${{ secrets.CODECOV_TOKEN }}
verbose: true
# test_linux_arm64:
# name: Test (Linux, arm64)
# runs-on: ubuntu-latest
# strategy:
# matrix:
# python-tag:
# - cp310-manylinux_aarch64
# - cp311-manylinux_aarch64
# steps:
# - uses: actions/checkout@v4
# with:
# submodules: true
# - name: Set up QEMU
# id: qemu
# uses: docker/setup-qemu-action@v3
# with:
# platforms: arm64
# - name: Build manylinux wheels
# uses: pypa/[email protected]
# env:
# CIBW_ARCHS: aarch64
# CIBW_BUILD: ${{ matrix.python-tag }}
# CIBW_BUILD_VERBOSITY: 2
# CIBW_BEFORE_BUILD: pip install cython
# CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
# CIBW_TEST_REQUIRES: importlib-resources
# with:
# output-dir: dist
# - uses: actions/upload-artifact@v3
# with:
# name: wheels
# path: dist/*
test_osx_x86:
name: Test (OSX)
runs-on: macos-12
env:
OS: OSX
_PYTHON_HOST_PLATFORM: macosx-10.9-x86_64
strategy:
matrix:
include:
- python-version: 3.7
python-release: v3.7
python-impl: CPython
- python-version: 3.8
python-release: v3.8
python-impl: CPython
- python-version: 3.9
python-release: v3.9
python-impl: CPython
- python-version: '3.10'
python-release: 'v3.10'
python-impl: CPython
- python-version: '3.11'
python-release: 'v3.11'
python-impl: CPython
- python-version: '3.12'
python-release: 'v3.12'
python-impl: CPython
- python-version: pypy-3.7
python-release: v3.7
python-impl: PyPy
- python-version: pypy-3.8
python-release: v3.8
python-impl: PyPy
- python-version: pypy-3.9
python-release: v3.9
python-impl: PyPy
- python-version: pypy-3.10
python-release: v3.10
python-impl: PyPy
steps:
- name: Checkout code
uses: actions/checkout@v4
with:
submodules: true
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Show Python build environment
run: arch -x86_64 python -m sysconfig
- name: Update pip
run: python -m pip install -U pip wheel setuptools
- name: Install Python requirements
run: python -m pip install -r .github/workflows/requirements.txt
- name: Build C extension
run: arch -x86_64 pip install -e . --no-build-isolation
- name: Install test requirements
run: python -m pip install -r pyhmmer/tests/requirements.txt
if: matrix.python-impl == 'CPython'
- name: Test with coverage
run: python -m coverage run -m unittest pyhmmer.tests -vv
- name: Upload to Codecov
uses: codecov/codecov-action@v4
if: matrix.python-impl == 'CPython'
with:
flags: ${{ matrix.python-release }}
env_vars: OS
name: test-python-${{ matrix.python-version }}
fail_ci_if_error: false
token: ${{ secrets.CODECOV_TOKEN }}
codecov_curl_args: "--globoff"
verbose: true