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test.yml
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name: Test
on:
- push
- pull_request
jobs:
test_linux:
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: 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
steps:
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Cache Python requirements
uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ matrix.python-version }}
restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
- name: Cache built C files
uses: actions/cache@v2
with:
path: build
key: ${{ runner.os }}-build-${{ matrix.python-version }}
restore-keys: ${{ runner.os }}-build-${{ matrix.python-version }}
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
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: python setup.py build_ext --inplace --debug -j0
- 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 discover -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_osx:
name: Test (OSX)
runs-on: macos-latest
env:
OS: OSX
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: 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
steps:
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Cache Python requirements
uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ matrix.python-version }}
restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
- name: Cache built C files
uses: actions/cache@v2
with:
path: build
key: ${{ runner.os }}-build-${{ matrix.python-version }}
restore-keys: ${{ runner.os }}-build-${{ matrix.python-version }}
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
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 python setup.py build_ext --inplace --debug
- 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 discover -vv
- name: Upload to Codecov
uses: codecov/codecov-action@v3
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