rename strains.py
to strain.py
#362
Workflow file for this run
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name: Build and test Python package | |
on: | |
push: | |
branches: | |
- main | |
- dev | |
paths: | |
- bin/** | |
- src/** | |
- tests/** | |
- setup.py | |
- .github/workflows/build.yml | |
pull_request: | |
branches: | |
- main | |
- dev | |
paths: | |
- bin/** | |
- src/** | |
- tests/** | |
- setup.py | |
- .github/workflows/build.yml | |
types: | |
- opened | |
- reopened | |
- synchronize | |
- ready_for_review | |
jobs: | |
smoke_test: | |
name: Smoke test on ubuntu for python 3.10 | |
runs-on: ubuntu-latest | |
if: github.event.pull_request.draft == false | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python 3.10 | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.10' | |
- name: Python info | |
shell: bash -l {0} | |
run: | | |
which python3 | |
python3 --version | |
- name: Upgrade pip and install dependencies | |
run: | | |
python3 -m pip install --upgrade pip setuptools | |
pip install build pytest wheel | |
- name: Build the package | |
run: python -m build | |
- name: Install nplinker | |
run: | | |
pip install $(ls dist/nplinker*.whl) | |
install-nplinker-deps --run-on-github | |
- name: Run unit tests | |
run: pytest -v | |
build: | |
needs: smoke_test | |
name: Build for (${{ matrix.python-version }}, ${{ matrix.os }}) | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ['ubuntu-latest'] | |
python-version: ['3.9', '3.11'] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v3 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Python info | |
shell: bash -l {0} | |
run: | | |
which python3 | |
python3 --version | |
- name: Upgrade pip and install dependencies | |
run: | | |
python3 -m pip install --upgrade pip setuptools | |
pip install build pytest wheel | |
- name: Build the package | |
run: python -m build | |
- name: Install nplinker | |
run: | | |
pip install $(ls dist/nplinker*.whl) | |
install-nplinker-deps --run-on-github | |
- name: Run unit tests | |
run: pytest -v | |
sonarcloud: | |
name: SonarCloud | |
needs: smoke_test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.10' | |
- name: Python info | |
shell: bash -l {0} | |
run: | | |
which python3 | |
python3 --version | |
- name: Upgrade pip and setuptools | |
run: | | |
python3 -m pip install --upgrade pip setuptools wheel | |
- name: Install nplinker and its dependencies | |
run: | | |
python3 -m pip install .[dev] | |
install-nplinker-deps --run-on-github | |
- name: Check style against standards using ruff | |
run: ruff . | |
- name: Run unit tests with coverage | |
run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/ | |
- name: Correct coverage paths | |
run: sed -i "s+$PWD/++g" coverage.xml | |
- name: SonarCloud Scan | |
uses: SonarSource/sonarcloud-github-action@master | |
env: | |
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} | |
SONAR_TOKEN: ${{secrets.SONAR_TOKEN }} |