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Freeze tests for Python 3.8/Ubuntu 20.04
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name: Python tests | ||
# This workflow is triggered on pushes and PRs to the repository. | ||
# Only run if we changed a Python file | ||
on: | ||
push: | ||
branches: | ||
- dev | ||
pull_request: | ||
release: | ||
types: [published] | ||
|
||
# Cancel if a newer run is started | ||
concurrency: | ||
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
cancel-in-progress: true | ||
|
||
jobs: | ||
pytest: | ||
runs-on: ubuntu-20.04 | ||
steps: | ||
- uses: actions/checkout@v3 | ||
name: Check out source-code repository | ||
|
||
- name: Set up Python 3.8 | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: "3.8" | ||
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||
- name: Install python dependencies | ||
run: | | ||
python -m pip install --upgrade pip -r requirements-dev.txt | ||
pip install -e . | ||
- name: Downgrade git to the Ubuntu official repository's version | ||
run: | | ||
sudo apt remove git git-man | ||
sudo add-apt-repository --remove ppa:git-core/ppa | ||
sudo apt install git | ||
- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v1 | ||
with: | ||
version: "latest-everything" | ||
|
||
- name: Test with pytest | ||
run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core | ||
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||
- uses: codecov/codecov-action@v1 | ||
name: Upload code coverage report | ||
with: | ||
if: success() | ||
token: ${{ secrets.CODECOV_TOKEN }} |