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Freeze tests for Python 3.8/Ubuntu 20.04
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Aratz committed Nov 30, 2022
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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"

- 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

- uses: codecov/codecov-action@v1
name: Upload code coverage report
with:
if: success()
token: ${{ secrets.CODECOV_TOKEN }}

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