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pytest.yml
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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:
paths:
- '**.py'
pull_request:
paths:
- '**.py'
jobs:
pytest:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.6, 3.7, 3.8]
steps:
- uses: actions/checkout@v2
name: Check out source-code repository
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Install python dependencies
run: |
python -m pip install --upgrade pip -r requirements-dev.txt
pip install -e .
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
mkdir /tmp/nextflow
cd /tmp/nextflow
wget -qO- get.nextflow.io | bash
sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
- name: Test with pytest
run: python3 -m pytest --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 }}