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Merge pull request #93 from sanger-bentley-group/feature/cache-getmls… #65

Merge pull request #93 from sanger-bentley-group/feature/cache-getmls…

Merge pull request #93 from sanger-bentley-group/feature/cache-getmls… #65

Workflow file for this run

# Runs test related tasks.
name: test
on:
push:
branches: [ main, dev ]
pull_request:
branches: [ main, dev ]
jobs:
test:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 pytest pytest-cov
pip install biopython pandas
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest
run: |
python3 -m pytest --cov=./ --cov-report=xml
- uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: ./coverage.xml
env_vars: OS,PYTHON
name: codecov-upload
fail_ci_if_error: true
verbose: true
- uses: actions/setup-java@v3
with:
distribution: 'zulu'
java-version: '17'
- name: Install Nextflow
run: |
# Install latest version of Nextflow
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/bin
- name: Regression tests
run: ./tests/regression_tests.sh