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Refactor branch

Refactor branch #18

Workflow file for this run

name: pytest
on: [pull_request]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v1
with:
python-version: 3.8
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pipenv codecov
pip install -r requirements.txt
pipenv install --dev
- name: pull reference data
run: |
curl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz -o tests/test_data/hs37d5.fa.gz
- name: gunzip data
run: |
gunzip tests/test_data/*.gz
- name: Test with pytest
run: |
pytest -vv --cov . --cov scripts/ --cov utils/