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snipit.yml
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name: snipit
on: [push, pull_request]
defaults:
run:
shell: bash -l {0}
jobs:
run_snipit_test:
name: snipit test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest"]
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.x'
- name: Install dependencies
run: |
python -m pip install --upgrade pip && pip install --upgrade setuptools
- name: Display Python version
run: python -c "import sys; print(sys.version)"
- name: Install snipit
run: pip3 install -e .
- name: Check snipit version
run: snipit --version
- name: Run snipit with test data
run: snipit docs/test_2.fasta | tee snipit.log
- name: Run snipit output snps
run: snipit docs/test_2.fasta -s | tee snipit_snps.log