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ci-test.yml
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name: Integration Tests
on:
pull_request: # Run on all pull requests
push:
branches: # Run on any push to main or development
- main
- development
jobs:
build:
runs-on: ubuntu-latest
strategy:
fail-fast: False
matrix:
python-version: [ "3.8", "3.9" ]
steps:
- uses: actions/checkout@v2
- name: Setup Conda with Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v2
with:
miniconda-version: "latest"
activate-environment: test
python-version: ${{ matrix.python-version }}
- name: Install conda packages
shell: bash -l {0}
run: |
conda info
conda list
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install mamba -y
mamba install pip 'htslib>=1.13' 'bcftools>=1.13' 'samtools>=1.13' bamtools minimap2 bedtools fasttree iqtree pyqt snpeff -y
conda list
- name: Setup python packages
shell: bash -l {0}
run: |
python --version
python -m pip install .
- name: Run Tests
shell: bash -l {0}
run: pytest