Update writers.py #32
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name: Test Preprimer | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout code | |
uses: actions/checkout@v2 | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: '3.x' | |
- name: Install dependencies | |
run: | | |
pip install -e . # install the preprimer package | |
pip install -r requirements.txt # Ensure pytest is listed here | |
- name: Set up conda | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
python-version: '3.12' # Replace with your Python version | |
- name: Install mamba and environment dependencies | |
shell: bash -l {0} | |
run: | | |
conda init bash | |
source ~/.bashrc | |
conda config --add channels bioconda | |
conda config --add channels conda-forge | |
conda install mamba -n base -c conda-forge | |
mamba create -n preprimer me-pcr exonerate pytest blast | |
source activate preprimer # Activate the environment | |
python -m pytest tests/test.py # Run the tests within the environment |