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fixed contig mode filetype detection and implemeted first unit pytests #5

fixed contig mode filetype detection and implemeted first unit pytests

fixed contig mode filetype detection and implemeted first unit pytests #5

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: Python application
on:
push:
branches: [ "master", "v1.5.0" ]
pull_request:
branches: [ "master", "v1.5.0" ]
permissions:
contents: read
jobs:
build:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.12
uses: actions/setup-python@v4
with:
python-version: "3.12"
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install ncbi-blast+ clustalw -y
sudo apt-get install python3-pip python3-numpy python3-pandas -y
python3 -m pip install --upgrade pip setuptools
pip3 install pytest "biopython>=1.7,<1.78"
if [ -f requirements.txt ]; then
pip3 install -r requirements.txt;
else
pip3 install -e .
fi
- name: Test with pytest
run: |
pytest -o log_cli=true --basetemp=tmp-pytest