test_run.yml

name: Python package

on: [ push , pull_request]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11"]

    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install flake8 pytest
          pip install .
      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --exit-zero --count --select=E9,F63,F7,F82 --show-source --statistics
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
      - name: Download test omamer db file
        run: |
          wget -O Homininae.h5 'https://omabrowser.org/All/Homininae.h5'
      - name: Download sample fasta file
        run: |
         wget -O human_sample.fa 'https://rest.uniprot.org/uniprotkb/search?format=fasta&query=%28%28proteome%3AUP000005640%29%29&size=200'
         head -n 10 human_sample.fa
      - name: Test 
        run: |
          ls -l
          omamer search --db Homininae.h5 --query human_sample.fa --out human_sample.omamer
          cat human_sample.omamer