run_circhemy_ci.yml

name: CI tests

on:
  push:
  pull_request:
  schedule:
    - cron: '0 11 * * *'


concurrency:
  group: ci-tests-${{ github.ref }}-1
  cancel-in-progress: true

jobs:
  Main:
    strategy:
      matrix:
        #os: [macos-14]
        os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13]
        #python-version: ["3.11"]
        python-version: ["3.8", "3.8", "3.9", "3.10", "3.11", "3.12"]
    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
    steps:
    - name: Create files
      uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        architecture: 'x64'
    - name: Updating setuptools
      run: |
         python3 -m pip install -U pip setuptools
    - name: Updating pip
      run: |
         python3 -m pip install --upgrade pip
    - name: Installing circhemy & Python dependencies
      run: |
         python3 -m pip install ./ -v
    - name: Check if circhemy starts
      run: |
         circhemy --version
         which circhemy
    - name: Download circhemy database
      run: |
         circhemy download
    - name: Running circhemy convert test
      run: |
         cat `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_query.results | circhemy convert  -q STDIN -i circBase -o CircAtlas2 circBase Genome > convert_output
    - name: Checking generated output against gold output
      run: |
         diff `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_convert.results convert_output
    - name: Running circhemy query test
      run: |
         circhemy query -o  circBase -b *atf6 -g hg38 | cut -f1 > query_output
    - name: Checking generated output against gold output
      run: |
         diff `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_query.results query_output

    runs-on: ${{ matrix.os }}