dev-tests.yml

name: dev-tests

on:
  push:
    branches:
      - '**'
      - '!main'
      - '!master'
    tags-ignore:
      - '*'
  pull_request:
    branches:
      - '**'
      - '!main'
      - '!master'

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.12'] #'3.7', '3.8', '3.9', '3.10', '3.11',

    steps:
    - uses: actions/checkout@v3
    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        miniconda-version: "latest"
        auto-update-conda: true
        python-version: ${{ matrix.python-version }}
        activate-environment: xpresspipe

    - name: Install system dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y libssl-dev

    - name: Install dependencies
      shell: bash -l {0}
      run: |
        conda clean --all
        conda env update --file requirements.yml --name xpresspipe
        conda activate xpresspipe
        pip install .
        pip install codecov flake8

    - name: Run test_arguments.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_arguments.py

    - name: Run test_utils.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_utils.py

    - name: Run test_bam.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_bam.py

    - name: Run test_modifyGTF.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_modifyGTF.py

    - name: Run test_truncateGTF.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_truncateGTF.py

    - name: Run test_metagene.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_metagene.py

    - name: Run test_periodicity.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_periodicity.py

    - name: Run test_complexity.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_complexity.py

    - name: Run test_rrnaProbe.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_rrnaProbe.py

    - name: Run test_help.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_help.py

    - name: Run test_pipelines.py
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage run -a tests/test_pipelines.py

    - name: Generate coverage report
      shell: bash -l {0}
      run: |
        conda activate xpresspipe
        coverage report
        bash <(curl -s https://codecov.io/bash) -cF python