main-tests.yml

name: Main Branch

on:
  push:
    branches:
      - main 
  pull_request:
    branches:
      - main

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

    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 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
  
      - 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

      - name: Generate conda version report 
        shell: bash -l {0}
        run: |
          conda activate xpresspipe
          conda list --explicit > conda-spec-file.txt
          cat conda-spec-file.txt

      - name: Generate R packages version report
        shell: bash -l {0}
        run: |
          conda activate xpresspipe
          Rscript -e 'write.table(as.data.frame(installed.packages()), "R-packages-version-report.txt", sep="\t")'
          cat R-packages-version-report.txt