build.yml

name: build

on: [push]

jobs:
  build1-Calculating-coverage:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.9
        uses: actions/setup-python@v2
        with:
          python-version: "3.9"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install coveralls coverage codecov wheel
          pip install .
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
      - name: Test with coverage
        run: |
          coverage run -a ./gff3tool/bin/gff3_QC.py -g example_file/example.gff3 -f example_file/reference.fa -o error.txt
          coverage run -a ./gff3tool/bin/gff3_fix.py -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3
          coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt
          coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt
          coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt
          coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt
          coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto
          coverage run -a ./gff3tool/bin/gff3_sort.py -g example_file/example.gff3 -og example-sorted.gff3
          coverage run -a ./gff3tool/bin/gff3_to_fasta.py -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences
      - name: after success
        env: 
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          coverage report
          coveralls --service=github
          codecov
  
  build2-Checking-links:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: Set up Ruby
        uses: ruby/setup-ruby@v1
        with:
          ruby-version: "3.0"
          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
      - name: Install dependencies
        run: gem install awesome_bot
      - name: Checking links
        run: awesome_bot --allow-redirect --allow-dupe README.md docs/*.md
          
  build3-Testing-functions:
    strategy:
      matrix:
        os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
    runs-on: ${{ matrix.os }}
    
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.9
        uses: actions/setup-python@v2
        with:
          python-version: "3.9"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install wheel
          pip install --no-cache-dir gff3tool
          pip install .
      - name: script
        run: |
          gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o error.txt
          gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3
          gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt
          gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt
          gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt
          gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt
          gff3_merge -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto
          gff3_sort -g example_file/example.gff3 -og example-sorted.gff3
          gff3_to_fasta -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences