Develop #103
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: set up python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8.10" | |
| - name: install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --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: test gen_reads | |
| run: python gen_reads_runner.py -R 101 -o test -r data/H1N1.fasta | |
| job-valBAM: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Execute validateBAM.py | |
| run: | | |
| cd ${{ github.workspace }}/utilities | |
| python validateBam.py ../data/baby.bam | |
| - run: echo "🍏 This job's status is ${{ job.status }}." | |
| job-valFQ: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Execute validateFQ.py | |
| run: | | |
| pip install biopython | |
| cd ${{ github.workspace }}/utilities | |
| python validateFQ.py ../data/baby.fastq | |
| - run: echo "🍏 This job's status is ${{ job.status }}." | |
| # job-computegc: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Check out repository code | |
| # uses: actions/checkout@v2 | |
| # - name: Execute compute_gc.py | |
| # run: | | |
| # pip install numpy | |
| # pip install biopython | |
| # pip install pandas | |
| # cd ${{ github.workspace }}/utilities | |
| # python compute_gc.py -i ../data/small.genomecov -r ../data/ecoli.fa -o gcop | |
| # - run: echo "🍏 This job's status is ${{ job.status }}." | |