python-package.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python package

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.7, 3.8, 3.9]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install
      run: |
        python -m pip install --upgrade pip
        python -m pip install flake8 pytest
        pip install -r requirements_dev.txt
        python setup.py build_ext --inplace
        pip install -v .
#    - 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
      run: |
        nosetests -v
        pysamstats --help
        pysamstats --type coverage fixture/test.bam > coverage.txt
        pysamstats --type coverage --output=coverage.txt fixture/test.bam
        pysamstats --type coverage --output=coverage.h5 --format=hdf5 fixture/test.bam
        pysamstats --type coverage --fields=pos,reads_all fixture/test.bam > coverage_fields.txt
        pysamstats --type coverage_binned --fasta=fixture/ref.fa fixture/test.bam > coverage_binned.txt
        pysamstats --type coverage_binned --fasta=fixture/ref.fa --output=coverage_binned.txt fixture/test.bam
        pysamstats --type coverage_binned --fasta=fixture/ref.fa --output=coverage_binned.h5 --format=hdf5 fixture/test.bam
        pysamstats --type=coverage --min-mapq=27 --min-baseq=17 --no-dup --no-del fixture/test.bam > coverage_filtered.txt
        pysamstats --type=coverage_binned --fasta=fixture/ref.fa --min-mapq=27 --no-dup fixture/test.bam > coverage_binned_filtered.txt