old_contents: from sequana.scripts import coverage
  from nose.plugins.attrib import attr
  from sequana import sequana_data
  
  #@attr("skip")
  class TestPipeline(object):
  
      @classmethod
      def setup_class(klass):
          """This method is run once for each class before any tests are run"""
          klass.prog = "sequana_coverage"
          klass.params = {'prog': klass.prog}
  
      @classmethod
      def teardown_class(klass):
          """This method is run once for each class _after_ all tests are run"""
          import os
          # local nosetests execution
          try:os.remove('README')
          except:pass
          try:os.remove('quality.rules')
          except:pass
          try:os.remove('config.yaml')
          except:pass
  
      def _test_version(self):
          coverage.main([self.prog, '--version'])
  
      def test_help(self):
          try:
              coverage.main([self.prog, '--help'])
              assert False
          except SystemExit:
              pass
          else:
              raise Exception
  
      def test_input(self):
          filename = sequana_data('virus.bed', 'data')
          reference = sequana_data('tofill.fa', 'data')
          coverage.main([self.prog, '-i', filename, "-o"]) # "-r", reference])
  
  
  
new_contents: from sequana.scripts import coverage
  from sequana import sequana_data
  import pytest
  
  prog = "sequana_coverage"
  
  @pytest.fixture
  def coveragefix():
      import os
      # local nosetests execution
      try:os.remove('README')
      except:pass
      try:os.remove('quality.rules')
      except:pass
      try:os.remove('config.yaml')
      except:pass
  
  
  def test_version():
      try:
          coverage.main([prog, '--version'])
          assert False
      except SystemExit:
          pass
      else:
          raise Exception
  
  
  def test_help():
      try:
          coverage.main([prog, '--help'])
          assert False
      except SystemExit:
          pass
      else:
          raise Exception
  
  
  def test_input(tmpdir):
  
      import os
      directory = tmpdir.mkdir("report")
      name = directory.__str__()
  
      filename = sequana_data('virus.bed', 'data')
      reference = sequana_data('tofill.fa', 'data')
      coverage.main([prog, '-i', filename, "-o", "--output-directory", name])
      assert os.path.exists(name + os.sep + "coverage_mapping.chrom1.html")
  
subject: Fix tests to use pytest