old_contents: 
  import subprocess
  import os
  import sys
  import shutil
  import re
  
  src_dir = os.getenv('SRC_DIR')
  
  test_pkg = 'msmtools'
  cover_pkg = test_pkg
  
  # matplotlib headless backend
  with open('matplotlibrc', 'w') as fh:
      fh.write('backend: Agg')
  
  
  def coverage_report():
      fn = '.coverage'
      assert os.path.exists(fn)
      build_dir = os.getenv('TRAVIS_BUILD_DIR')
      dest = os.path.join(build_dir, fn)
      print( "copying coverage report to", dest)
      shutil.copy(fn, dest)
      assert os.path.exists(dest)
  
      # fix paths in .coverage file
      with open(dest, 'r') as fh:
          data = fh.read()
      match= '"/home/travis/miniconda/envs/_test/lib/python.+?/site-packages/.+?/({test_pkg}/.+?)"'
      repl = '"%s/\\1"' % build_dir
      data = re.sub(match, repl, data)
      os.unlink(dest)
      with open(dest, 'w+') as fh:
         fh.write(data)
  
  nose_run = "nosetests {test_pkg} -vv" \
             " --with-coverage --cover-inclusive --cover-package={cover_pkg}" \
             " --with-doctest --doctest-options=+NORMALIZE_WHITESPACE,+ELLIPSIS" \
             .format(test_pkg=test_pkg, cover_pkg=cover_pkg).split(' ')
  
  res = subprocess.call(nose_run)
  
  
  # move .coverage file to git clone on Travis CI
  if os.getenv('TRAVIS', False):
     coverage_report()
  
  sys.exit(res)
  
  
new_contents: 
  import subprocess
  import os
  import sys
  import shutil
  import re
  
  src_dir = os.getenv('SRC_DIR')
  
  test_pkg = 'msmtools'
  cover_pkg = test_pkg
  
  # matplotlib headless backend
  with open('matplotlibrc', 'w') as fh:
      fh.write('backend: Agg')
  
  
  def coverage_report():
      fn = '.coverage'
      assert os.path.exists(fn)
      build_dir = os.getenv('TRAVIS_BUILD_DIR')
      dest = os.path.join(build_dir, fn)
      print( "copying coverage report to", dest)
      shutil.copy(fn, dest)
      assert os.path.exists(dest)
  
      # fix paths in .coverage file
      with open(dest, 'r') as fh:
          data = fh.read()
      match= '"/home/travis/miniconda/envs/_test/lib/python.+?/site-packages/.+?/({test_pkg}/.+?)"'.format(test_pkg=test_pkg)
      repl = '"%s/\\1"' % build_dir
      data = re.sub(match, repl, data)
      os.unlink(dest)
      with open(dest, 'w+') as fh:
         fh.write(data)
  
  nose_run = "nosetests {test_pkg} -vv" \
             " --with-coverage --cover-inclusive --cover-package={cover_pkg}" \
             " --with-doctest --doctest-options=+NORMALIZE_WHITESPACE,+ELLIPSIS" \
             .format(test_pkg=test_pkg, cover_pkg=cover_pkg).split(' ')
  
  res = subprocess.call(nose_run)
  
  
  # move .coverage file to git clone on Travis CI
  if os.getenv('TRAVIS', False):
     coverage_report()
  
  sys.exit(res)
  
  
subject: fix cov