You can no longer do PyFile(inputStream) directly from Jython code. This is because a PyFile that gets an InputStream [INSERT REAL REASON], so that the recommended approach is to replace code like:

from java.io import FileInputStream
from org.python.core import PyFile
fis = FileInputStream("error.txt")
pyf = PyFile(fis)

with code like:

from java.io import FileInputStream
from org.python.core.util import FileUtil
fis = FileInputStream("error.txt")
pyf = FileUtil.wrap(fis)