fix python3 string/bytes error when using --printLogs

[johnbradley]

Adds decode('utf-8') method call to fix the following error:

  .../toil/utils/toilStatus.py", line 83, in printJobLog
    msg += fH.read()
TypeError: can only concatenate str (not "bytes") to str

This fix is already being used in leader.py FailedJobsException:

toil/src/toil/leader.py

Lines 79 to 80 in 993be0c

	with job.getLogFileHandle(jobStore) as fH:
	msg += fH.read().decode('utf-8')

Let me know if you would prefer a new function to abstract out this duplication.

For testing the bug I added an example CWL workflow that always fails.

Fixes problem raised in #3004

[adamnovak]

This looks great! I'll pull it in for testing.

[DailyDreaming]

@johnbradley Thanks for putting in this fix!

[adamnovak]

The Gitlab tests are all failing due to the absence of the pytz module. It isn't installed because installing our dependencies bails out, because http-parser can't install, becuase it goes looking for setuptools.Feature and can't find it.

Collecting http-parser
  Downloading http-parser-0.8.3.tar.gz (83 kB)
    ERROR: Command errored out with exit status 1:
     command: /builds/databiosphere/toil/venv/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1bte35b_/http-parser/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1bte35b_/http-parser/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-1bte35b_/http-parser/pip-egg-info
         cwd: /tmp/pip-install-1bte35b_/http-parser/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-1bte35b_/http-parser/setup.py", line 19, in <module>
        from setuptools import setup, find_packages, Extension, Feature
    ImportError: cannot import name 'Feature'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Between the last successful job and this one we changed from setuptools 45 to 56. In 46 they removed Feature (see https://github.com/pypa/setuptools/blob/master/CHANGES.rst#v4600 and pypa/setuptools#65); now http-parser is completely broken and not installable.

We either need to make Toil require setuptools <46, or fix http-parser and pymesos.

[adamnovak]

OK I stacked this on top of current master which passed CI; I think this will pass too.