Error in running python setup.py test - NameError: global name 'which' is not defined

[EPKok]

Hi John,

Thanks for developing fast5tools. I have an error when running python setup.py test. It shows that the global name 'which' is not defined. Part of the error message is shown below:

======================================================================
ERROR: test_get_start_time_template (tests.test_f5class.TestFast5Class)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/projects/kokep/kokep/devel/fast5tools/tests/test_f5class.py", line 210, in test_get_start_time_template
    self.f5.get_start_time("template")
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 963, in get_start_time
    return self.get_read_events_start_time(readtype=which,index=0)
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 986, in get_read_events_start_time
    return self.f5[self._get_location_path(which,"Events")].attrs["start_time"]
NameError: global name 'which' is not defined

======================================================================
ERROR: test_get_start_time_complement (tests.test_f5class.TestFast5Class)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/projects/kokep/kokep/devel/fast5tools/tests/test_f5class.py", line 213, in test_get_start_time_complement
    self.f5.get_start_time("complement")
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 963, in get_start_time
    return self.get_read_events_start_time(readtype=which,index=0)
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 986, in get_read_events_start_time
    return self.f5[self._get_location_path(which,"Events")].attrs["start_time"]
NameError: global name 'which' is not defined

======================================================================
ERROR: test_get_start_time_template (tests.test_f5class.TestFast5Class)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/projects/kokep/kokep/devel/fast5tools/tests/test_f5class.py", line 210, in test_get_start_time_template
    self.f5.get_start_time("template")
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 963, in get_start_time
    return self.get_read_events_start_time(readtype=which,index=0)
  File "/mnt/projects/kokep/kokep/devel/fast5tools/fast5tools/f5class.py", line 986, in get_read_events_start_time
    return self.f5[self._get_location_path(which,"Events")].attrs["start_time"]
NameError: global name 'which' is not defined

----------------------------------------------------------------------
Ran 1360 tests in 20.230s

FAILED (errors=31)
Test failed: <unittest.runner.TextTestResult run=1360 errors=31 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1360 errors=31 failures=0> 

The full run and error log files are attached below:
run.log
err.log

Wonder how I could fix this issue? Thanks in advance.

[JohnUrban]

I just saw this issue.

Did you ever resolve it?

I likely need to update the tests -- its been a while.

There is a good chance, you will be able to do what you want w/ fast5tools anyway regardless of those tests.

Let me know what you're trying to do -- perhaps I can advise.