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RuntimeError: generator raised StopIteration #41

Closed sebastian-luna-valero closed 4 years ago

sebastian-luna-valero commented 5 years ago

Hi,

After releasing version 0.5.4, it looks like Jenkins tests are failing for:

Both throwing: RuntimeError: generator raised StopIteration

The major change with this release is that we are using Python 3.7 instead of Python 3.6.

I think we are hitting this: https://stackoverflow.com/questions/51700960/runtimeerror-generator-raised-stopiteration-every-time-i-try-to-run-app

Any suggestions?

Best regards, Sebastian

Acribbs commented 5 years ago

From the solution provided on stack overflow for generators:

try:
    yield next(seq)
except StopIteration:
    return

should work and I can apply these changes. However, I think there are further issues with the conda package for cgat-apps 0.5.4. It seems like we are unable to run any code that requires cython code.(please see comments in https://github.com/cgat-developers/cgat-flow/pull/96).

In the meantime can we not just rebuild cgat-apps for python 3.6 only.

Acribbs commented 4 years ago

Hi Sebastian,

Im not having any luck debugging this. I fixed bed2bed but the FastaIterator is still failing. I just cant work it out as far as I can see I have modified the data to reflect the change in generators as above without any luck (See AC-itererror branch)

Any suggestions would be greatly appreciated

Acribbs commented 4 years ago

Managed to find the issue, fixed with #49