Error when trying to update BOF step 1 (1.8)

[Christiansj83]

AttributeError Traceback (most recent call last)
in ()
----> 1 bofdat_step1 = update.make_new_BOF(model_so,False,True,dna_coefficients,rna_coefficients,protein_coefficients,)

~/.local/lib/python3.6/site-packages/BOFdat-0.1.7-py3.6.egg/BOFdat/util/update.py in make_new_BOF(model, update_model, update_NGAM, *args, **kwargs)
159 ppi_coeff, h2o_coeff, atp_coeff = [], [], []
160 remove_keys = []
--> 161 for k, v in base_biomass.iteritems():
162 if k.id == 'ppi_c':
163 ppi_coeff.append(v)

AttributeError: 'dict' object has no attribute 'iteritems'

[EBosi]

Hi, the issue here is that python 3 has dictionaries with an efficient .items() method which is equivalent to .iteritems() of python 2 (i.e. using a generator).
To make it compatible for both python version you should replace all instances of dict.iteritems with

from future.utils import iteritems

for (k, v) in iteritems(dict):

[jclachance]

Christian did raise some interesting concerns:
1- Compatibility with Python3 has to be reviewed for most of the code
2- What do we want to do with the Update module of BOFdat. I think it is useful for users to have such functionality but ad hoc functions can easily be generated that will better suit their needs also.

Any thoughts?

[EBosi]

Hi JC,
1- yes, it's kinda boring but it should be done. The module future helps a lot, here are some idioms which should work for both versions (http://python-future.org/compatible_idioms.html), but I think you should look at futurize (http://python-future.org/automatic_conversion.html)
2- that's the thing, I see it as a cozy wrapper function which does what I could do, but in a snap