Cannot interpret DEpairs as a list

[saubhagya-gatech]

Dear developers,

I am not able to use DEpairs as a list (DEpairs=[1,2,3]) as it throws following error suggesting that DEpairs argument needs to be an integer. However, it worked perfectly fine in Robertson_no_pysb example where I passed DEpairs a list. Any help will be appreciated.

Codes looks like:

run_dream(sampled_parameter_names, likelihood, niterations=niterations, nchains=nchains,
multitry=False, gamma_levels=4, adapt_gamma=True, history_thin=1, model_name='S_14_5chain', verbose=True,
DEpairs=[1,2,3],hardboundaries =True, start_random=False, start=starts)

Error message:

File "dreams_run.py", line 74, in
DEpairs=[1,2,3],hardboundaries =True, start_random=False, start=starts)
File "/home/7s2/.local/lib/python3.6/site-packages/pydream/core.py", line 64, in run_dream
step_instance = Dream(model=model, variables=parameters, verbose=verbose, mp_context=mp_context, **kwargs)
File "/home/7s2/.local/lib/python3.6/site-packages/pydream/Dream.py", line 150, in init
self.DEpairs = np.linspace(1, DEpairs, num=DEpairs, dtype=int) #This is delta in original Matlab code
File "<array_function internals>", line 6, in linspace
File "/home/7s2/.local/lib/python3.6/site-packages/numpy/core/function_base.py", line 121, in linspace
.format(type(num)))

Thanks
Saubhagya

[ortega2247]

Hi Saubhagya, thanks for reporting this issue.

I think the problem is that the docs are outdated. It is not necessary to pass a list to the DEpairs argument since PyDREAM would automatically generate an evenly spaced array from 1 to the integer value that you set DEpairs: https://github.com/LoLab-VU/PyDREAM/blob/9beedddd511361abe6390e51f9d749a10d9392b7/pydream/Dream.py#L150
In your example you used a DEpairs = [1,2,3], you could get that setting by using DEpairs=3

I think we should updated the documentation. Please let me know if you have any comments or issues with pydream.

Best,

Oscar

[saubhagya-gatech]

Ah ok, my bad. Thanks for the prompt reply. Is this the best place to ask any other query (which might be due to me doing something wrong) or is there a mailing list or google group?

[ortega2247]

No problem! You can ask questions here or use the pysb gitter: https://gitter.im/pysb/pysb?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge