LimbDark object can't be pickled, stops sampling in the transit example

[aditya-sengupta]

Describe the bug
When trying to run exoplanet/docs/tutorials/transit.py, execution is stopped at the sampling stage on line 155: the stated error is TypeError: cannot pickle 'exoplanet.theano_ops.driver.LimbDark' object.

To Reproduce
cd into docs/tutorials and run python transit.py: output is reproduced below.

optimizing logp for variables: [b, r, u, logP, t0, mean]
106it [00:01, 82.32it/s, logp=2.479354e+04]
message: Desired error not necessarily achieved due to precision loss.
logp: 24787.977771807487 -> 24793.53942561123
Auto-assigning NUTS sampler...
Initializing NUTS using adapt_full...
/Users/adityasengupta/opt/anaconda3/envs/oracle/lib/python3.8/site-packages/pymc3/step_methods/hmc/quadpotential.py:503: UserWarning: QuadPotentialFullAdapt is an experimental feature
  warnings.warn("QuadPotentialFullAdapt is an experimental feature")
Multiprocess sampling (2 chains in 2 jobs)
NUTS: [b, r, u, logP, t0, mean]
Traceback (most recent call last):
  File "transit.py", line 149, in <module>
    trace = pm.sample(
  File "/Users/adityasengupta/opt/anaconda3/envs/oracle/lib/python3.8/site-packages/pymc3/sampling.py", line 545, in sample
    trace = _mp_sample(**sample_args, **parallel_args)
  File "/Users/adityasengupta/opt/anaconda3/envs/oracle/lib/python3.8/site-packages/pymc3/sampling.py", line 1470, in _mp_sample
    sampler = ps.ParallelSampler(
  File "/Users/adityasengupta/opt/anaconda3/envs/oracle/lib/python3.8/site-packages/pymc3/parallel_sampling.py", line 432, in __init__
    step_method_pickled = pickle.dumps(step_method, protocol=-1)
TypeError: cannot pickle 'exoplanet.theano_ops.driver.LimbDark' object

Expected behavior
The same output as in the docs at https://docs.exoplanet.codes/en/stable/tutorials/transit/.

Your setup (please complete the following information):

• Version of exoplanet: 0.4.0
• Operating system: Mac OS Catalina v10.15.7
• Python version & installation method (pip, conda, etc.): Python 3.8.5, installation via pip in a conda env (+ git clone to get the file)

Additional context
Add any other context about the problem here.

[dfm]

Thanks!

This is a duplicate of #115 and it was fixed in #120. This will be included in the next release if you don't want to build from source.

[LucieScharre]

Hello,
I'm a student trying to use this package for a project. I have not used github before and am experiencing the same issue! I have tried to implement the fix #120, but am just getting new error messages. Should the approach work of just replacing exoplanet directory (installed using pip) with the new version I've downloaded from here?

I'm getting this error message then:
ImportError: cannot import name 'driver' from 'exoplanet.theano_ops' (/Applications/anaconda3/lib/python3.7/site-packages/exoplanet/theano_ops/init.py)

I'm not the most experienced coder and don't know to what extent I should mess around with the source code.

[aditya-sengupta]

Looks like it's still running the pip installed version; try the following (in some directory you want to use for this)

git clone https://github.com/exoplanet-dev/exoplanet
cd exoplanet
git submodule update --init --recursive
python setup.py develop

[dfm]

I'll also plan on making a pip release early next week so that it'll be easier to use then. Thanks for your patience!!

[LucieScharre]

That would be great as I still can't get it to work, just getting new error messages... Thank both of you so much!

[LucieScharre]

Are there any obvious fixes for [Errno 32] Broken pipe?

[aditya-sengupta]

Have `pm.sample` use only one core

…

On Sat, Nov 14, 2020 at 4:48 AM LucieScharre ***@***.***> wrote: Are there any obvious fixes for [Errno 32] Broken pipe? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#124 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIK476Q4AJF4NTYGTUZCZS3SPZ4A7ANCNFSM4TRIGJTA> .

[dfm]

The package on PyPI has been updated so you should be able to get the new version using

python -m pip install -U exoplanet

For other errors (like a broken pipe) can you open a new issue with an example that demonstrates the problem? Then it'll be easier for me to look into it!

[LucieScharre]

It now works with the new version! Thank you for fixing it so quickly!

[LucieScharre]

Do you by any chance have examples of how to fit just one planet to the data? No worries if not! Just struggling a little with a working translation to only one planet

[dfm]

Take a look at the examples on the case studies page to see if those are enough to get you started: https://gallery.exoplanet.codes/en/latest/