PyMC3 has been renamed PyMC

canyon289 commented 3 years ago

Hi, PyMC3 has been renamed PyMC. If this affects you and you have questions, or you want someone to direct your rage at I'm available! Do let me know how i, or any of the PyMC devs can help.

Ravin

catrionamurray commented 2 years ago

Hi! I'm trying to use exoplanet with PyMC (v4) and I'm having trouble with defining the limb-darkening coeffs: u_ld = xo.distributions.QuadLimbDark("u", testval=np.array(init_u)) Throws an error when defined under pm.Model() where pm is pyMC not pyMC3.


---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
~/opt/anaconda3/envs/py38/lib/python3.8/site-packages/pymc3/model.py in get_context(cls, error_if_none)
    320         try:
--> 321             candidate = cls.get_contexts()[-1]  # type: Optional[T]
    322         except IndexError as e:

IndexError: list index out of range

During handling of the above exception, another exception occurred:

TypeError                                 Traceback (most recent call last)
~/opt/anaconda3/envs/py38/lib/python3.8/site-packages/pymc3/distributions/distribution.py in __new__(cls, name, *args, **kwargs)
     85         try:
---> 86             model = Model.get_context()
     87         except TypeError:

~/opt/anaconda3/envs/py38/lib/python3.8/site-packages/pymc3/model.py in get_context(cls, error_if_none)
    325             if error_if_none:
--> 326                 raise TypeError("No %s on context stack" % str(cls))
    327             return None

TypeError: No <class 'pymc3.model.Model'> on context stack

During handling of the above exception, another exception occurred:

TypeError                                 Traceback (most recent call last)
/var/folders/6k/5j78gjkn74b4xb382c27jzwr0000gn/T/ipykernel_64514/3843441120.py in <module>
     17 
     18 # fit MCMC transit
---> 19 map_soln, model,[period,r,t0,b_ip,u_ld,mean] = fit_transit(x,y,yerr,init_r,init_t0, init_period,init_b,init_mean,init_u,period_error)
     20 # plot the fit
     21 plot_fit(x,y,yerr,map_soln)

~/Documents/Postdoc/CUBoulder/chromatic_fitting/src/recover_transit.py in fit_transit(x, y, yerr, init_r, init_t0, init_period, init_b, init_mean, init_u, period_error, fixed_var)
     86             u_ld = xo.distributions.QuadLimbDark("u", testval=np.array(init_u), observed=np.array(init_u))
     87         else:
---> 88             u_ld = xo.distributions.QuadLimbDark("u", testval=np.array(init_u))
     89 
     90         #         r = pm.Uniform(

~/opt/anaconda3/envs/py38/lib/python3.8/site-packages/pymc3/distributions/distribution.py in __new__(cls, name, *args, **kwargs)
     86             model = Model.get_context()
     87         except TypeError:
---> 88             raise TypeError(
     89                 "No model on context stack, which is needed to "
     90                 "instantiate distributions. Add variable inside "

TypeError: No model on context stack, which is needed to instantiate distributions. Add variable inside a 'with model:' block, or use the '.dist' syntax for a standalone distribution.

dfm commented 2 years ago

Yeah - exoplanet does not work with PyMC v4. You'll need to stick with PyMC3!

vandalt commented 2 years ago

Hi, I'm not sure this is the best place to ask my question (sorry if it's not). I was wondering if there were plans to make exoplanet compatible with PyMC v4 or if the JAX backend (exo4jax I think?) was the main path forward in the future?

Thank you!

dfm commented 2 years ago

Great question and this is a good place to ask!

So far, I have updated all the backend packages (exoplanet-core, and celerite2) to be compatible with PyMC v4. This means that in principle it shouldn't be too hard to get the main package updated, but I haven't had the bandwidth to work on it!

For my own work, I've mostly been hacking on the JAX implementation (which is really more of a separate project, name TBD :D), but I definitely want to make sure that this package stays up to date. Maybe it makes sense to open a separate issue or PR to track these changes...

dfm commented 2 years ago

Quick update here that I'm working on the update to pymc v4 over here: https://github.com/exoplanet-dev/exoplanet/pull/271

exoplanet-dev / exoplanet

PyMC3 has been renamed PyMC #234