Closed AlexAndorra closed 3 years ago
Hi @AlexAndorra I am willing to update the notebooks dealing with Variational Inference and restyling according to the guide. I have one question though - do we need to re-run the notebooks on the current state of the PyMC3 codebase or running them on the latest released version (3.8)?
Great, thanks for answering so quickly Sayam! Actually, we're rerunning and restyling all the notebooks prior to releasing 3.9.0 (see https://github.com/pymc-devs/pymc3/pull/3955) so it'd be awesome if you could help us out here with the VI notebooks (or any others you like) -- just make sure to tell us which you're working on in the comments π
Le ven. 12 juin 2020 Γ 19:59, Sayam Kumar notifications@github.com a Γ©crit :
Hi @AlexAndorra https://github.com/AlexAndorra I am willing to update the notebooks dealing with Variational Inference and restyling according to the guide. I have one question though - do we need to re-run the notebooks on the current state of the PyMC3 codebase or running them on the latest released version (3.8)?
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I can work on rugby, radon (multilevel_modeling
) and model comparison ones. I like the first two because after rerunning them I will be able to update the ArviZ examples with the new InferenceData objects (see https://github.com/arviz-devs/arviz/issues/1132). Regarding the third one, I am very familiar with loo/waic api and therefore I don't expect to find many issues (nor spend too much time on it).
Thanks @OriolAbril ! Actually, I think @Sayam753 already updated the rugby NB. Now that pymc-devs/pymc3#3955 is merged, he'll probably open a new PR and it should be merged in master pretty soon π
For the radon NB, it should be quick: I updated it a couple of months ago and it was reviewed so I think it's a false positive -- the More chains (4000) than draws (2)
warning is because of a known ArviZ issue that we didn't have time to look at yet, and I don't expect many plots to be wrong. But it's alway good to have a second pair of eyes!
Finally, I think you're the perfect person for the model_comparison
NB π
I will open a PR regarding rugby notebook and will be happy @OriolAbril reviewing the same.
Great! Please ping me in the PR and I'll review :)
Count on me to fix the model comparison and model averaging notebooks.
I am working on the GP notebooks.
I submitted a PR for weibull_aft. It's my first PR so will greatly appreciate if one of you can review it! @AlexAndorra Thanks.
Should we transfer this to pymc-examples? It doesn't show as an option if I click transfer issue ->
.
Sounds good, I think I can transfer the issue
closing this in favour of the tracker project and all the other issues (each notebook has its own issue now)
[BEGINNER-FRIENDLY] Our notebooks gallery is quite big, so:
FutureWarnings
that should be addressed (not listed).So this issue is here to signal it would be nice if people want to take some time updating and re-running the notebooks below with PyMC 3.9, according to this style page π Do it in small batches though, to not get bored and enjoy it π Thanks a lot in advance for your help and don't hesitate to ask your questions below! PyMCheers π
Here is an up-to-date list of the most outdated and problematic NBs (those not listed here should be checked for style and updating accordingly):
Exotic
blackbox_external_likelihood
needs Cythonconvolutional_vae_keras_advi
needs KerasOther Issues
GLM
theano.gof.fg.MissingInputErrorGLM-poisson-regression
KeyError: "['hpd_2.5', 'hpd_97.5'] not in index"GLM-negative-binomial-regression
KeyError: "['hpd_97.5', 'hpd_2.5'] not in index"GLM-model-selection
KeyError: 'var names: "[\'sd_log__\'] are not present" in dataset'GP-MaunaLoa2
ValueError: Units 'M' and 'Y' are no longer supportedGP-MaunaLoa
ValueError: Units 'M' and 'Y' are no longer supported, as they do not represent unambiguous timedelta values durations.GP-TProcess
runs but has way too many divergences; timed out after 14_000 secondsPyMC3_tips_and_heuristic
KeyError: Rhatdependent_density_regression
AttributeError: 'DataFrame' object has no attribute 'range'hierarchical_partial_pooling
not enough values to unpack (expected 2, got 1)lda-advi-aevb
TypeError: init() got an unexpected keyword argument 'n_topics'marginalized_gaussian_mixture_model
AttributeError: 'Rectangle' object has no property 'normed'GLM-logistic
AttributeError: 'Rectangle' object has no property 'normed'model_averaging
FileNotFoundError: File ../data/milk.csv does not existmodel_comparison
AttributeError: 'ELPDData' object has no attribute 'WAIC'multilevel_modeling
More chains (4000) than draws (2) and some plots may be wrongprofiling
has a shape errorrugby_analytics
ValueError: not enough values to unpack (expected 2, got 1)sampling_callback
has a shape error (looks like a threading problem)survival_analysis
cell 11 raises a NotImplementedError in numpy/pandasweibull_aft
AttributeError: module 'statsmodels' has no attribute 'datasets'ODE_with_manual_gradients
ValueError: array must not contain infs or NaNs