Update GP NBs to use standard notebook style #3978

bwengals · 2020-06-23T07:21:40Z

Updates the examples to use the standard notebook style, #3959, as outlined here.

Should figure sizes / font sizes also be standardized? @michaelosthege @AlexAndorra.

review-notebook-app · 2020-06-23T07:21:46Z

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AlexAndorra

This is great, thanks for your help @bwengals !
LGTM, except for:

Is it expected that the GP for classification example seems less able to recover the true f than in the earlier version of the NB? Would you consider the performance in the new version good enough?
I'm not sure you ran black_nbconvert on the NB (see NB style Wiki)
Oddly enough, test_matrix_multiplication is failing, but I don't see how that's related to the changes you did here 🤔

michaelosthege · 2020-06-23T12:35:53Z

Looks great! Can you add assert all(r_hat < 1.03) or similar after the samplings?

bwengals · 2020-06-24T06:18:21Z

@AlexAndorra I think the original problem was just easier, those variations around 0.5 were hard to pick up with the small data set. I added more data and fixed the random seed so the results are better.

Nope, totally forgot about black_nbconvert, thanks! I'll see if that test still fails after fixing the other things.

@michaelosthege that's a good idea, will add that.

AlexAndorra

Thanks @bwengals ! This is almost ready, just added some comments below.

I think the original problem was just easier, those variations around 0.5 were hard to pick up with the small data set. I added more data and fixed the random seed so the results are better.

Ow ok, thanks, that's good to know! You can even write a quick line about that in the NB if you feel like it -- always nice to highlight where a model could fail 🙂

Regarding the tests: this has been fixed and merged, so if you merge master onto your branch, tests should pass now 😉

review-notebook-app · 2020-06-24T09:19:02Z

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AlexAndorra commented on 2020-06-24T09:19:01Z
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I don't think you need to reset the seed here, at it's done at the top of the NB

bwengals commented on 2020-06-24T21:26:18Z
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good call, will fix and rerun it

review-notebook-app · 2020-06-24T09:19:03Z

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AlexAndorra commented on 2020-06-24T09:19:02Z
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I don't think you need to reset the seed here, at it's done at the top of the NB

bwengals commented on 2020-06-24T21:28:05Z
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I reset it here because it's generating a new batch of fake data, it got a little confusing if I ran a few other cells before the new example. Will add a note explaining this

review-notebook-app · 2020-06-24T09:19:04Z

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AlexAndorra commented on 2020-06-24T09:19:03Z
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I think you need plt.legend() to display the legend

bwengals commented on 2020-06-24T21:31:12Z
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fixed

bwengals · 2020-06-24T21:26:19Z

good call, will fix and rerun it

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bwengals · 2020-06-24T21:28:06Z

I reset it here because it's generating a new batch of fake data, it got a little confusing if I ran a few other cells before the new example. Will add a note explaining this

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bwengals · 2020-06-24T21:31:13Z

fixed

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AlexAndorra

Thanks @bwengals, this looks great now!
Just run black_nbconvert again (the new cells are not formatted) and merge master in your branch so that the tests pass, and then we're good to go 🎉

michaelosthege · 2020-06-25T10:45:48Z

@bwengals to fix the failing test:

git checkout master
git pull
git checkout gp-latent-nb-style-update
git merge master

bwengals · 2020-06-25T20:36:25Z

thanks @michaelosthege, much appreciated, pushed

Should I keep going with this PR for the other GP notebooks? Or is 1 PR / 1 Notebook better?

michaelosthege · 2020-06-25T20:40:51Z

thanks @michaelosthege, much appreciated, pushed

Should I keep going with this PR for the other GP notebooks? Or is 1 PR / 1 Notebook better?

I think multiple related NBs per PR are fine, but as this is done, let's merge it already

bwengals · 2020-06-25T21:21:38Z

@AlexAndorra whoops forgot about black again!

OK that sounds good, next one I'll bundle the other GP NBs together.

* Update GP NBs to use standard notebook style (pymc-devs#3978) * update gp-latent nb to use arviz * rerun, run black * rerun after fixes from comments * rerun black * rewrite radon notebook using ArviZ and xarray (pymc-devs#3963) * rewrite radon notebook using ArviZ and xarray Roughly half notebook has been updated * add comments on xarray usage * rewrite 2n half of notebook * minor fix * rerun notebook and minor changes * rerun notebook on pymc3.9.2 and ArviZ 0.9.0 * remove unused import * add change to release notes * SMC: refactor, speed-up and run multiple chains in parallel for diagnostics (pymc-devs#3981) * first attempt to vectorize smc kernel * add ess, remove multiprocessing * run multiple chains * remove unused imports * add more info to report * minor fix * test log * fix type_num error * remove unused imports update BF notebook * update notebook with diagnostics * update notebooks * update notebook * update notebook * Honor discard_tuned_samples during KeyboardInterrupt (pymc-devs#3785) * Honor discard_tuned_samples during KeyboardInterrupt * Do not compute convergence checks without samples * Add time values as sampler stats for NUTS (pymc-devs#3986) * Add time values as sampler stats for NUTS * Use float time counters for nuts stats * Add timing sampler stats to release notes * Improve doc of time related sampler stats Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com> Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com> * Drop support for py3.6 (pymc-devs#3992) * Drop support for py3.6 * Update RELEASE-NOTES.md Co-authored-by: Colin <ColCarroll@users.noreply.github.com> Co-authored-by: Colin <ColCarroll@users.noreply.github.com> * Fix Mixture distribution mode computation and logp dimensions Closes pymc-devs#3994. * Add more info to divergence warnings (pymc-devs#3990) * Add more info to divergence warnings * Add dataclasses as requirement for py3.6 * Fix tests for extra divergence info * Remove py3.6 requirements * follow-up of py36 drop (pymc-devs#3998) * Revert "Drop support for py3.6 (pymc-devs#3992)" This reverts commit 1bf867e. * Update README.rst * Update setup.py * Update requirements.txt * Update requirements.txt Co-authored-by: Adrian Seyboldt <aseyboldt@users.noreply.github.com> * Show pickling issues in notebook on windows (pymc-devs#3991) * Merge close remote connection * Manually pickle step method in multiprocess sampling * Fix tests for extra divergence info * Add test for remote process crash * Better formatting in test_parallel_sampling Co-authored-by: Junpeng Lao <junpenglao@gmail.com> * Use mp_ctx forkserver on MacOS * Add test for pickle with dill Co-authored-by: Junpeng Lao <junpenglao@gmail.com> * Fix keep_size for arviz structures. (pymc-devs#4006) * Fix posterior pred. sampling keep_size w/ arviz input. Previously posterior predictive sampling functions did not properly handle the `keep_size` keyword argument when getting an xarray Dataset as parameter. Also extended these functions to accept InferenceData object as input. * Reformatting. * Check type errors. Make errors consistent across sample_posterior_predictive and fast_sample_posterior_predictive, and add 2 tests. * Add changelog entry. Co-authored-by: Robert P. Goldman <rpgoldman@sift.net> * SMC-ABC add distance, refactor and update notebook (pymc-devs#3996) * update notebook * move dist functions out of simulator class * fix docstring * add warning and test for automatic selection of sort sum_stat when using wassertein and energy distances * update release notes * fix typo * add sim_data test * update and add tests * update and add tests * add docs for interpretation of length scales in periodic kernel (pymc-devs#3989) * fix the expression of periodic kernel * revert change and add doc * FIXUP: add suggested doc string * FIXUP: revertchanges in .gitignore * Fix Matplotlib type error for tests (pymc-devs#4023) * Fix for issue 4022. Check for support for `warn` argument in `matplotlib.use()` call. Drop it if it causes an error. * Alternative fix. * Switch from pm.DensityDist to pm.Potential to describe the likelihood in MLDA notebooks and script examples. This is done because of the bug described in arviz-devs/arviz#1279. The commit also changes a few parameters in the MLDA .py example to match the ones in the equivalent notebook. * Remove Dirichlet distribution type restrictions (pymc-devs#4000) * Remove Dirichlet distribution type restrictions Closes pymc-devs#3999. * Add missing Dirichlet shape parameters to tests * Remove Dirichlet positive concentration parameter constructor tests This test can't be performed in the constructor if we're allowing Theano-type distribution parameters. * Add a hack to statically infer Dirichlet argument shapes Co-authored-by: Brandon T. Willard <brandonwillard@users.noreply.github.com> Co-authored-by: Bill Engels <w.j.engels@gmail.com> Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Co-authored-by: Osvaldo Martin <aloctavodia@gmail.com> Co-authored-by: Adrian Seyboldt <aseyboldt@users.noreply.github.com> Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com> Co-authored-by: Colin <ColCarroll@users.noreply.github.com> Co-authored-by: Brandon T. Willard <brandonwillard@users.noreply.github.com> Co-authored-by: Junpeng Lao <junpenglao@gmail.com> Co-authored-by: rpgoldman <rpgoldman@goldman-tribe.org> Co-authored-by: Robert P. Goldman <rpgoldman@sift.net> Co-authored-by: Tirth Patel <tirthasheshpatel@gmail.com> Co-authored-by: Brandon T. Willard <971601+brandonwillard@users.noreply.github.com>

update gp-latent nb to use arviz

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AlexAndorra reviewed Jun 23, 2020

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lucianopaz mentioned this pull request Jun 23, 2020

Set different almost equal tolerance depending on floatX #3980

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5 tasks

rerun, run black

332746e

AlexAndorra requested changes Jun 24, 2020

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rerun after fixes from comments

bfb271f

AlexAndorra approved these changes Jun 25, 2020

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Merge branch 'master' into gp-latent-nb-style-update

d322843

rerun black

d513f2e

AlexAndorra merged commit f93b5e7 into master Jun 26, 2020

AlexAndorra deleted the gp-latent-nb-style-update branch June 26, 2020 09:02

AlexAndorra mentioned this pull request Jul 7, 2020

[WIP] Updated GP notebooks #4005

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kyleabeauchamp added this to the 3.9.3 milestone Jul 28, 2020

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Update GP NBs to use standard notebook style #3978

Update GP NBs to use standard notebook style #3978

bwengals commented Jun 23, 2020

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Update GP NBs to use standard notebook style #3978

Update GP NBs to use standard notebook style #3978

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