add glossary example as orphan page #4797

OriolAbril · 2021-06-21T12:18:19Z

Depending on what your PR does, here are a few things you might want to address in the description:

important background, or details about the implementation
- Creates a glossary page so that we can already start adding terms and definitions there.
  Choosing where within the docs it will be will come later. If we separate building
  of examples and docs, I think we should still keep a single glossary in the main docs, we can
  then link to term from the notebooks too using intersphinx. The main/only drawback is that
  notebooks that need to add new terms to the glossary need an auxiliary PR to pymc3 repo.
- We could also do that the other way around, glossary in pymc-examples, link from pymc3 docs with
  intersphinx.
- Another somewhat too ambitious alternative would be to host a Bayesian glossary (single web, non
  versioned) so that we can then link there from pymc3, arviz, bambi docs... I think @canyon289
  has wanted something like that for a long time
linting/style checks have been run

ricardoV94 · 2021-06-21T12:44:13Z

Can't we keep two glossaries, one for pymc-examples and the other for pymc3 docs?

Edit: I see, we only need a PR to pymc3 if a new glossary item is needed? That sounds reasonable

OriolAbril · 2021-06-21T12:57:58Z

Yes, I think two glossaries would be confusing and end up being more work. notebooks will be able to link to any term in the glossary without any problem, and users clicking will go to the main pymc3 docs. Side note, in practice I am not sure this will have much of an effect though, we could for example keep the exact same navbar in both docs, so that visually everything looks basically the same, in pymc3 docs, the examples and tutorials would be external links, in pymc-examples the other way around

What is not possible (from any of the two) is linking to terms that are not yet defined, so if new notebooks need to add terms to the glossary, they need an extra PR to pymc3 repo (or viceversa, maybe the main docs are more stable and it makes more sense to host the glossary in pymc-examples which is where more new terms will be added 🤔 ) to add the term so that then it can be referenced in the notebook

ricardoV94 · 2021-06-21T13:03:01Z

Yes I think the pymc3 docs is a better place for the glossary.

Edit: I see you actually said the opposite haha :D I will refrain from misreading you again in this PR

OriolAbril · 2021-06-21T13:17:22Z

Yes I think the pymc3 docs is a better place for the glossary.

Edit: I see you actually said the opposite haha :D I will refrain from misreading you again in this PR

I actually don't know where it would be better!

ricardoV94 · 2021-06-26T07:03:11Z

Do you want me to push here the terms that will be used in #4783?

michaelosthege · 2021-07-24T19:35:54Z

@OriolAbril what shall we do with this PR ?

Sayam753 · 2021-07-24T20:48:03Z

Another somewhat too ambitious alternative would be to host a Bayesian glossary (single web, non
versioned) so that we can then link there from pymc3, arviz, bambi docs... I think @canyon289
has wanted something like that for a long time

Creating a dedicated repository in PyMC just for glossary seems like a good option to me.
And then we can decide either adding it as a submodule or just linking it from the documentation.

OriolAbril · 2021-07-27T03:42:59Z

I think we can start trying out the glossary here (thus merge this) and if we see that having a glossary as an independent webpage or having it rendered via pymc-examples works better then move the page.

It isn't yet ready to be merged though. I can start fixing some syntax from the distributions dev guide which is so far the only page that has terms so that someone else can then add the definitions.

@Sayam753 do we already have PR doc preview for v4?

Sayam753 · 2021-07-27T19:17:31Z

@Sayam753 do we already have PR doc preview for v4?

Yes, preview - https://pymc3-fork.readthedocs.io/en/latest/

But it is on my fork. I'll roll out a PR later this week, adding support of RTD on main. I guess it will be just a yml file.

OriolAbril · 2021-07-29T11:54:06Z

docs/source/developer_guide_implementing_distribution.md

@@ -84,12 +84,12 @@ blah = BlahRV()

 Some important things to keep in mind:

-1. Everything inside the `rng_fn` method is pure Python code (as are the inputs) and should not make use of other `Aesara` symbolic ops. The random method should make use of the `rng` which is a Numpy    {`class`}`~numpy.random.RandomState`, so that samples are reproducible.
+1. Everything inside the `rng_fn` method is pure Python code (as are the inputs) and should not make use of other `Aesara` symbolic ops. The random method should make use of the `rng` which is a Numpy    {class}`~numpy.random.RandomState`, so that samples are reproducible.


just to double check, v4 uses RandomState or Generator?

Both can be used. By default RVs use / create RandomStates

OriolAbril · 2021-07-29T11:55:40Z

docs/source/developer_guide_implementing_distribution.md

@@ -280,7 +280,7 @@ The latter kind of test (if warranted) can be performed with the aid of `pymc3_r
 This kind of test only makes sense if there is a good independent generator reference (i.e., not just the same composition of numpy / scipy python calls that is done inside `rng_fn`).

 Finally, when your `rng_fn` is doing something more than just calling a `numpy` or `scipy` method, you will need to setup an equivalent seeded function with which to compare for the exact draws (instead of relying on `seeded_[scipy|numpy]_distribution_builder`).
-You can find an example in {`class`}`~pymc3.tests.test_distributions_random.TestWeibull`, whose `rng_fn` returns `beta * np.random.weibull(alpha, size=size)`.
+You can find an example in {class}`~pymc3.tests.test_distributions_random.TestWeibull`, whose `rng_fn` returns `beta * np.random.weibull(alpha, size=size)`.


now the syntax for these links is correct, but tests are not part of the documentation, so they don't render as links as their destination doesn't exist.

OriolAbril · 2021-07-29T11:56:53Z

docs/source/glossary.md

+Functional Programming
+  Functional programming is writing pure functions
+Dispatching
+  Choosing which implementation of an operation is used


@ricardoV94 or anyone else who feels like it, please add the right definitions, relevant links... I have left the two example terms and defintions I added originally to show a bit what is possible.

codecov · 2021-07-29T12:05:34Z

Codecov Report

Merging #4797 (4c9ebf7) into main (ea263f6) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #4797   +/-   ##
=======================================
  Coverage   74.06%   74.06%           
=======================================
  Files          86       86           
  Lines       13864    13864           
=======================================
  Hits        10269    10269           
  Misses       3595     3595

Impacted Files	Coverage Δ
pymc3/parallel_sampling.py	`86.28% <0.00%> (-1.01%)`	⬇️
pymc3/backends/report.py	`91.60% <0.00%> (+2.09%)`	⬆️

docs/source/glossary.md

Co-authored-by: Ricardo Vieira <[email protected]>

ricardoV94 mentioned this pull request Jun 25, 2021

Add V4 distribution implementation developer guide #4783

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OriolAbril force-pushed the init_glossary branch from b7132ef to f5804e4 Compare July 29, 2021 11:52

OriolAbril commented Jul 29, 2021

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OriolAbril requested a review from ricardoV94 July 29, 2021 11:57

OriolAbril mentioned this pull request Aug 2, 2021

Glossary terms #4899

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OriolAbril added 2 commits August 26, 2021 18:02

add glossary example as orphan page

188244a

fixes to distribution guide and add glossary skeleton

e848a21

OriolAbril force-pushed the init_glossary branch from b8461f8 to e848a21 Compare August 26, 2021 15:02

ricardoV94 reviewed Aug 27, 2021

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OriolAbril and others added 2 commits August 27, 2021 13:56

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Co-authored-by: Ricardo Vieira <[email protected]>

fix indentation

4c9ebf7

michaelosthege approved these changes Aug 28, 2021

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OriolAbril merged commit 529a317 into main Aug 28, 2021

OriolAbril deleted the init_glossary branch August 28, 2021 08:52

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add glossary example as orphan page #4797

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add glossary example as orphan page #4797

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