Remove notebooks, replace with pymc-examples submodule

[MarcoGorelli]

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[MarcoGorelli]

for now I've put the submodule in docs/source, later it could be taken out with (Michael had mentioned nbsphinx_link)

[MarcoGorelli]

I still can't see anything from the 'tutorials' and 'examples' tabs, but I can't see anything there when I build the docs from master either - @ColCarroll is there a way to check that they're correct?

The rest (e.g. the quickstart button linking to the API quickstart) works fine

EDIT

Sorry Colin, just saw your reply about this - will try again and'll let you know!

[codecov]

Codecov Report

Merging #4348 (1e8b9ea) into master (b7b145d) will increase coverage by 0.09%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #4348      +/-   ##
==========================================
+ Coverage   87.85%   87.95%   +0.09%     
==========================================
  Files          88       88              
  Lines       14495    14499       +4     
==========================================
+ Hits        12734    12752      +18     
+ Misses       1761     1747      -14     

Impacted Files	Coverage Δ
pymc3/plots/posteriorplot.py	95.65% <0.00%> (+74.59%)	⬆️

[MarcoGorelli]

@ColCarroll works now! A few screenshots:

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After clicking "quickstart":

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After clicking "tutorials":

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Clicking "using shared variables":

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Clicking 'variational inference' from the homepage:

[twiecki]

LGTM, definitely release-notes worthy.

[fonnesbeck]

We should probably move the python script examples out, as well as the notebooks.

[MarcoGorelli]

Sure, done here and in pymc-devs/pymc-examples#5

[MarcoGorelli]

@fonnesbeck @twiecki what about examples/data, which is used by pm.get_data? Unless there's a plan to deprecate, I think that would need to stay here (though we could move just the examples scripts)

[fonnesbeck]

I think it makes sense to keep all the examples together. If the examples get imported as a submodule by default, nothing should break, should it? We can add an informative error message if pymc-examples is for some reason not installed.

[MarcoGorelli]

If the examples get imported as a submodule by default

Not sure what you mean here - the submodule is available if you clone the repo and then do git submodule update --init --recursive, but I don't think it would be part of the PyPI package

Anyway, that feels like a separate discussion - I've reverted changes to pymc3/examples, they can be moved in a separate PR if desired, this one will only touch the notebooks

[MarcoGorelli]

Anyway, that feels like a separate discussion - I've reverted changes to pymc3/examples, they can be moved in a separate PR if desired, this one will only touch the notebooks

Hey - re-reading this, I think I may have come across as rude - sorry about this, please allow me to rephrase:

I think that moving notebooks out of PyMC3 and putting pymc-examples as a git submodule in their place allows for the docs to keep being built relatively seamlessly. Furthermore, it doesn't change packaging because docs/source/notebooks are already kept out of the PyPI package.

On the other hand, pymc3/examples are currently part of the PyPI package, and so moving them out requires a bit more thought and discussion. Hence, I'd rather keep that to a separate PR so as to not delay moving the notebooks out for too long as well as too not make this PR even bigger. However, I'm happy to address pymc/examples here as well if you prefer

[fonnesbeck]

That's fine, it can be a separate PR, as long as they eventually move over. I don't think the .py scripts in the examples folder get used very much, so its unlikely to be disruptive. The location of the associated data is something to discuss, however, as some of the datasets are used in tests.

[MarcoGorelli]

Sure, thanks - I've opened #4352 for moving out pymc3/examples. The data used by tests would go in pymc3/tests/data, the rest would be downloaded from the pymc-examples repo

[fonnesbeck]

That's probably a reasonable solution. Thanks.

[MarcoGorelli]

Marking as draft because this breaks with the latest reorganisations in pymc-examples, will get back to it

[MarcoGorelli]

works again 🎉

NOTE

This requires pymc-devs/pymc-examples#10 to be merged in order to work if you want to try building the docs locally

[AlexAndorra]

LGTM, thanks @MarcoGorelli !

[AlexAndorra]

BTW, can I merge or do we wait for Colin's review?

[twiecki]

@AlexAndorra Merge away.