Remove notebooks, replace with pymc-examples submodule #4348

MarcoGorelli · 2020-12-17T08:26:12Z

No description provided.

review-notebook-app · 2020-12-17T08:26:19Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

docs/source/index.rst

MarcoGorelli · 2020-12-17T08:30:37Z

docs/source/sphinxext/gallery_generator.py

+        os.path.join(
+            os.path.dirname(os.path.dirname(srcdir)), "docs", "source", "pymc-examples", "notebooks"
+        )


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

MarcoGorelli · 2020-12-17T08:44:50Z

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 · 2020-12-17T08:55:05Z

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 · 2020-12-17T10:42:45Z

@ColCarroll works now! A few screenshots:

After clicking "quickstart":

After clicking "tutorials":

Clicking "using shared variables":

Clicking 'variational inference' from the homepage:

twiecki · 2020-12-17T12:22:44Z

LGTM, definitely release-notes worthy.

fonnesbeck · 2020-12-17T13:25:22Z

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

MarcoGorelli · 2020-12-17T13:47:31Z

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

MarcoGorelli · 2020-12-17T14:21:31Z

@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 · 2020-12-17T15:15:48Z

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 · 2020-12-17T15:32:54Z

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 · 2020-12-17T16:35:40Z

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 · 2020-12-17T19:28:13Z

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 · 2020-12-18T14:51:56Z

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 · 2020-12-18T15:15:52Z

That's probably a reasonable solution. Thanks.

MarcoGorelli · 2020-12-19T09:13:37Z

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

… remove-notebooks

MarcoGorelli · 2020-12-19T09:29:12Z

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 · 2020-12-19T10:46:31Z

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

twiecki · 2020-12-19T10:58:32Z

@AlexAndorra Merge away.

MarcoGorelli requested a review from ColCarroll December 17, 2020 08:26

🔥 remove notebooks from pymc3, replace with pymc-examples submodule

611bb1c

MarcoGorelli force-pushed the remove-notebooks branch from a905780 to 611bb1c Compare December 17, 2020 08:34

MarcoGorelli commented Dec 17, 2020

View reviewed changes

MarcoGorelli added 2 commits December 17, 2020 10:34

change notebook output_html

f55ad70

revert href change

9a3d6e8

twiecki approved these changes Dec 17, 2020

View reviewed changes

📝 release notes

7e0c3a3

MarcoGorelli added 2 commits December 17, 2020 13:43

🚚 move examples to pymc-examples

ef6f027

checkout submodule at main

cd6d41c

MarcoGorelli added 2 commits December 17, 2020 14:09

noop

1a8d336

🔥 remove test_examples

00e5817

MarcoGorelli added 2 commits December 17, 2020 14:24

keep examples/data for now, so pm.get_data keeps working

0a4b23d

keep examples/__init__.py so get_data still works

11ea4ee

revert removing examples

6af422b

revert removing test_examples

c98c5d7

MarcoGorelli mentioned this pull request Dec 18, 2020

Remove pymc3/examples #4352

Merged

MarcoGorelli marked this pull request as draft December 19, 2020 09:13

MarcoGorelli added 2 commits December 19, 2020 09:26

fixup so docs work with latest pymc-examples reorg

7434b8f

Merge branch 'remove-notebooks' of github.com:MarcoGorelli/pymc3 into…

fdb0199

… remove-notebooks

MarcoGorelli marked this pull request as ready for review December 19, 2020 09:29

🎨

1e8b9ea

AlexAndorra approved these changes Dec 19, 2020

View reviewed changes

AlexAndorra merged commit 34447a7 into pymc-devs:master Dec 19, 2020

MarcoGorelli deleted the remove-notebooks branch December 19, 2020 11:38

paw-lu mentioned this pull request Apr 8, 2021

Unable to get notebook sections to appear in build docs #4619

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Remove notebooks, replace with pymc-examples submodule #4348

Remove notebooks, replace with pymc-examples submodule #4348

MarcoGorelli commented Dec 17, 2020

review-notebook-app bot commented Dec 17, 2020

MarcoGorelli Dec 17, 2020

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

codecov bot commented Dec 17, 2020 •

edited

Loading

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

twiecki commented Dec 17, 2020

fonnesbeck commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020

fonnesbeck commented Dec 17, 2020 •

edited

Loading

MarcoGorelli commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

fonnesbeck commented Dec 17, 2020

MarcoGorelli commented Dec 18, 2020

fonnesbeck commented Dec 18, 2020

MarcoGorelli commented Dec 19, 2020 •

edited

Loading

MarcoGorelli commented Dec 19, 2020 •

edited

Loading

AlexAndorra left a comment

AlexAndorra commented Dec 19, 2020

twiecki commented Dec 19, 2020

Remove notebooks, replace with pymc-examples submodule #4348

Remove notebooks, replace with pymc-examples submodule #4348

Conversation

MarcoGorelli commented Dec 17, 2020

review-notebook-app bot commented Dec 17, 2020

MarcoGorelli Dec 17, 2020

Choose a reason for hiding this comment

MarcoGorelli commented Dec 17, 2020 • edited Loading

EDIT

codecov bot commented Dec 17, 2020 • edited Loading

Codecov Report

MarcoGorelli commented Dec 17, 2020 • edited Loading

twiecki commented Dec 17, 2020

fonnesbeck commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020

fonnesbeck commented Dec 17, 2020 • edited Loading

MarcoGorelli commented Dec 17, 2020

MarcoGorelli commented Dec 17, 2020 • edited Loading

fonnesbeck commented Dec 17, 2020

MarcoGorelli commented Dec 18, 2020

fonnesbeck commented Dec 18, 2020

MarcoGorelli commented Dec 19, 2020 • edited Loading

MarcoGorelli commented Dec 19, 2020 • edited Loading

NOTE

AlexAndorra left a comment

Choose a reason for hiding this comment

AlexAndorra commented Dec 19, 2020

twiecki commented Dec 19, 2020

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

codecov bot commented Dec 17, 2020 •

edited

Loading

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

fonnesbeck commented Dec 17, 2020 •

edited

Loading

MarcoGorelli commented Dec 17, 2020 •

edited

Loading

MarcoGorelli commented Dec 19, 2020 •

edited

Loading

MarcoGorelli commented Dec 19, 2020 •

edited

Loading