Port do and observe functions from PyMC-Experimental

[juanitorduz]

Related to pymc-devs/pymc-extras#237
Closes #5443

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📚 Documentation preview 📚: https://pymc--6879.org.readthedocs.build/en/6879/

[ricardoV94]

I removed the "closes", because we will need a PR that deprecates the functionality in pymc_experimental in favor of pymc

[ricardoV94]

Let's do the following: rename model/model.py to model/basic.py. Keep all public variables that were present in model.py available in model.__init__.py (so existing code isn't broken)

[codecov]

Codecov Report

Merging #6879 (dc4b774) into main (dfb05b6) will increase coverage by 0.08%.
The diff coverage is 95.76%.

❗ Current head dc4b774 differs from pull request most recent head 404ba19. Consider uploading reports for the commit 404ba19 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main    pymc-devs/pymc#6879      +/-   ##
==========================================
+ Coverage   92.05%   92.14%   +0.08%     
==========================================
  Files          96      100       +4     
  Lines       16446    16796     +350     
==========================================
+ Hits        15140    15476     +336     
- Misses       1306     1320      +14     

Files Changed	Coverage Δ
pymc/model/core.py	91.29% <ø> (ø)
pymc/pytensorf.py	92.17% <85.71%> (-0.59%)	⬇️
pymc/model/transform/basic.py	95.00% <95.00%> (ø)
pymc/model/transform/conditioning.py	96.03% <96.03%> (ø)
pymc/model/fgraph.py	96.89% <96.89%> (ø)
pymc/__init__.py	100.00% <100.00%> (ø)
pymc/backends/__init__.py	89.18% <100.00%> (ø)
pymc/backends/arviz.py	96.48% <100.00%> (ø)
pymc/backends/base.py	85.83% <100.00%> (ø)
pymc/backends/mcbackend.py	100.00% <100.00%> (ø)
... and 21 more

[twiecki]

How about model/core.py (formerly model.py), model/transform.py and model/fgraph.py?

[juanitorduz]

How about model/core.py (formerly model.py), model/transform.py and model/fgraph.py?

I am easy! Just provide your feedback and I will change it accordingly :)

[ricardoV94]

transform should be a submodule. We want to implement many things, and the file would become messy quickly

[twiecki]

transform should be a submodule. We want to implement many things, and the file would become messy quickly

Sure, just model/transform/ then

[ricardoV94]

A good check that you are not breaking anything is to not change any of the imports in tests (things should be importable from the same "path" after your PR).

[juanitorduz]

A good check that you are not breaking anything is to not change any of the imports in tests (things should be importable from the same "path" after your PR).

Yes! Thanks for the feedback! I will revert and fix the last commit which does exactly that 😅

[juanitorduz]

@ricardoV94, while I fix the mypy errors (yay!)... I would appreciate feedback on the new module structure (all tests are passing now). Thanks :)

[ricardoV94]

Just a small refactor suggestion, otherwise looks great!

[ricardoV94]

Ah we also need to list the new functionality in the docs! And make sure that we show the old model stuff now that the paths have changed

[juanitorduz]

Ah we also need to list the new functionality in the docs! And make sure that we show the old model stuff now that the paths have changed

What exactly do I need to change? Is there an example PR?

[ricardoV94]

I don't know about a template PR. The goal is for the functionality to be discoverable in the API docs: https://pymcio--6879.org.readthedocs.build/projects/docs/en/6879/api.html

Just need to add some entries in the docs indexes, somewhere here: https://github.com/pymc-devs/pymc/tree/main/docs/source/api

This may be useful: https://www.pymc.io/projects/docs/en/stable/contributing/build_docs.html

[juanitorduz]

@ricardoV94 I tried changing the structure in the docs but I am not seeing this locally (see adde6d2). I will need some support here 🙏

[juanitorduz]

After 4d7b805, I can see the docs:

• https://pymcio--6879.org.readthedocs.build/projects/docs/en/6879/api/model/core.html
• https://pymcio--6879.org.readthedocs.build/projects/docs/en/6879/api/model/transform/conditioning.html

but not on the API page.

[juanitorduz]

Ok! I think 96e6c2b fixed the API entry page.

[twiecki]

Just making sure we're making this available from the global namespace so that we can do pm.do and pm.observe?

[juanitorduz]

Just making sure we're making this available from the global namespace so that we can do pm.do and pm.observe?

They should be available after 2fa700b

[ricardoV94]

I pushed the following changes:

• Reverted changes in imports, so the PR shows less changes
• Updated docstring examples that still showed pymc_experimental imports
• Added __all__ to the new modules
• Rebased from main

Should be good to go when tests pass

[juanitorduz]

Thank you very much @ricardoV94 😀 !