Merge AePPL into logprob submodule

[ricardoV94]

There are still some redundancies to clean, namely in distributions/transforms and distributions/logprob but this should get us 99% there.

TODO

• Figure out if we want an explicit license note for this submodule

Major / Breaking Changes

• PyMC no longer depends on Aeppl. Relevant dispatch methods can be found in pymc.logprob.abstract

[codecov]

Codecov Report

Merging #6334 (5cd0c6a) into main (0654e7f) will decrease coverage by 0.11%.
The diff coverage is 91.61%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #6334      +/-   ##
==========================================
- Coverage   94.26%   94.14%   -0.12%     
==========================================
  Files         111      132      +21     
  Lines       24004    26714    +2710     
==========================================
+ Hits        22627    25150    +2523     
- Misses       1377     1564     +187     

Impacted Files	Coverage Δ
pymc/tests/logprob/test_joint_logprob.py	0.00% <0.00%> (ø)
pymc/tests/sampling/test_forward.py	100.00% <ø> (ø)
pymc/tests/logprob/utils.py	54.87% <54.87%> (ø)
pymc/logprob/tensor.py	87.03% <87.03%> (ø)
pymc/tests/logprob/test_scan.py	93.51% <93.51%> (ø)
pymc/logprob/joint_logprob.py	95.52% <95.52%> (ø)
pymc/logprob/rewriting.py	97.05% <97.05%> (ø)
pymc/logprob/scan.py	97.35% <97.35%> (ø)
pymc/logprob/abstract.py	97.56% <97.56%> (ø)
pymc/tests/logprob/test_tensor.py	99.24% <99.24%> (ø)
... and 37 more

[twiecki]

We should probably add copyright notices at the top linking to aeppl.

[ricardoV94]

We should probably add copyright notices at the top linking to aeppl.

Top of what? Each file?

[michaelosthege]

We should probably add copyright notices at the top linking to aeppl.

Top of what? Each file?

I'd place the license in the __init__.py of the logprob module, and possibly also as a LICENSE.txt file inside the logprob module

At the top of each file we have license notices in other parts of the codebase too.

[ricardoV94]

At the top of each file we have license notices in other parts of the codebase too.

I am not a fan of those, do we need them as well?

[ricardoV94]

BTW anyone feel free to push the license stuff, I would appreciate the help.

[michaelosthege]

@ricardoV94 I amended the license stuff.

I also cancelled the CI because I didn't fix the tests. You can find the previous CI results with the error messages here: https://github.com/pymc-devs/pymc/actions/runs/3539685445

[twiecki]

I amended the license stuff.

I think we should add it at the top of every new file we copy.

[Armavica]

@ricardoV94 Out of curiosity what is the icdf story? Also it looks like you missed five documentation links in pymc/distributions/transforms.py (search for "aeppl")

[ricardoV94]

@ricardoV94 Out of curiosity what is the icdf story?

They already existed in Aeppl, I brought them to where we define the other distribution specific methods. Does that make sense?

Also it looks like you missed five documentation links in pymc/distributions/transforms.py (search for "aeppl")

I didn't want to touch those yet, but maybe I should. I haven't figured out where they should live...

[twiecki]

@brandonwillard @rlouf this is how we think licensing and attribution are correct. Please let us know if you disagree. We plan to merge by EOD. You can still give feedback after that of course.

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[rlouf]

For files that are copied almost verbatim you should paste the full license at the beginning of the file, is that what you suggested above?

For the record, that doesn't mean I am ethically ok with this or approve any of this, I am just making sure proper attribution is given.

[michaelosthege]

For files that are copied almost verbatim you should paste the full license at the beginning of the file, is that what you suggested above?

Yes, at the top of all files in logprob we now have this notice:

#   MIT License
#
#   Copyright (c) 2021-2022 aesara-devs
#
#   The full transcript of the AePPL license can be found in pymc/logprob/LICENSE_AEPPL.txt

[twiecki]

@michaelosthege I think @rlouf means to include the full license, not just a reference. I'm personally don't mind that. Did you have a reference for just referencing the license?

[michaelosthege]

@michaelosthege I think @rlouf means to include the full license, not just a reference. I'm personally don't mind that. Did you have a reference for just referencing the license?

@lucianopaz looked it up, but I agree that we can just paste the whole thing.

While we're at it, we can also rebase on main, which should fix that flaky test.

[brandonwillard]

People, stop tagging me on your work. I want nothing to do with any of your activities (PyMC or otherwise), and give absolutely no explicit or implicit approval or consent to any of it.

@twiecki, you in particular are well aware of this, but you keep doing it. I don't want to have to block you, but I definitely will. The same goes for any follow-ups to this comment.