Remove deprecated modules #111

ferrine · 2022-12-12T14:43:02Z

Motivation for these changes

These modules/functions were not used anymore or moved to a different place long time ago

closes Remove deprecated modules and functions #62
closes pytensor.graph.sched is not referenced anywhere #110
closes Remove MRG_RandomStream? #120
closes Remove deprecated pytensor.tensor.nnet,signal #124
closes Consider removing deprecated config api #125
closes Do we still need to support Sympy? #128

Checklist

Explain motivation and implementation 👆
Make sure that the pre-commit linting/style checks pass.
Link relevant issues, preferably in nice commit messages.
The commits correspond to relevant logical changes. Note that if they don't, we will rewrite/rebase/squash the git history before merging.
Are the changes covered by tests and docstrings?
Fill out the short summary sections 👇

Major / Breaking Changes

None

Bugfixes / New features

None

Docs / Maintenance

Deprecated functionality is removed

ferrine · 2022-12-13T11:59:15Z

hits the #119 issue

ferrine · 2022-12-13T15:35:34Z

@ricardoV94 I want to make this PR fat, that will get rid of everything we do not want to support, I'll continue opening issues to validate we indeed want to remove some part of the code. Does it resonate with you? Opening small individual PRs is overwhelming

pytensor/utils.py

ricardoV94 · 2022-12-13T18:04:42Z

@ricardoV94 I want to make this PR fat, that will get rid of everything we do not want to support, I'll continue opening issues to validate we indeed want to remove some part of the code. Does it resonate with you? Opening small individual PRs is overwhelming

Sure. I am going to "request changes", because you mention this PR closes #120 but it doesn't yet.

ricardoV94

It doesn't yet close #120

ferrine · 2022-12-13T20:42:10Z

@ricardoV94 I want to make this PR fat, that will get rid of everything we do not want to support, I'll continue opening issues to validate we indeed want to remove some part of the code. Does it resonate with you? Opening small individual PRs is overwhelming

Sure. I am going to "request changes", because you mention this PR closes #120 but it doesn't yet.

I open issues when I discover something new, so there will me more referenced issues

twiecki · 2022-12-14T12:32:28Z

Are we keeping conv2d?

ferrine · 2022-12-14T12:37:01Z

Are we keeping conv2d?

We do, we even continue testing that
https://github.com/pymc-devs/pytensor/pull/111/files#diff-faff1af3d8ff408964a57b2e475f69a6b7c7b71c9978cccc8f471798caac2c88R80
The moved file is here pytensor/tensor/conv/abstract_conv.py

ferrine · 2022-12-14T12:37:49Z

I've added https://pypi.org/project/pyDeprecate/ to the dependencies so whenever we decide deprecating things or change arguments we can follow semantic versioning with that

michaelosthege

Wow, so many deletions! That's awesome.

michaelosthege · 2022-12-14T16:50:43Z

doc/conf.py

 # html4_writer added to Fix colon & whitespace misalignment
 # https://github.com/readthedocs/sphinx_rtd_theme/issues/766#issuecomment-513852197
-html4_writer = True
+# https://github.com/readthedocs/sphinx_rtd_theme/issues/766#issuecomment-629666319
+# html4_writer = False


This whole comment can be removed because the whitespace problem is now taken care of by the pymc-sphinx-theme

…ct/pyDeprecate/)

ferrine · 2022-12-15T11:42:28Z

I've modified mypy script to reflect the updated fileset as suggested in #77 by @michaelosthege

ricardoV94 · 2022-12-15T13:45:32Z

Now this is some house cleaning alright!

ferrine · 2022-12-16T06:50:40Z

Who is going to press the nuke button?

codecov-commenter · 2022-12-16T08:17:27Z

Codecov Report

Merging #111 (8558e3b) into main (e2ae99e) will increase coverage by 5.53%.
The diff coverage is 84.21%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #111      +/-   ##
==========================================
+ Coverage   74.45%   79.99%   +5.53%     
==========================================
  Files         179      151      -28     
  Lines       49235    43980    -5255     
  Branches    10426     9310    -1116     
==========================================
- Hits        36660    35181    -1479     
+ Misses      10275     6637    -3638     
+ Partials     2300     2162     -138

Impacted Files	Coverage Δ
pytensor/compile/profiling.py	`74.83% <ø> (+0.28%)`	⬆️
pytensor/configparser.py	`86.36% <ø> (+1.41%)`	⬆️
pytensor/gradient.py	`76.82% <ø> (-0.20%)`	⬇️
pytensor/graph/op.py	`86.59% <ø> (ø)`
pytensor/graph/rewriting/basic.py	`64.50% <ø> (-0.54%)`	⬇️
pytensor/graph/rewriting/db.py	`85.90% <ø> (-0.48%)`	⬇️
pytensor/graph/rewriting/utils.py	`95.34% <ø> (+2.49%)`	⬆️
pytensor/misc/pkl_utils.py	`79.48% <ø> (ø)`
pytensor/printing.py	`50.52% <ø> (+0.11%)`	⬆️
pytensor/scalar/basic.py	`79.12% <ø> (+0.01%)`	⬆️
... and 25 more

ricardoV94

Everything else seems good for me, just an error in the docs that were changed

doc/library/tensor/basic.rst

…ywhere

ferrine · 2022-12-16T18:55:44Z

nuke

twiecki · 2022-12-16T21:48:52Z

Epic.

twiecki approved these changes Dec 12, 2022

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ferrine mentioned this pull request Dec 13, 2022

Make sure all deprecations are properly removed #114

Open

ferrine force-pushed the remove-deprecated branch from 31f5367 to aef730a Compare December 13, 2022 13:19

ricardoV94 added the maintenance label Dec 13, 2022

ricardoV94 reviewed Dec 13, 2022

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ricardoV94 marked this pull request as draft December 13, 2022 18:25

ferrine force-pushed the remove-deprecated branch 4 times, most recently from e24e4be to 8cbea97 Compare December 14, 2022 09:22

ferrine requested a review from michaelosthege December 14, 2022 11:37

ferrine force-pushed the remove-deprecated branch from 8cbea97 to c9c0f35 Compare December 14, 2022 12:24

ferrine force-pushed the remove-deprecated branch 2 times, most recently from f45900b to 55a0f0a Compare December 14, 2022 12:46

ferrine marked this pull request as ready for review December 14, 2022 12:46

ferrine force-pushed the remove-deprecated branch 5 times, most recently from 451af01 to aee9de7 Compare December 14, 2022 18:13

michaelosthege reviewed Dec 14, 2022

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ferrine force-pushed the remove-deprecated branch from 63cc0ca to 2472877 Compare December 14, 2022 21:39

ferrine added 4 commits December 15, 2022 14:19

remove deprecated module pytensor/link/jax/jax_linker.py

0b92f87

remove deprecated pytensoor.change_flags

efe448c

remove test for a scipy deprecated submodule

bac999d

remove deprecation utility, favor pydeprecate (https://pypi.org/proje…

b007aca

…ct/pyDeprecate/)

ferrine force-pushed the remove-deprecated branch from 8ac9871 to 8f0a4f2 Compare December 15, 2022 11:40

ricardoV94 requested changes Dec 16, 2022

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doc/library/tensor/basic.rst Outdated Show resolved Hide resolved

ferrine added 12 commits December 16, 2022 13:32

manual curation of docs to eliminate 90% of warnings

ac2694b

remove sympy support

4c598f8

remove gpu related script pytensor/misc/latence_gpu_transfert.py

05a8db2

remove unused internal argument

1aef521

remove pytensor/sandbox/solve.py as it is marked deprecated

a84cee7

remove pytensor/sandbox/fourier.py as it is marked deprecated

040054a

refactor deprecated api

17adb0a

remove deprecated type from pytensor/sparse/type.py

393cafd

bring back deprecated configvals

64b356e

remove deleted files from mypy script and improve the structure

0398c03

remove toposort from pytensor/graph/utils.py it was not referenced an…

61a6e4a

…ywhere

remove D from pytensor/graph/utils.py it was not referenced anywhere

2c413f3

ferrine force-pushed the remove-deprecated branch from 8558e3b to 2c413f3 Compare December 16, 2022 10:33

ricardoV94 approved these changes Dec 16, 2022

View reviewed changes

ferrine merged commit 2c1d7aa into main Dec 16, 2022

ferrine deleted the remove-deprecated branch December 16, 2022 18:55

ricardoV94 mentioned this pull request Jan 5, 2023

Do we need pickler from pytensor? #132

Open

ricardoV94 mentioned this pull request May 17, 2023

Efficient Conv Ops were removed accidentally #305

Open

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Remove deprecated modules #111

Remove deprecated modules #111

ferrine commented Dec 12, 2022 •

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twiecki commented Dec 16, 2022

Remove deprecated modules #111

Remove deprecated modules #111

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ferrine commented Dec 12, 2022 • edited Loading

Motivation for these changes

Checklist

Major / Breaking Changes

Bugfixes / New features

Docs / Maintenance

ferrine commented Dec 13, 2022

ferrine commented Dec 13, 2022

ricardoV94 commented Dec 13, 2022

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