[BLD] Add support for NumPy 2.0 wheels #629

matthewfeickert · 2024-06-18T09:20:51Z

Types of changes

Resolves #626.

Add numpy>=2.0.0 to build-system requires to build NumPy 1.x and 2.x compatible
wheels.
- c.f. https://numpy.org/doc/stable/dev/depending_on_numpy.html#numpy-2-0-specific-advice
- As NumPy 2.0 is Python 3.9+, also need to conditionally support oldest-supported-numpy for Python 3.8.
Remove wheel from build-system requires as it is never required and injected automatically by setuptools only when needed.
- c.f. https://learn.scientific-python.org/development/guides/packaging-classic/
Remove setup_requires metadata from setup.py as it is deprecated and should defer to PEP 517/518.
- c.f. https://learn.scientific-python.org/development/guides/packaging-classic/#pep-517518-support-high-priority
Use np.inf to avoid AttributeErrors with NumPy 2.0. Avoids

  AttributeError: `np.infty` was removed in the NumPy 2.0 release. Use `np.inf` instead.

  AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead.

Motivation and context / Related issue

Numpy 2.0 compatibility #626

How has this been tested (if it applies)

On my fork all tests (.github/workflows/build_tests.yml) and wheel builds (.github/workflows/build_wheels.yml) are passing.

Locally I tested by

uv pip install --upgrade -e . && python -c 'import ot'

PR checklist

I have read the CONTRIBUTING document.
The documentation is up-to-date with the changes I made (check build artifacts).
All tests passed, and additional code has been covered with new tests.
I have added the PR and Issue fix to the RELEASES.md file.

matthewfeickert · 2024-06-18T09:43:20Z

@rflamary It looks like things are going to pass on my fork (thumbs pressed) so can you enable the CI on my PR (as I'm a first timer)? I'm going to be offline for the next several hours.

codecov · 2024-06-18T12:11:40Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.67%. Comparing base (cba9c7b) to head (f34309b).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #629   +/-   ##
=======================================
  Coverage   96.67%   96.67%           
=======================================
  Files          85       85           
  Lines       16836    16836           
=======================================
  Hits        16276    16276           
  Misses        560      560

rflamary

This is great thanks @matthewfeickert

Could you also update teh setup.py? I know the toml file is enough but it is importnant to remain synchronized

rflamary · 2024-06-18T12:44:23Z

Also if you put "build wheels" in the commit text it should build the wheels in the PR

matthewfeickert · 2024-06-18T15:30:49Z

(Sorry, I force pushed and I forgot that doing so reset the approval of the CI permissions.)

* Add numpy>=2.0.0 to build-system requires to build NumPy 1.x and 2.x compatible wheels. - c.f. https://numpy.org/doc/stable/dev/depending_on_numpy.html#numpy-2-0-specific-advice - As NumPy 2.0 is Python 3.9+, also need to conditionally support 'oldest-supported-numpy' for Python 3.8. * Remove wheel from build-system requires as it is never required and injected automatically by setuptools only when needed. - c.f. https://learn.scientific-python.org/development/guides/packaging-classic/

* Remove setup_requires as it is deprecated and should defer to PEP 517/518. - c.f. https://learn.scientific-python.org/development/guides/packaging-classic/#pep-517518-support-high-priority

* Avoids: AttributeError: `np.infty` was removed in the NumPy 2.0 release. Use `np.inf` instead. AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead.

matthewfeickert · 2024-06-18T16:34:45Z

setup.py

@@ -69,7 +69,6 @@
    license='MIT',
    scripts=[],
    data_files=[],
-    setup_requires=["oldest-supported-numpy", "cython>=0.23"],


Could you also update the setup.py? I know the toml file is enough but it is important to remain synchronized.

setup_requires is deprecated and indeed trying to use it actually breaks a NumPy 2.0 build, so this needs to get removed. The build-system information in pyproject.toml supersedes it.

c.f. https://learn.scientific-python.org/development/guides/packaging-classic/#pep-517518-support-high-priority

matthewfeickert · 2024-06-18T17:13:52Z

Okay, as I now have all tests and wheel builds passing on my fork, this PR should be ready for CI and review.

pyproject.toml

matthewfeickert · 2024-06-18T19:23:05Z

setup.py

@@ -69,7 +69,6 @@
    license='MIT',
    scripts=[],
    data_files=[],
-    setup_requires=["oldest-supported-numpy", "cython>=0.23"],
    install_requires=["numpy>=1.16", "scipy>=1.6"],
    python_requires=">=3.6",


The requires-python metadata here is incorrect compared to reality as pot v0.9.3 only provides wheels for Python 3.7+ and the tests are only for Python 3.8+

POT/.github/workflows/build_tests.yml

Line 25 in cba9c7b

python-version: ["3.8", "3.9", "3.10", "3.11"]

As @henryiii has covered elsewhere (can't remember which blog) the purpose of requires-python (python_requires in setuptools) is to provide guards to keep older CPython versions from installing releases that could contain unrunnable code and to avoid backtracking unhelpfully in dependency resolves.

This should get updated, but this is also a separate (adjacent) scope issue than NumPy 2.0, so I'll open up PR #630 for this.

thanks we need to cleanup stuff

rflamary · 2024-06-19T07:52:15Z

Wheels are building, thanks so much @matthewfeickert !

https://github.com/PythonOT/POT/actions/runs/9578068455

matthewfeickert · 2024-06-19T08:04:23Z

That's great! :D

Thanks for the super speedy and responsive review. It was a great first time contributing to the project!

matthewfeickert force-pushed the build/numpy-1-x-2-x-compatible-wheel branch from 826b40c to d392abf Compare June 18, 2024 09:32

matthewfeickert marked this pull request as ready for review June 18, 2024 09:45

rflamary reviewed Jun 18, 2024

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matthewfeickert force-pushed the build/numpy-1-x-2-x-compatible-wheel branch from f6e3cdf to 49556f9 Compare June 18, 2024 15:21

matthewfeickert requested a review from rflamary June 18, 2024 15:22

matthewfeickert force-pushed the build/numpy-1-x-2-x-compatible-wheel branch from 49556f9 to 2923485 Compare June 18, 2024 15:37

matthewfeickert added 4 commits June 18, 2024 11:28

build: Remove setup_requires metadata

1a83b3e

* Remove setup_requires as it is deprecated and should defer to PEP 517/518. - c.f. https://learn.scientific-python.org/development/guides/packaging-classic/#pep-517518-support-high-priority

fix: Use np.inf to avoid AttributeError

c801e41

* Avoids: AttributeError: `np.infty` was removed in the NumPy 2.0 release. Use `np.inf` instead. AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead.

docs: Add NumPy 2.0 support to release notes

f34309b

matthewfeickert force-pushed the build/numpy-1-x-2-x-compatible-wheel branch from 2923485 to f34309b Compare June 18, 2024 16:32

matthewfeickert commented Jun 18, 2024

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matthewfeickert commented Jun 18, 2024

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matthewfeickert mentioned this pull request Jun 18, 2024

[BLD] Update requires-python metadata to Python 3.7 #630

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matthewfeickert changed the title ~~build: Add support for NumPy 2.0 wheels~~ [BLD] Add support for NumPy 2.0 wheels Jun 18, 2024

rflamary approved these changes Jun 19, 2024

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rflamary merged commit 61d751b into PythonOT:master Jun 19, 2024
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matthewfeickert deleted the build/numpy-1-x-2-x-compatible-wheel branch June 19, 2024 07:39

matthewfeickert mentioned this pull request Jun 19, 2024

[CI] Remove redundant CIBW_BEFORE_BUILD #631

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[BLD] Add support for NumPy 2.0 wheels #629

[BLD] Add support for NumPy 2.0 wheels #629

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[BLD] Add support for NumPy 2.0 wheels #629

[BLD] Add support for NumPy 2.0 wheels #629

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Types of changes

Motivation and context / Related issue

How has this been tested (if it applies)

PR checklist

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