Upgrade scipy to 1.10.1

[mkoeppe]

📚 Description

The upgrade also includes upgrades of meson, meson_python, and pythran.

Closes #34842

📝 Checklist

• I have made sure that the title is self-explanatory and the description concisely explains the PR.
• I have linked an issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation accordingly.

⌛ Dependencies

[codecov-commenter]

Codecov Report

Patch coverage has no change and project coverage change: -0.02 ⚠️

Comparison is base (05329f6) 88.59% compared to head (64987b3) 88.58%.

❗ Current head 64987b3 differs from pull request most recent head 439ea59. Consider uploading reports for the commit 439ea59 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop   #35082      +/-   ##
===========================================
- Coverage    88.59%   88.58%   -0.02%     
===========================================
  Files         2140     2140              
  Lines       396998   396998              
===========================================
- Hits        351740   351683      -57     
- Misses       45258    45315      +57     

see 25 files with indirect coverage changes

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[mkoeppe]

doctest failure in doc/de/a_tour_of_sage/index.rst is unrelated

[kiwifb]

Looks good to me and scipy 1.10.0 works fine here.

[kiwifb]

Looks good to me.

[kiwifb]

Let me know if that was an abuse of the workflow.

[mkoeppe]

Starting a review and approving the changes is exactly the right procedure. Thanks!

[kiwifb]

It wouldn't be the first time that numpy or scipy gives us a small change in a minor release, so I am doing some more checks.

[kiwifb]

I cannot see any problem with it. Once I removed all the warnings I got from matplotlib 3.7.0.

[mkoeppe]

Thanks! Also works without problems on macOS

[vbraun]

Doesn't build on OSX for me: http://build.sagemath.org/#/builders/54/builds/16

  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  Traceback (most recent call last):
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_
process.py", line 144, in prepare_metadata_for_build_wheel
      hook = backend.prepare_metadata_for_build_wheel
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'mesonpy' has no attribute 'prepare_metadata_for_build_wheel'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_
process.py", line 351, in <module>
      main()
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_
process.py", line 333, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_
process.py", line 148, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/var/tmp/sage/build/meson_python-0.12.1/src/mesonpy/__init__.py"
, line 1054, in wrapper
      return func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/var/tmp/sage/build/meson_python-0.12.1/src/mesonpy/__init__.py"
, line 1115, in build_wheel
      with _project(config_settings) as project:
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/contextlib.py", line 137, in __enter__
      return next(self.gen)
             ^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/var/tmp/sage/build/meson_python-0.12.1/src/mesonpy/__init__.py"
, line 1011, in _project
      with Project.with_temp_working_dir(
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/contextlib.py", line 137, in __enter__
      return next(self.gen)
             ^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/var/tmp/sage/build/meson_python-0.12.1/src/mesonpy/__init__.py", line 785, in with_temp_working_dir
      yield cls(source_dir, tmpdir, build_dir, meson_args)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/var/tmp/sage/build/meson_python-0.12.1/src/mesonpy/__init__.py", line 588, in __init__
      arch, *other = filter(None, (x.strip() for x in archflags.split('-arch')))
      ^^^^^^^^^^^^
  ValueError: not enough values to unpack (expected at least 1, got 0)
  error: subprocess-exited-with-error
  
  <C3><97> Preparing metadata (pyproject.toml) did not run successfully.
  <E2><94><82> exit code: 1
  <E2><95><B0><E2><94><80>> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/bin/python3 /Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpz5dlgfng

[mkoeppe]

I think this is misconfigured on your buildbot. Do you set ARCHFLAGS to the empty string?
https://github.com/mesonbuild/meson-python/blob/release-0.12/mesonpy/__init__.py#L586

[mkoeppe]

Anyway I'm working on a PR for meson-python that makes this more robust

[github-actions]

Documentation preview for this PR is ready! 🎉
Built with commit: 439ea59