build/pkgs/numpy 2.0.1, scipy 1.13.1, cmake 3.30.2, gsl 2.8, meson 1.5.1, meson_python 0.16.0, ninja_build 1.12.1, openblas 0.3.28, pybind11 2.13.1, pythran 0.16.1

[mkoeppe]

• https://numpy.org/doc/stable/release/2.0.0-notes.html

• https://scipy.github.io/devdocs/release/1.13.1-notes.html

• Fixes using numpy 2.0 #38242

📝 Checklist

• The title is concise and informative.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation and checked the documentation preview.

⌛ Dependencies

• Depends on provide compatibility with numpy 2.0 #38250 (merged here)
• Depends on build/pkgs/setuptools_scm: Upgrade to 8.1.0, fix dependency typing_extensions, change some packages to wheel #38226 (merged here)

[github-actions]

Documentation preview for this PR (built with commit f62f88b; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

[mkoeppe]

Tests at https://github.com/mkoeppe/sage/actions/runs/10059877764

[kwankyu]

I get

sage -t --warn-long 69.9 --random-seed=274666681782489637879204037307995713165 src/sage/graphs/generic_graph.py
**********************************************************************
File "src/sage/graphs/generic_graph.py", line 15996, in sage.graphs.generic_graph.GenericGraph.?
Failed example:
    (graphs.FruchtGraph()).clustering_coeff(weight=True)                  # needs networkx
Expected:
    {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0,
     3: 0.3333333333333333, 4: 0.3333333333333333,
     5: 0.3333333333333333, 6: 0.3333333333333333,
     7: 0.3333333333333333, 8: 0, 9: 0.3333333333333333,
     10: 0.3333333333333333, 11: 0}
Got:
    {0: np.float64(0.3333333333333333),
     1: np.float64(0.3333333333333333),
     2: 0,
     3: np.float64(0.3333333333333333),
     4: np.float64(0.3333333333333333),
     5: np.float64(0.3333333333333333),
     6: np.float64(0.3333333333333333),
     7: np.float64(0.3333333333333333),
     8: 0,
     9: np.float64(0.3333333333333333),
     10: np.float64(0.3333333333333333),
     11: 0}
**********************************************************************
File "src/sage/graphs/generic_graph.py", line 16006, in sage.graphs.generic_graph.GenericGraph.?
Failed example:
    (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2],                # needs networkx
                                            weight=True)
Expected:
    {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0}
Got:
    {0: np.float64(0.3333333333333333), 1: np.float64(0.3333333333333333), 2: 0}
**********************************************************************
1 item had failures:
   2 of 1269 in sage.graphs.generic_graph.GenericGraph.?
    [3915 tests, 2 failures, 23.88 s]
----------------------------------------------------------------------
sage -t --warn-long 69.9 --random-seed=274666681782489637879204037307995713165 src/sage/graphs/generic_graph.py  # 2 doctests failed
----------------------------------------------------------------------

[mkoeppe]

https://github.com/mkoeppe/sage/actions/runs/10437086696/job/28902874363#step:11:5246

#29 3702.4   [sagemath_doc_html-none]   [spkg-install] [rings_num] Could not import extension matplotlib.sphinxext.plot_directive (exception: /sage/local/var/lib/sage/venv-python3.9/lib64/python3.9/site-packages/matplotlib/_path.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZN3agg10curve3_div4initEdddddd)

likewise on other platforms

same or similar to matplotlib/matplotlib#28357

[mkoeppe]

Set to "disputed" 3 weeks ago.

• In favor: @mkoeppe (PR author), @kwankyu (reviewer, build/pkgs/numpy 2.0.1, scipy 1.13.1, cmake 3.30.2, gsl 2.8, meson 1.5.1, meson_python 0.16.0, ninja_build 1.12.1, openblas 0.3.28, pybind11 2.13.1, pythran 0.16.1 #38227 (comment))
• Against: @tobiasdiez (presumed from setting label to "needs work" and https://groups.google.com/g/sage-devel/c/sVcJiJdUxRs/m/TmOVq2U3AwAJ), @dimpase (presumed from side comment "demand by Tobias Diez on #38227" is for keeping existent practices #38648)