Set cython directive binding=True

[tobiasdiez]

Continuation of #26254. This is needed for better integration of Cython functions and thereby unlocks a few further documentation improvements (#27578, #30884, #31309, ...).

Moreover, binding=True is the default in Cython 3.

📝 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

• Remove duplicate 'doc-html' target from CI #40357

[github-actions]

Documentation preview for this PR (built with commit c3de821; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

[tobiasdiez]

@dcoudert The test for del_vertex that you have added in #39271 (and only that test) fails now with binding=True. Do you have an idea why/how to fix this?

sage -t --warn-long 5.0 --random-seed=162462718596100674006260289682106403625 src/sage/graphs/base/static_sparse_backend.pyx
**********************************************************************
Error: Failed example:: Got: 
Traceback (most recent call last):
  File "/Users/runner/miniconda3/envs/sage-dev/lib/python3.11/site-packages/sage/doctest/forker.py", line 730, in _run
    self.compile_and_execute(example, compiler, test.globs)
  File "/Users/runner/miniconda3/envs/sage-dev/lib/python3.11/site-packages/sage/doctest/forker.py", line 1154, in compile_and_execute
    exec(compiled, globs)
  File "<doctest sage.graphs.base.static_sparse_backend.StaticSparseBackend.del_vertex[3]>", line 1, in <module>
    g.del_vertex('a')
  File "static_sparse_backend.pyx", line 1546, in sage.graphs.base.static_sparse_backend.StaticSparseBackend.del_vertex
TypeError: an integer is required

    g.del_vertex('a')
Expected:
    Traceback (most recent call last):
    ...
    ValueError: graph is immutable; please change a copy instead (use function copy())
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/Users/runner/miniconda3/envs/sage-dev/lib/python3.11/site-packages/sage/doctest/forker.py", line 730, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/runner/miniconda3/envs/sage-dev/lib/python3.11/site-packages/sage/doctest/forker.py", line 1154, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.base.static_sparse_backend.StaticSparseBackend.del_vertex[3]>", line 1, in <module>
        g.del_vertex('a')
      File "static_sparse_backend.pyx", line 1546, in sage.graphs.base.static_sparse_backend.StaticSparseBackend.del_vertex
    TypeError: an integer is required
**********************************************************************
1 item had failures:
   1 of   9 in sage.graphs.base.static_sparse_backend.StaticSparseBackend.del_vertex
    [198 tests, 1 failure, 0.24s wall]

[dcoudert]

Got it, and it's my fault: methods add_vertex and del_vertex are defined twice in StaticSparseBackend.
The solution is to remove the duplicates lines 1512-1546.

[tobiasdiez]

Got it, and it's my fault: methods add_vertex and del_vertex are defined twice in StaticSparseBackend. The solution is to remove the duplicates lines 1512-1546.

Thanks a lot, that worked!

[tobiasdiez]

The CI runs for sage-the-distro are red, but I think it's just because it doesn't recognize the changed compilation options correctly and does an incremental build, without recompiling the necessary cython modules.

[dcoudert]

This looks good to me but I'm not sure how to double check that on my laptop. Any advise is more than welcome.

[tobiasdiez]

Thanks!

Since all cython modules need to be recompiled, either make sagelib-clean (+ build) or sage -ba should do the trick.

[dcoudert]

It compiles well on Fedora 39 and passes tests (make ptest).

LGTM.

[dcoudert]

I hope the tests I did are sufficient

[tobiasdiez]

Thanks for the review!