sagemathgh-36238: `sage -t`: Distinguish .pxd from .pyx in doctest basenames
    
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These basenames are used in the stats file, recording test failures and
running times in `~/.sage/timings2.json`.
Currently, `element.pyx` and `element.pxd` have the same basename, and
so they clobber each other in the stats file. It depends on the order of
execution which of the two wins. This affects `sage -t --failed` and the
sort order according to running times.

Here we disambiguate them by adding a suffix for .pxd and .pxi files.

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example "Fixes sagemath#12345". -->
Cherry-picked from sagemath#35095, where the stats are used for creating records
of known test failures of the modularized distributions.
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URL: sagemath#36238
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee

…senames

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<!-- Describe your changes here in detail -->
These basenames are used in the stats file, recording test failures and
running times in `~/.sage/timings2.json`.
Currently, `element.pyx` and `element.pxd` have the same basename, and
so they clobber each other in the stats file. It depends on the order of
execution which of the two wins. This affects `sage -t --failed` and the
sort order according to running times.

Here we disambiguate them by adding a suffix for .pxd and .pxi files.

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes sagemath#12345". -->
Cherry-picked from sagemath#35095, where the stats are used for creating records
of known test failures of the modularized distributions.
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appropriately. -->

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URL: sagemath#36238
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee

sagemathgh-36264: `sage --fixdoctests --update-known-test-failures`; silence modularized distributions in CI
    
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The distributions `sagemath-repl` and `sagemath-categories` run parts of
the testsuite in a virtual environment created by `tox` when
SAGE_CHECK=yes. This also runs as part of the Build & Test CI.

Here we make several improvements:
- Support SAGE_CHECK=warn
- Invoke the doctester with `--baseline-stats-path={toxinidir}/known-
test-failures.json`
- Make the tests silent unless new test failures, not recorded in the
`known-test-failures.json`, are encountered

To help maintain the `known-test-failures.json`, we also add new
features to the command `sage --fixdoctests`.
- `sage --fixdoctests --update-known-test-failures` reads the stats
files generated by the doctester in the virtual environments and writes
updated `known-test-failures.json` files to the source tree
- doctester stats now also include a field `ntests` - number of doctests
of a module that were run

`sage --fixdoctests` also receives new switches `--distribution all`,
`--fixed-point`, `--verbose`, `--no-diff` and some other improvements.

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- Part of: sagemath#29705
- Cherry-picked from: sagemath#35095
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### ⌛ Dependencies

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- Depends on sagemath#36263 (merged here)
- Depends on sagemath#36238 (merged here)

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URL: sagemath#36264
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe

sagemathgh-36123: Upgrade numpy to 1.26.0, setuptools to 68.2.2
    
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NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility.

1.26.0 was released 2023-09-16.

As NumPy has changed its build system from setuptools-pinned-to-an-
ancient-version to meson_python, we get rid of our ancient version of
`setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the
same (current) version.

- [x] Check portability run:
https://github.com/mkoeppe/sage/actions/runs/5959239800
- [ ] Check SAGE_FAT_BINARY

<!-- Why is this change required? What problem does it solve? -->
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example "Fixes sagemath#12345". -->
Resolves sagemath#34816
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- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies
- Depends on sagemath#36112 (for the `meson_python` upgrades, merged here)
- Depends on sagemath#35404 (merged here as
part of above)
- Depends on sagemath#35810 (merged here as part of above)
- Depends on sagemath#36110 (merged here)
- Depends on sagemath#36263 (merged here)
- Depends on sagemath#36238 (merged here)
- Depends on sagemath#36255 (merged here)
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URL: sagemath#36123
Reported by: Matthias Köppe
Reviewer(s):

gh-36123: Upgrade numpy to 1.26.0, setuptools to 68.2.2
    
<!-- ^^^^^
Please provide a concise, informative and self-explanatory title.
Don't put issue numbers in there, do this in the PR body below.
For example, instead of "Fixes #1234" use "Introduce new method to
calculate 1+1"
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<!-- Describe your changes here in detail -->

NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility.

1.26.0 was released 2023-09-16.

As NumPy has changed its build system from setuptools-pinned-to-an-
ancient-version to meson_python, we get rid of our ancient version of
`setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the
same (current) version.

- [x] Check portability run:
https://github.com/mkoeppe/sage/actions/runs/5959239800
- [ ] Check SAGE_FAT_BINARY

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes #12345". -->
Resolves #34816
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appropriately. -->

### 📝 Checklist

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- [x] The title is concise, informative, and self-explanatory.
- [x] The description explains in detail what this PR is about.
- [x] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies
- Depends on #36112 (for the `meson_python` upgrades, merged here)
- Depends on #35404 (merged here as
part of above)
- Depends on #35810 (merged here as part of above)
- Depends on #36110 (merged here)
- Depends on #36263 (merged here)
- Depends on #36238 (merged here)
- Depends on #36255 (merged here)
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- #34567: ...
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URL: #36123
Reported by: Matthias Köppe
Reviewer(s):