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Fix minor documentation formatting issues in dancing links #34567

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Kerl13 opened this issue Sep 21, 2022 · 8 comments
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Fix minor documentation formatting issues in dancing links #34567

Kerl13 opened this issue Sep 21, 2022 · 8 comments

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@Kerl13
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Kerl13 commented Sep 21, 2022

Component: documentation

Author: Martin Pépin

Branch: 1c9e627

Reviewer: Frédéric Chapoton

Issue created by migration from https://trac.sagemath.org/ticket/34567

@Kerl13 Kerl13 added this to the sage-9.8 milestone Sep 21, 2022
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Kerl13 commented Sep 21, 2022

Author: Martin Pépin

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Reviewer: Frédéric Chapoton

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comment:3

ok, feu vert

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vbraun commented Sep 29, 2022

Changed branch from u/MartinPepin/dancing_links_docs_formatting to 1c9e627

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Changed commit from 1c9e627 to none

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comment:5

Is it normal that build/pkgs/configure/checksums.ini and build/pkgs/configure/package-version.txt were modified in this ticket?

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comment:6

hmm, no. But this is the last commit that Volker has closed before the release.

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Kerl13 commented Sep 30, 2022

comment:7

These files are not modified on u/MartinPepin/dancing_links_docs_formatting at least.

By the way, what's the usual practice regarding merged branches? Can I remove the branch on trac or is there a policy to keep them?

vbraun pushed a commit that referenced this issue Mar 26, 2023
    
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### 📚 Description

Made small edits to the PR template, making it concise and tidy overall.

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URL: #35141
Reported by: Kwankyu Lee
Reviewer(s): Kwankyu Lee, Tobias Diez
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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Partial fix for pycodestyle E221, done using autopep8.

E221 multiple spaces before operator

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URL: #35355
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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The update #35184 broke the docs
upload. Hopefully this is fixed with this PR.

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URL: #35356
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik, Kwankyu Lee
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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Follow-up from #35322.
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URL: #35366
Reported by: Matthias Köppe
Reviewer(s): Gonzalo Tornaría
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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### 📚 Description

This is a follow-up on:
- #35110

As preparation for #35322, which is changing more packages to implicit
namespace packages, we remove `.all` imports from these packages
throughout the Sage library.

This is part of:
- #29705

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- Depends on #35418
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URL: #35372
Reported by: Matthias Köppe
Reviewer(s): Gonzalo Tornaría
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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openblas 0.3.22 is broken, see:
- #35371
- scipy/scipy#18208
- OpenMathLib/OpenBLAS#3976

We reject it.

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URL: #35377
Reported by: Matthias Köppe
Reviewer(s): John H. Palmieri
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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`matrix_modn_dense_float.pyx` had single backticks in one of the
docstrings which was causing it to render as LaTeX text, while it was
intended to be monospace formatted. The missing backticks are added to
fix this.

Fixes #35363

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URL: #35382
Reported by: Karan Handa
Reviewer(s): Matthias Köppe
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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The source tarballs made by `make dist` contain a git repository.
We update the remotes.
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As discussed in https://groups.google.com/g/sage-devel/c/TsHnvmkdrR8
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URL: #35384
Reported by: Matthias Köppe
Reviewer(s): John H. Palmieri
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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Adding the command `sage --tox -e cython-lint`.
See https://pypi.org/project/cython-lint/

There are many failures, so it is not run by default.
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URL: #35385
Reported by: Matthias Köppe
Reviewer(s): Frédéric Chapoton
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
In sage/src/sage/libs/eclib/mwrank.pyx
Line 843 should read 'minumum' instead of 'minimum'.

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URL: #35390
Reported by: yukibl
Reviewer(s): Matthias Köppe
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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URL: #35405
Reported by: Marc Mezzarobba
Reviewer(s): Matthias Köppe
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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### 📚 Description

fix all pep8 E303 warning in the folders whose name starts with the
letter m

purely done with autopep8:

```
$ autopep8 -i --select=E303 src/sage/m*/*.py
$ autopep8 -i --select=E303 src/sage/m*/*/*.py
```

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URL: #35409
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert
vbraun pushed a commit that referenced this issue Apr 6, 2023
    
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### 📚 Description

Follow-up from #35056. Currently no
codecov reports are displayed because the doc deployment workflow is
failing and codecov by default only adds its checks if all other checks
are passing. We change this setting so that codecov checks are always
added, regardless of other failing tests.

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URL: #35412
Reported by: Tobias Diez
Reviewer(s): Kwankyu Lee, Matthias Köppe, Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
Related to sagemath#36801 , but this does not resolve that one. Instead:

* modify the function to respect `_repr_pretty_` just like IPython
* implement `_repr_pretty_` for `Sequence` and `PolynomialSequence`
* Add notes that `_repr_` and `cr=` and `cr_str=` of `Sequence` are
mostly unused
* Add `# need sage.groups` (automatic fix by sage-fixdoctests)

When sagemath#36801 is implemented part of this would be redundant (because
`Sequence` derives from `list`)

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- [x] fix doc tests
- [x] explain meaning of `cr=True` in `Sequence` constructor


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URL: sagemath#39027
Reported by: user202729
Reviewer(s): Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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Next set of formatting fixes in `manifolds`. Hopefully this time a bit
more interesting but still small enough for review ;-)

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URL: sagemath#39099
Reported by: Tobias Diez
Reviewer(s): gmou3, Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
Tiny fix.


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URL: sagemath#39127
Reported by: user202729
Reviewer(s): Martin Rubey, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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URL: sagemath#39157
Reported by: user202729
Reviewer(s): Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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Small improvements to the Meson-based CI workflow:
- Add check that all dependencies are installed via conda (and are not
pulled-in from pypi). This copies the same check from the conda
workflow, as a preparation to delete the latter.
- In case of error, upload the meson build logs to make it easier to
investigate errors.

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URL: sagemath#39176
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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Fixes sagemath#39072

Alternative to sagemath#39116.

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URL: sagemath#39179
Reported by: Kwankyu Lee
Reviewer(s): Kwankyu Lee, Marc Culler, Tobias Diez, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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preemptively as the new year is around the corner!

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URL: sagemath#39190
Reported by: Kwankyu Lee
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
* for some reason the proper header is needed to open the HTML file on
my machine.
* It's reported that `webbrowser.open()` doesn't work when called on a
file path, rather an URI is needed
(sagemath#38946)


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URL: sagemath#39193
Reported by: user202729
Reviewer(s): Martin Rubey
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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Fixes the issue raised in
sagemath/website#480 (comment)

I manually edited the release
https://github.com/sagemath/sage/releases/tag/10.5 generated by an
workflow implemented in sagemath/website#480 to
correct the changelog https://github.com/sagemath/website/blob/master/sr
c/changelogs/sage-10.5.txt, which is now in good shape. But see, for
example, https://github.com/sagemath/sage/releases/tag/10.4 that
contains all changes in betas and rcs.

This PR is for automatic generation of a release that contains only
changes from the last release.

test:
https://github.com/kwankyu/sage/releases
https://github.com/kwankyu/sage/actions/runs/12485317339/job/34844199681

### 📝 Checklist

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URL: sagemath#39194
Reported by: Kwankyu Lee
Reviewer(s): Soham Rane
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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With these changes it should now be possible to run doctests via pytest:
e.g. `pytest --doctest src/sage/manifolds`.

There are still a lot of errors since pytests handles a few things
differently (most notable it doesn't isolate tests from each other).
These issues will be fixed in follow-ups.

I've also moved the pytest config from `src` to the root for better
vscode integration. Added also a bit of typing information in the
doctest framework.

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URL: sagemath#39206
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
… in multiple files

    
Discovered via pytest, which follows stricter rules when parsing
doctests.

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URL: sagemath#39209
Reported by: Tobias Diez
Reviewer(s): Martin Rubey
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
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URL: sagemath#39210
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
    
Similarly to sagemath#39216, we avoid the conversion to `short_digraph` when the
input graph is an instance of `StaticSparseBackend`.

Furthermore, we use the new `PairingHeap_of_n_integers` data structure
(sagemath#39046) instead of a `priority_queue` to emulate a max-heap. This is
slightly faster this way and cleaner.


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URL: sagemath#39217
Reported by: David Coudert
Reviewer(s): Travis Scrimshaw
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 1, 2025
Looks like the file path has changed some time earlier.

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URL: sagemath#39238
Reported by: user202729
Reviewer(s): Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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Use pkg-config to find more dependencies, and add version constraints
(mostly) as specified in the `spkg-configure` scripts.

Now only the packages without pkg-config info use `find_library` (refs
sagemath#39064)

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- sagemath#37447 for the updated conda lock files

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URL: sagemath#38993
Reported by: Tobias Diez
Reviewer(s): Antonio Rojas, Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
When there is an error during importing `sage.all`, then it is just
hidden but sage's are no longer available. This is very hard to debug
and misleading during development. For this reason the fallback to
`repl.all` is removed.

Furthermore, a ruff exception for "unused imports" is added for all
files, since these files always contains many unused imports.

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URL: sagemath#39011
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
Related to sagemath#36801 , but this does not resolve that one. Instead:

* modify the function to respect `_repr_pretty_` just like IPython
* implement `_repr_pretty_` for `Sequence` and `PolynomialSequence`
* Add notes that `_repr_` and `cr=` and `cr_str=` of `Sequence` are
mostly unused
* Add `# need sage.groups` (automatic fix by sage-fixdoctests)

When sagemath#36801 is implemented part of this would be redundant (because
`Sequence` derives from `list`)

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- [x] fix doc tests
- [x] explain meaning of `cr=True` in `Sequence` constructor


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URL: sagemath#39027
Reported by: user202729
Reviewer(s): Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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Next set of formatting fixes in `manifolds`. Hopefully this time a bit
more interesting but still small enough for review ;-)

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URL: sagemath#39099
Reported by: Tobias Diez
Reviewer(s): gmou3, Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
Tiny fix.


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URL: sagemath#39127
Reported by: user202729
Reviewer(s): Martin Rubey, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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URL: sagemath#39157
Reported by: user202729
Reviewer(s): Tobias Diez
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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Small improvements to the Meson-based CI workflow:
- Add check that all dependencies are installed via conda (and are not
pulled-in from pypi). This copies the same check from the conda
workflow, as a preparation to delete the latter.
- In case of error, upload the meson build logs to make it easier to
investigate errors.

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URL: sagemath#39176
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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Fixes sagemath#39072

Alternative to sagemath#39116.

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URL: sagemath#39179
Reported by: Kwankyu Lee
Reviewer(s): Kwankyu Lee, Marc Culler, Tobias Diez, user202729
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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preemptively as the new year is around the corner!

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URL: sagemath#39190
Reported by: Kwankyu Lee
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
* for some reason the proper header is needed to open the HTML file on
my machine.
* It's reported that `webbrowser.open()` doesn't work when called on a
file path, rather an URI is needed
(sagemath#38946)


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URL: sagemath#39193
Reported by: user202729
Reviewer(s): Martin Rubey
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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Fixes the issue raised in
sagemath/website#480 (comment)

I manually edited the release
https://github.com/sagemath/sage/releases/tag/10.5 generated by an
workflow implemented in sagemath/website#480 to
correct the changelog https://github.com/sagemath/website/blob/master/sr
c/changelogs/sage-10.5.txt, which is now in good shape. But see, for
example, https://github.com/sagemath/sage/releases/tag/10.4 that
contains all changes in betas and rcs.

This PR is for automatic generation of a release that contains only
changes from the last release.

test:
https://github.com/kwankyu/sage/releases
https://github.com/kwankyu/sage/actions/runs/12485317339/job/34844199681

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URL: sagemath#39194
Reported by: Kwankyu Lee
Reviewer(s): Soham Rane
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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With these changes it should now be possible to run doctests via pytest:
e.g. `pytest --doctest src/sage/manifolds`.

There are still a lot of errors since pytests handles a few things
differently (most notable it doesn't isolate tests from each other).
These issues will be fixed in follow-ups.

I've also moved the pytest config from `src` to the root for better
vscode integration. Added also a bit of typing information in the
doctest framework.

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URL: sagemath#39206
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
… in multiple files

    
Discovered via pytest, which follows stricter rules when parsing
doctests.

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URL: sagemath#39209
Reported by: Tobias Diez
Reviewer(s): Martin Rubey
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
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URL: sagemath#39210
Reported by: Tobias Diez
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
    
Similarly to sagemath#39216, we avoid the conversion to `short_digraph` when the
input graph is an instance of `StaticSparseBackend`.

Furthermore, we use the new `PairingHeap_of_n_integers` data structure
(sagemath#39046) instead of a `priority_queue` to emulate a max-heap. This is
slightly faster this way and cleaner.


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URL: sagemath#39217
Reported by: David Coudert
Reviewer(s): Travis Scrimshaw
vbraun pushed a commit to vbraun/sage that referenced this issue Jan 3, 2025
Looks like the file path has changed some time earlier.

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URL: sagemath#39238
Reported by: user202729
Reviewer(s): Tobias Diez
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