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Merge updates from add_new_skew_hadamard_matrices #2

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MatteoCati
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Sandstorm831 and others added 27 commits February 15, 2023 00:21
### 📚 Description

Changes the `:trac:` role to point to github instead, and changes
deprecation and stopgap warnings.  Changes all the resulting urls that
are printed in doctests, as well as various comments in code.

Does not update the developer documentation to explain how to use
github.

URL: sagemath#35015
Reported by: roed314
Reviewer(s): Kwankyu Lee, Matthias Köppe, roed314
gh-pr-34960: Improve camera positioning for threejs
    
Fixes sagemath#34822.

The template says that we are not yet accepting PRs. But I will just go
ahead.
    
URL: sagemath#34960
Reported by: Kwankyu Lee
Reviewer(s): Dima Pasechnik
gh-pr-34963: Add doctest for sagemath#20847
    
Closes sagemath#20847.
    
URL: sagemath#34963
Reported by: Marc Mezzarobba
Reviewer(s): Lorenz Panny
gh-pr-34967: show explicit formulas in documentation of WeierstrassIsomorphism
    
Fixes sagemath#34439.
    
URL: sagemath#34967
Reported by: Lorenz Panny
Reviewer(s): Kwankyu Lee
gh-pr-34968: compute matrix kernels modulo composites
    
Fixes sagemath#34862.
    
URL: sagemath#34968
Reported by: Lorenz Panny
Reviewer(s): Lorenz Panny, Travis Scrimshaw
gh-pr-34970: add is_supergreedy() to linear extensions
    
This is my pull request originally created on trac, which I thought
pushing on github.
Fixes sagemath#24700
    
URL: sagemath#34970
Reported by: Rohan Garg
Reviewer(s): Dima Pasechnik, Rohan Garg, Tobias Diez
gh-pr-34972: Cross-link matrix methods image and column_space
    
This is my pull request originally created on trac, which I thought
pushing on github.
Fixes sagemath#33548
    
URL: sagemath#34972
Reported by: Rohan Garg
Reviewer(s): Marc Mezzarobba
gh-pr-34974: SignedPermutation should allow iterables as input
    
This is my pull request originally which addresses the issue sagemath#34923
Fixes sagemath#34923
    
URL: sagemath#34974
Reported by: Rohan Garg
Reviewer(s): Travis Scrimshaw
gh-pr-34982: add .torsion_basis() method to EllipticCurve_finite_field
    
Fixes sagemath#34718.
    
URL: sagemath#34982
Reported by: Lorenz Panny
Reviewer(s): roed314
Fixes sagemath#24682.

URL: sagemath#34986
Reported by: MatteoCati
Reviewer(s): David Coudert
@MatteoCati MatteoCati merged commit 6ee79be into add_hadamard_matrices_up_to_1000 Feb 21, 2023
MatteoCati pushed a commit that referenced this pull request Mar 27, 2023
sagemathgh-35114: libgap: Remove some GC hazards
    
### 📚 Description

Trac branch `u/gh-collares/gap-gc` from sagemath#34701, now migrated to GitHub.
Currently based atop sagemath#35093; will rebase once that is merged.

The rest of the description below is copied from sagemath#34701:

A refactor in sagemath#27946 introduced "unprotected" (not surrounded by
`GAP_Enter`/`GAP_Leave`) `GAP_ValueGlobalVariable` calls. I believe this
might be a GC hazard, because after updating to GAP 4.12.1 I started
seeing aarch64 crashes on NixOS infrastructure such as:

```
#0  0x0000fffff79740e8 in wait4 ()
#1  0x0000fffff5dc6b78 in print_enhanced_backtrace ()
#2  0x0000fffff5dc8190 in sigdie ()
sagemath#3  0x0000fffff5dcb1c0 in cysigs_signal_handler ()
sagemath#4  0x0000fffff7ffb7cc in __kernel_rt_sigreturn ()
sagemath#5  0x0000ffff99a0bf28 in ConvString ()
sagemath#6  0x0000000000000000 in ?? ()
sagemath#7  0x0000000000000000 in ?? ()
sagemath#8  0x0000000000000000 in ?? ()
sagemath#9  0x0000ffff99989930 in Pr ()
sagemath#10 0x0000ffff9998aa18 in CloseOutput ()
sagemath#11 0x0000ffff99884828 in capture_stdout () at /build/sage-
src-9.7/pkgs/sagemath-standard/sage/libs/gap/element.pyx:154
...
```
I also see cases where `capture_stdout` throws errors such as
`sage.libs.gap.util.GAPError: Error, Length: <list> must be a list (not
the integer 255)` and then crashes. Both types of errors are fixed by
this ticket.

Note that I am nesting `GAP_Enter`/`GAP_Leave` calls because I didn't
remove the preexisting calls inside `capture_stdout`. That's because I
feared removing the innermost calls might create a new footgun (and I
believe nested `GAP_Enter`/`GAP_Leave` calls are explicitly supported),
but removing them should cause no problem. Removing them might even be
preferable for performance reasons, I don't know.

Fixes sagemath#34701

### 📝 Checklist

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appropriately -->
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here to help! -->

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

### ⌛ Dependencies
<!-- List all open pull requests that this PR logically depends on -->
<!--
- #xyz: short description why this is a dependency
- #abc: ...
-->
- sagemath#35093: GAP 4.12.2 upgrade, which touches the same function and should
land first.
    
URL: sagemath#35114
Reported by: Mauricio Collares
Reviewer(s): Dima Pasechnik
MatteoCati pushed a commit that referenced this pull request Aug 10, 2024
Remove excessive blank lines around INPUT, OUTPUT, EXAMPLES, and before
docstring ending """. (#2)
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8 participants