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Recreate 36964 #5

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Recreates changes from 36964 once 37796 has been merged.

Check that the diff with develop is currently empty. So, essentially this just reverts 37796 but returns the authorship to the original authors and sets commit messages in git blame correctly (to the extent possible.)

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Documentation preview for this PR is ready! 🎉
Built with commit: df78533

Release Manager and others added 29 commits May 31, 2024 22:11
    
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- Cherry-picked from sagemath#35095.

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URL: sagemath#38071
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
…date `# needs`

    
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- Cherry-picked from sagemath#35095.

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URL: sagemath#38074
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
    
as another move towards removal of the "Algebra" class, using "Parent"
framework instead.

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URL: sagemath#38078
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
This fixes all warnings for pep8 E302 in `algebras` and `categories`
folders :
```
E302 expected 2 blank lines, found 0 or 1.
```

This was purely scripted using `autopep8`.

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URL: sagemath#38079
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
this is removing empty lines in the `libs` folder in `.pyx` files, for
compliance with pep8 E302 and E305

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URL: sagemath#38080
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
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as seen in

https://github.com/sagemath/sage/actions/runs/9234699215/job/25408704331
#:~:text=bash%3A%20line%201%3A%20cd%3A%20./worktree%2Dimage%3A%20No%20su
ch%20file%20or%20directory

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URL: sagemath#38082
Reported by: Kwankyu Lee
Reviewer(s):
…l_doc'

    
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- Cherry-picked from sagemath#37900

Includes style fixes from there as well.

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URL: sagemath#38086
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
…ilt our own toolchain

    
The GMP configure test should link against our own libstdc++ instead of
the (too old) system libstdc++


Fixes sagemath#38085
    
URL: sagemath#38087
Reported by: Volker Braun
Reviewer(s):
…repair Coverage.py upload

    
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test-long (90 minutes) runs after a successful test-new (10 minutes).
This is the critical path (100 minutes), longer than build-docs-pdf (85
minutes). We split it into multiple parallel jobs (33 minutes), merging
the coverage files in a job afterwards (6 minutes).

This also repairs the Coverage.py upload, which apparently got broken.

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URL: sagemath#38090
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
    
```
**********************************************************************
File "src/sage/features/__init__.py", line 384, in
sage.features.Feature.hide
Failed example:
    len(list(graphs.fusenes(2)))  # optional - benzene, needs
sage.graphs
Expected nothing
Got:
    1
**********************************************************************
1 item had failures:
   1 of   6 in sage.features.Feature.hide
    [146 tests, 1 failure, 3.74 s]
**********************************************************************
```

Comes from 1ade282
    
URL: sagemath#38091
Reported by: Volker Braun
Reviewer(s):
    
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URL: sagemath#38092
Reported by: gmou3
Reviewer(s): Matthias Köppe
    
Just adding a little comment in the doc on the link to Borel and Laplace
formal transforms.

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URL: sagemath#38093
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
…t, remove deprecated global import

    
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- The change to use `lazy_import` was cherry-picked from sagemath#37900
- The global import was deprecated in sagemath#32647 (2021)

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URL: sagemath#38095
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
    
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All deprecated 2019-2022.

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URL: sagemath#38099
Reported by: Matthias Köppe
Reviewer(s): Frédéric Chapoton
    
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Fixes sagemath#37996.

We remove this function

```python
def nitpick_patch_config(app):
    """
    Patch the default config for nitpicky
    [...] ensure that nitpicky is not considered as a Sphinx
    environment variable but rather as a Sage environment variable. As a
    consequence, changing it doesn't force the recompilation of the
entire
    documentation.
    """
    app.config.values['nitpicky'] = (False, 'sage')
    app.config.values['nitpick_ignore'] = ([], 'sage')
```
from `src/sage_docbuild/conf.py`.

The original purpose of the function seems to change `"env"` to `"sage"`
for `nitpicky` config variable. But the recent Sphinx is setting `""`
(empty string) instead of `"env"` by default. See
https://github.com/sphinx-doc/sphinx/blob/48cbb43e28efe82b198137042811e0
ade3599ae7/sphinx/config.py#L250C1-L250C41

- Hence  the function is already no-op. But this old and obsolete
function is the cause of sagemath#37996. Hence we simply remove it.

- To prepare for Sphinx 7.3.7, we also remove some code which seems to
have become obsolete when `sage -clone` was removed long time ago.

- Made some docstring up-to-date, to test incremental doc build.

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URL: sagemath#38100
Reported by: Kwankyu Lee
Reviewer(s):
    
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- Cherry-picked from sagemath#35095.

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URL: sagemath#38104
Reported by: Matthias Köppe
Reviewer(s): David Coudert, Kwankyu Lee, Matthias Köppe
    
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Fixes sagemath#37979 by handling passing along the index set for the special
cased rank 1 Cartan matrix.

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URL: sagemath#38105
Reported by: Travis Scrimshaw
Reviewer(s): Frédéric Chapoton
…, `database_knotinfo`, `matroid_database`

    
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Using `sage --package update-latest ... --commit`.

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URL: sagemath#38110
Reported by: Matthias Köppe
Reviewer(s): gmou3, Kwankyu Lee
    
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The change made in sagemath#37099 to accommodate the new design of
actions/{up,down}load-artifact@v4 broke the upload of macOS wheels to
PyPI (see https://github.com/sagemath/sage/actions/runs/9234698750/job/2
5408786962#step:8:23); this was masked so far because the build of macOS
wheels was broken until sagemath#36525.

Here we revert to using a separate job that uploads all platform wheels.
This uses the new keywords `pattern` and `merge-multiple` of
actions/download-artifact@v4

Example run:
https://github.com/mkoeppe/sage/actions/runs/9291646178/job/25572343853

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URL: sagemath#38111
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
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This is a bug in sagemath#37589. I  made other small edits.

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URL: sagemath#38121
Reported by: Kwankyu Lee
Reviewer(s):
Release Manager and others added 30 commits June 8, 2024 00:05
    
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URL: sagemath#38077
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
… files of existing distributions sagemath-{categories,...,tdlib}

    
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These directives at the top of the file inform developers about the
assignment of modules to pip-installable distributions.

As of this PR, there should be no change to the existing distributions
(sagemath-categories...) nor the monolithic build of the Sage library.

This is a portion of:
- sagemath#37901

In contrast to that PR, it has no dependencies.

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URL: sagemath#38088
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
    
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URL: sagemath#38103
Reported by: Matthias Köppe
Reviewer(s): gmou3, grhkm21, Matthias Köppe
    
Moved the file set_labels_by_changes.sh to to the .ci directory.
The workflow runs from the main repo.
Fixed bug, the correct labels will be added even if the feature branch
is behind.

sagemath#37262
sagemath#37262 (comment)
https://groups.google.com/g/sage-devel/c/w4IeYgXgVUc/m/Og7NP-3VAQAJ
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URL: sagemath#38114
Reported by: Aman Moon
Reviewer(s): Matthias Köppe
    
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which I think are already established.  But it is good to recommend
preferred styles to keep docstrings in consistent styles.

motivated by the comment:
sagemath#37821 (comment)

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sagemath#38068 (merged here)
    
URL: sagemath#38117
Reported by: Kwankyu Lee
Reviewer(s): gmou3, Kwankyu Lee
    
Weyl algebras elements cannot be hashed or compared, since the element
class is too barren.
This patch lets the element class inherit from IndexedFreeModuleElement,
which fixes this problem automatically.
    
URL: sagemath#38119
Reported by: Darij Grinberg
Reviewer(s): Travis Scrimshaw
…ats for stats

    
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Hopefully fixes sagemath#38116 @jhpalmieri

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URL: sagemath#38122
Reported by: Matthias Köppe
Reviewer(s):
…Field`, `is_RelativeNumberField`, `is_NumberFieldIdeal`, `is_NumberFieldFractionalIdeal`, `is_NumberFieldFractionalIdeal_rel`

    
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URL: sagemath#38124
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
    
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URL: sagemath#38125
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
…lection`, `is_ToricLattice`, `is_ToricLatticeElement`, `is_ToricLatticeQuotient`

    
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URL: sagemath#38126
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
    
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solves some items of wishlist in sagemath#37759

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URL: sagemath#38127
Reported by: Kwankyu Lee
Reviewer(s): Matthias Köppe
    
simplify code in various places by using more list comprehension, as
suggested by `ruff --select=PERF4`

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URL: sagemath#38131
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
…numerical/

    
fixing pycodestyle warning for blank lines in pyx files in `groups` and
`numerical` folders

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URL: sagemath#38132
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
fixing pycodestyle warning about blank lines in pyx files in `coding`
and `modules`

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URL: sagemath#38133
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
fixing pycodestyle warning for blank lines in pyx files in matrix folder

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URL: sagemath#38134
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
some care for blank lines in pyx files in `rings` (only partial here)

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URL: sagemath#38137
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
    
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- Cherry-picked from sagemath#35095.

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URL: sagemath#38143
Reported by: Matthias Köppe
Reviewer(s): David Coudert
…Uninstall/build changed packages; Linux Incremental: Update platforms

    
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Fixes handling of deletions/renames
- https://groups.google.com/g/sage-devel/c/tw6J8vU7IY0/m/IZxuGW8gBQAJ
- sagemath#36892 (comment)

When changes to packages are made, "CI Build&Test" now uses the same
logic as "CI Linux Incremental" for determining what SPKGs to uninstall
(so that spkg-configure.m4 is re-run) and what optional SPKGs to
install.

We update the platforms of "CI Linux Incremental" and remove the default
platform from there, to remove the duplication with "CI Build&Test".

- Also apparently fixes sagemath#37786

For a test run with a PR that actually makes changes to packages, see
- sagemath#38147

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URL: sagemath#38144
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
    
Separate ` ``x, y`` ` to ` ``x``, ``y`` ` and remove excessive newlines.
    
URL: sagemath#38145
Reported by: gmou3
Reviewer(s): gmou3, Kwankyu Lee
    
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CI Fix to fix the doctest dataflow warning that shows in all PRs:
sagemath#38143 (review)

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URL: sagemath#38146
Reported by: Matthias Köppe
Reviewer(s): David Coudert
….2.1, `onetbb` 2021.12.0

    
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Minor update

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- Depends on sagemath#38144 (merged here for testing purposes)
    
URL: sagemath#38147
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
…t is picked

    
On Debian 12 32-bit I get:
```
**********************************************************************
File "src/sage/geometry/polyhedral_complex.py", line 935, in
sage.geometry.polyhedral_complex.PolyhedralComplex._an_element_
Failed example:
    pc._an_element_().vertices_list()
Expected:
    [[0, 0], [0, 1/2], [1, 2]]
Got:
    [[0, 0], [1/3, 1/3], [1, 2]]
**********************************************************************
1 item had failures:
   1 of   4 in
sage.geometry.polyhedral_complex.PolyhedralComplex._an_element_
    [469 tests, 1 failure, 17.41 s]
----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/geometry/polyhedral_complex.py
# 1 doctest failed
----------------------------------------------------------------------
```
Just accept either of the two maximal cells
    
URL: sagemath#38148
Reported by: Volker Braun
Reviewer(s): Matthias Köppe
    
most of them scripted using `autopep8`, and a few ones by hand ; only in
`py` files

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URL: sagemath#38149
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert
…s over GF(2)

    
In response to issue sagemath#38150 I
have adjusted the request for columns over dense matrices over GF(2) by
replacing the standard call to columns with a transpose followed by a
request of rows.

This results in almost a 1000x speed up for large matrices (for the
example in the issue).

### Old Implementation

```py
sage: M2 = random_matrix(GF(2), 2, 2)
sage: %time _  = M2.columns()
CPU times: user 4.14 ms, sys: 1.67 ms, total: 5.81 ms
Wall time: 10.9 ms
sage: %time _  = M2.rows()
CPU times: user 109 µs, sys: 130 µs, total: 239 µs
Wall time: 1.39 ms
sage: M2 = random_matrix(GF(2), 200, 200)
sage: %time _  = M2.columns()
CPU times: user 87.9 ms, sys: 1.32 ms, total: 89.2 ms
Wall time: 88.3 ms
sage: %time _  = M2.rows()
CPU times: user 811 µs, sys: 96 µs, total: 907 µs
Wall time: 912 µs
sage: M2 = random_matrix(GF(2), 2000, 2000)
sage: %time _  = M2.columns()
CPU times: user 7.94 s, sys: 9.11 ms, total: 7.95 s
Wall time: 7.97 s
sage: %time _  = M2.rows()
CPU times: user 7.49 ms, sys: 770 µs, total: 8.26 ms
Wall time: 7.97 ms
```

### New Implementation

```py
sage: M2 = random_matrix(GF(2), 2, 2)
sage: %time _  = M2.columns()
CPU times: user 1.01 ms, sys: 261 µs, total: 1.27 ms
Wall time: 3.75 ms
sage: %time _  = M2.rows()
CPU times: user 54 µs, sys: 8 µs, total: 62 µs
Wall time: 65.1 µs
sage: M2 = random_matrix(GF(2), 200, 200)
sage: %time _  = M2.columns()
CPU times: user 1.09 ms, sys: 40 µs, total: 1.13 ms
Wall time: 1.13 ms
sage: %time _  = M2.rows()
CPU times: user 712 µs, sys: 15 µs, total: 727 µs
Wall time: 732 µs
sage: M2 = random_matrix(GF(2), 2000, 2000)
sage: %time _  = M2.columns()
CPU times: user 9.07 ms, sys: 746 µs, total: 9.82 ms
Wall time: 9.54 ms
sage: %time _  = M2.rows()
CPU times: user 7.82 ms, sys: 687 µs, total: 8.51 ms
Wall time: 8.18 ms
```

Fixes sagemath#38150
    
URL: sagemath#38152
Reported by: Giacomo Pope
Reviewer(s): grhkm21
    
just a few small codes changes in the modified file, some for pep8
compliance, some for micro-optimisation

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URL: sagemath#38156
Reported by: Frédéric Chapoton
Reviewer(s): Matthias Köppe
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Latest in the 3.2 series

- https://www.openssl.org/news/openssl-3.2-notes.html

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- Depends on sagemath#38144 (merged here
for testing)

URL: sagemath#38157
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
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