Upgrade pypi packages to the lastest version by cxzhong · Pull Request #41926 · sagemath/sage

cxzhong · 2026-03-30T14:03:35Z

Some pypi packages are not well maintained from 2024. I have upload them once. and I have fixed some typos. and delete some packages does not fit python3.12+

📝 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

…e specifications

github-actions · 2026-03-30T17:40:19Z

Documentation preview for this PR (built with commit 5716efd; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

cxzhong · 2026-03-31T09:23:58Z

many sage-the-distro packages seems unmaintenence for a while.

cxzhong · 2026-03-31T15:14:32Z

bs4 needs typing_extension for all python3, so typing_extension is standard for all python

…version_requirements.txt (#17) * Initial plan * Fix bootstrap installation issues - Remove exceptiongroup from hypothesis dependencies (built into Python 3.11+) - Add meson to bootstrap package list to generate version_requirements.txt Agent-Logs-Url: https://github.com/cxzhong/sage/sessions/32dbf026-e8eb-426c-aad0-c23f2cbf31a0 Co-authored-by: cxzhong <14092175+cxzhong@users.noreply.github.com> --------- Co-authored-by: anthropic-code-agent[bot] <242468646+Claude@users.noreply.github.com> Co-authored-by: cxzhong <14092175+cxzhong@users.noreply.github.com>

cxzhong · 2026-04-01T05:45:12Z

The fails caused by mpmath 1.4.1 deprecation warnings. It almostly good now

Add warning filters for deprecated functions in mpmath and pyparsing

cxzhong · 2026-04-01T09:19:57Z

This is ready for review now.

gmou3 · 2026-04-02T08:58:32Z

I could review all packages that are straightforward updates, i.e., with changes only to:

checksums.ini
package-version.txt

The rest would be too hard for me to properly check.

cxzhong · 2026-04-02T09:03:39Z

I could review all packages that are straightforward updates, i.e., with changes only to:

checksums.ini

package-version.txt

The rest would be too hard for me to properly check.

Thank you. and there are also some typos, some dependencies relations change. since 2024, I think the sage-the-distro is not well maintained. And some packages are very old.

dimpase · 2026-04-02T22:59:29Z

why was this removed?

because now, beautifulsoup4 is a standard package which will rely typing_extension for all python version. so we must install typing_extension for all python versions.

why? on Gentoo I use system python with system typing_extensions. Why would I all of a sudden need to install it? It's already there.

and beautifulsoup4, too.

The sage-the-distro pypi packages need to be self-contained. And now for python>=3.12, actually we do not install typing_extension. but beatifulsoup4 needs typing_extension for all python version in their pyproject.toml. and the spkg-configure is used to do not install typing_extension when python>=3.11. But now we need it for all python version, I think this file is useless

the clean way out here would be to use the same set-up as for the rust-dependent packages. But OK, it can wait

cxzhong · 2026-04-05T18:47:14Z

maybe I will try to edit sagelib dependency file for this and #41120

cxzhong · 2026-04-05T18:57:05Z

@dimpase Now I have solve the conflict with #41120, please help me relabel this and #41120

cxzhong · 2026-04-05T19:06:19Z

because they both try to edit the sagelib/dependency file

mantepse · 2026-04-15T13:05:35Z

Most likely, this broke sage-shell-mode for emacs. Please help! In particular: how can I downgrade to check?

cxzhong · 2026-04-15T13:15:08Z

You just revert the commits of this PR to check? Can you reproduce how this breaks?

mantepse · 2026-04-15T14:07:17Z

Unfortunately, this won't work. I downgraded to sage 10.8, but Ipython will stay the same:

sage: import IPython
sage: IPython.__version__
'9.12.0'

mantepse · 2026-04-15T14:10:07Z

I found a hack:

sage -sh
pip install ipython==8.18.1

This works and shows that it is indeed a regression.

cxzhong · 2026-04-15T14:11:55Z

please run ./sage -pip install ipython==xxx.xxx

cxzhong · 2026-04-15T14:12:36Z

I found a hack:
sage -sh
pip install ipython==8.18.1
This works and shows that it is indeed a regression.

Can you describe the detail of regression? Thank you.

cxzhong · 2026-04-15T14:12:55Z

It seems ipython's upgrade break this

mantepse · 2026-04-15T14:18:11Z

The tab-completion in sage-shell-mode swallows the first letter of many (but not all) candidate completions.

cxzhong · 2026-04-15T14:21:27Z

OK, I will find the root cause and fix this

cxzhong · 2026-04-15T14:26:44Z

Observe: IPython 9.x changed ip.complete('ZZ.') to return completions as ['.CartesianProduct', '.Hom', ...] (dot-prefixed, no variable name) instead of the old ['ZZ.CartesianProduct', 'ZZ.Hom', ...]

mantepse · 2026-04-15T14:35:20Z

Here is an example. Eg., erator, ibers, etc.

In fact, it seems it does not just swallow the first letter. For example, ibers should be statistics_fibers.

cxzhong · 2026-04-15T14:38:31Z

It seems this part is also not maintained. Thank you for your report. IPython 9.0 changed this API

mantepse · 2026-04-15T14:46:47Z

Observe: IPython 9.x changed ip.complete('ZZ.') to return completions as ['.CartesianProduct', '.Hom', ...] (dot-prefixed, no variable name) instead of the old ['ZZ.CartesianProduct', 'ZZ.Hom', ...]

Wow, that was quick! The following seems to work!

def _completions_attributes(varname) -> list[str]:
    completions = ip.complete(f'{varname}.')[1]
    return [a[1:] for a in completions]

Upgrade pypi packages to the lastest version

256cd5b

cxzhong added c: build v: large labels Mar 30, 2026

cxzhong added 4 commits March 30, 2026 22:30

Fix dependency specifications for rpy2_rinterface and vcs_versioning

93517fd

Fix dependency specifications for numpy and ply packages

fcf0ec8

Refactor dependency specifications for numpy, ply, and pythran packages

28d378a

Remove importlib_metadata from dependencies and update related packag…

3f3d267

…e specifications

cxzhong added 2 commits March 31, 2026 16:43

fix some unused dependencies

9961dc0

fix the outdated patch

2889098

cxzhong added 3 commits March 31, 2026 18:14

fix some build issues

976be96

fix a format issue

6ee6bea

roman-numerals-py to roman-numerals

8f91d15

cxzhong and others added 3 commits March 31, 2026 23:15

remove some unused packages for python3.12+

6127839

remove unused file

2e8a42b

Ignore deprecation warnings for mpmath

c9ced41

Add warning filters for deprecated functions in mpmath and pyparsing

cxzhong marked this pull request as ready for review April 1, 2026 09:19

github-actions bot added the s: needs review label Apr 1, 2026

cxzhong requested review from dimpase and tobiasdiez April 2, 2026 08:32

Add new tarball and checksum for clarabel package

2e25469

cxzhong requested a review from gmou3 April 2, 2026 08:46

dimpase reviewed Apr 2, 2026

View reviewed changes

cxzhong removed the s: positive review label Apr 5, 2026

resolve conflict with 41120

5716efd

github-actions bot added s: needs review and removed s: needs work labels Apr 5, 2026

cxzhong requested a review from dimpase April 5, 2026 18:55

dimpase approved these changes Apr 5, 2026

View reviewed changes

dimpase added s: positive review c: build and removed c: build s: needs review labels Apr 5, 2026

vbraun merged commit 19f95db into sagemath:develop Apr 8, 2026
33 of 38 checks passed

github-actions bot removed the s: positive review label Apr 8, 2026

cxzhong deleted the Upgrade-pypi-packages branch April 9, 2026 04:44

cxzhong mentioned this pull request Apr 15, 2026

Fix the compatibility of IPython 9.0+ sagemath/sage-shell-mode#86

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