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update numpy to 2.2.3, scipy to 1.15.2 #39655

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merged 19 commits into from
Mar 22, 2025
Merged

update numpy to 2.2.3, scipy to 1.15.2 #39655

merged 19 commits into from
Mar 22, 2025

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dimpase
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@dimpase dimpase commented Mar 9, 2025

this is long overdue update.

It needs building tools bumped, too, thus dependencies

📝 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

build tools need a bump

This was referenced Mar 9, 2025
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@dimpase dimpase force-pushed the numpy223scipy1152 branch from 0a2a4bf to e42854b Compare March 9, 2025 22:53
@dcoudert
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I tried on macOS with python 3.12 and it seems ok to me.
Note that I had to manually download pythran from pypi.
Should we do more tests ? Otherwise, I'm ok to validate the 4 PRs.

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dimpase commented Mar 11, 2025

Note that I had to manually download pythran from pypi.

what exactly was happening? a wrong URL?

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dimpase commented Mar 11, 2025

@dcoudert - indeed, the URL was not correct.
911fcb3
should fix it

Matthias Koeppe and others added 16 commits March 11, 2025 10:32
@dimpase
pybind11: Update to 2.13.6, switch to wheel
b27da1a
@dimpase
version needed for scipy update
fe3e29d
@dimpase
pythran 0.17.0, switch to wheel
21fef4d
@dimpase
build/pkgs/ninja_build: Update to 1.12.1
f98e540
@dimpase
bump numpy to 2.2.3, scipy to 1.15.2
a7abfcf 
also fix a related doctest in graphs
@dimpase
correctly document location of conftest.py for pytest
a792b55
@dimpase
wrap ./configure in a wrapper saving conftest.py
7d543f8 
as autoconf's generated configure clobbers conftest*,
we are saving conftest.py from it by making a backup copy and then
restoring it after the real configure was run.
@dimpase
add the wrapper and real_configure to configure tarball
4ce11db
@dimpase
use ./bootstrap in building docker container
211789b
@dimpase
move wrapper creation to the better place
e0fd9c4
@user202729 @dimpase
also ADD configure_wrapper and conftest.py
acc9808
@dimpase
add comments suggested on #39373i by user202729
05fe4a3
@dimpase
Revert "use ./bootstrap in building docker container"
ce445f0 
This reverts commit 48a81bd.
@dimpase
typo fix
f4d90d9
@dimpase
correct version-requirements
783439e
@dimpase
correct package's wheel URL
e22f443
@dimpase dimpase force-pushed the numpy223scipy1152 branch from 9ee2dd2 to e22f443 Compare March 11, 2025 15:34
@dcoudert dcoudert mentioned this pull request Mar 11, 2025
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LGTM.

@dcoudert dcoudert mentioned this pull request Mar 11, 2025
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There is an error building scipy in some CI : https://github.com/sagemath/sage/actions/runs/13795446150/job/38585879952?pr=39655#step:9:2833
A wrong version of meson is used. I don't undestand why.

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dimpase commented Mar 12, 2025 •
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There is an error building scipy in some CI : https://github.com/sagemath/sage/actions/runs/13795446150/job/38585879952?pr=39655#step:9:2833 A wrong version of meson is used. I don't undestand why.

because the system meson was used, and the lower bound on the version was too low. The latest commit fixes it.

meson one of the few Python packages which are checked of presence on the OS in a different to the rest of them way.

I've also made it easy for you to bump your branch on #39676 to include this fix

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Documentation preview for this PR (built with commit 07e6461; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

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LGTM.

vbraun pushed a commit to vbraun/sage that referenced this pull request Mar 19, 2025
ec43db0 
sagemathgh-39655: update numpy to 2.2.3, scipy to 1.15.2
    
this is long overdue update.

It needs building  tools bumped, too, thus dependencies

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. -->

- [x] The title is concise and informative.
- [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 and checked the documentation
preview.

### ⌛ Dependencies
build tools need a bump
-  sagemath#39652 : pythran
- sagemath#39653 : ninja
-  sagemath#39654: pybind11
<!-- List all open PRs that this PR logically depends on. For example,
-->
<!-- - sagemath#12345: short description why this is a dependency -->
<!-- - sagemath#34567: ... -->
    
URL: sagemath#39655
Reported by: Dima Pasechnik
Reviewer(s): David Coudert
vbraun pushed a commit to vbraun/sage that referenced this pull request Mar 19, 2025
ffb7ab1 
sagemathgh-39676: update networkx to 3.4.2
    
With the update of numpy and scipy (sagemath#39655), we can update networkx to
version 3.4.2.

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. -->

- [x] The title is concise and informative.
- [x] 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

sagemath#39655
    
URL: sagemath#39676
Reported by: David Coudert
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this pull request Mar 22, 2025
e14b0a2 
sagemathgh-39676: update networkx to 3.4.2
    
With the update of numpy and scipy (sagemath#39655), we can update networkx to
version 3.4.2.

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. -->

- [x] The title is concise and informative.
- [x] 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

sagemath#39655
    
URL: sagemath#39676
Reported by: David Coudert
Reviewer(s): Dima Pasechnik
@vbraun vbraun merged commit 943b1b4 into sagemath:develop Mar 22, 2025
25 of 37 checks passed
@user202729 user202729 mentioned this pull request Mar 23, 2025
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