Update numpy to 1.24.3 #35081

mkoeppe · 2023-02-12T04:47:14Z

📚 Description

NumPy 1.24.x still supports Python 3.8 (see #35404).
https://github.com/numpy/numpy/releases

Closes #34816

📝 Checklist

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

⌛ Dependencies

Depends on Ignore deprecation warnings triggered by pythran 0.12.1 #35438

codecov-commenter · 2023-02-12T08:02:27Z

Codecov Report

Base: 88.59% // Head: 88.58% // Decreases project coverage by -0.02% ⚠️

Coverage data is based on head (6a2aeb4) compared to base (05329f6).
Patch has no changes to coverable lines.

❗ Current head 6a2aeb4 differs from pull request most recent head 4430324. Consider uploading reports for the commit 4430324 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop   #35081      +/-   ##
===========================================
- Coverage    88.59%   88.58%   -0.02%     
===========================================
  Files         2140     2140              
  Lines       396998   396961      -37     
===========================================
- Hits        351740   351648      -92     
- Misses       45258    45313      +55

Impacted Files	Coverage Δ
src/sage/plot/histogram.py	`96.77% <ø> (-3.23%)`	⬇️
src/sage/repl/ipython_extension.py	`80.13% <ø> (ø)`
src/sage/groups/affine_gps/euclidean_group.py	`88.88% <0.00%> (-11.12%)`	⬇️
...e/combinat/cluster_algebra_quiver/mutation_type.py	`50.00% <0.00%> (-4.64%)`	⬇️
src/sage/groups/affine_gps/affine_group.py	`96.62% <0.00%> (-2.25%)`	⬇️
src/sage/modular/hecke/algebra.py	`94.65% <0.00%> (-1.07%)`	⬇️
src/sage/schemes/elliptic_curves/hom_velusqrt.py	`94.09% <0.00%> (-0.79%)`	⬇️
src/sage/schemes/elliptic_curves/hom.py	`83.33% <0.00%> (-0.62%)`	⬇️
src/sage/sets/integer_range.py	`91.41% <0.00%> (-0.51%)`	⬇️
... and 22 more

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mkoeppe · 2023-02-12T13:45:02Z

@tornaria #34994 is merged here, but it looks like we need to take care of doctest failures due to FutureWarning: In the future np.bytes will be defined as the corresponding NumPy scalar. etc.

tornaria · 2023-02-12T19:27:33Z

@tornaria #34994 is merged here, but it looks like we need to take care of doctest failures due to FutureWarning: In the future np.bytes will be defined as the corresponding NumPy scalar. etc.

I upgraded to numpy 1.24.2 last week and I did not get any of these failures. Also, the backtraces seem to point to pythran, not sagemath, I don't install pythran with sagemath (should I? what am I missing?).

At some point I was starting to like python 3, but they really make an effort to show up. Sometimes it seems half the work is dealing with deprecation sh*t.

tornaria · 2023-02-12T19:37:32Z

I installed pythran (we are on 0.12.1). Now I get stuff like

    DeprecationWarning: msvccompiler is deprecated and slated to be removed in the future. Please discontinue use or file an issue with pypa/distutils describing your use case.

No, I don't have msvc installed here, thank you very much. Uninstalling pythran.

I abhor programs that change behaviour just because some library is installed.

Also, we have these lines in src/sage/alll.py:

# Ignore numpy warnings triggered by pythran
warnings.filterwarnings('ignore', category=DeprecationWarning,
                        module='pythran

Shouldn't that apply? Btw, that's the only reference to pythran in the sage library. Why is then installing pythran having any effect at all?

mkoeppe · 2023-02-14T20:09:51Z

I'm throwing in an update of pythran to see if that helps

mkoeppe · 2023-02-15T02:38:39Z

Yes, that fixed it.

kiwifb · 2023-02-21T22:30:35Z

This now "conflicts" with #34994 which includes all the doctests fixes I think. That PR is in Volker's current merge tree. I was wondering why I could not see the fortran warnings anymore. I would support the upgrade once #34994 is merged.

kiwifb · 2023-02-21T22:38:59Z

The stuff in here (or #34994) doesn't fix

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/plot/plot_field.py
**********************************************************************
File "src/sage/plot/plot_field.py", line 51, in sage.plot.plot_field.PlotField.__init__
Failed example:
    r.yvec_array
Expected:
    masked_array(data=[0.0, 0.70710678118..., 0.70710678118...,
                       0.89442719...],
                 mask=[False, False, False, False],
           fill_value=1e+20)
Got:
    masked_array(data=[0.        , 0.70710678, 0.70710678, 0.89442719],
                 mask=False,
           fill_value=1e+20)

and at least one similar failure in sage/plot/streamline_plot.py. Has it been attributed to something else?

tornaria · 2023-02-22T01:15:13Z

The stuff in here (or #34994) doesn't fix

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/plot/plot_field.py
**********************************************************************
File "src/sage/plot/plot_field.py", line 51, in sage.plot.plot_field.PlotField.__init__
Failed example:
    r.yvec_array
Expected:
    masked_array(data=[0.0, 0.70710678118..., 0.70710678118...,
                       0.89442719...],
                 mask=[False, False, False, False],
           fill_value=1e+20)
Got:
    masked_array(data=[0.        , 0.70710678, 0.70710678, 0.89442719],
                 mask=False,
           fill_value=1e+20)

and at least one similar failure in sage/plot/streamline_plot.py. Has it been attributed to something else?

I never saw anything like that.

mkoeppe · 2023-02-22T01:33:52Z

I've redone the branch on top of current #34994.

kiwifb · 2023-02-22T01:52:56Z

@tornaria pythran is a dependency of scipy, but it may not be useful at runtime as it is similar to cython as far as I can see. It is possible that the formatting in plot_field.py is coming from something else, but then what? And it was spotted as far back as December.

kiwifb · 2023-02-22T04:07:19Z

src/sage/plot/plot_field.py and sage/plot/streamline_plot.py formatting issues have disappeared by going from numpy 1.24.0 to 1.24.2. I was still on 1.24.0.

tornaria · 2023-04-04T16:12:19Z

For the record, I pushed #35438 to ignore all the deprecation warnings that I see when installing pythran (python 3.11, setuptools 67.6.1, numpy 1.24.2).

I can't really review the current PR since it's only changing a spkg, but FWIW I've been using 1.24.2 for a while without any trouble after #34994.

kiwifb

I have now been using 1.24.2 since the end of February without noticeable problems because of it.

mkoeppe · 2023-04-04T21:13:13Z

I've merged #35438 just in case.

mkoeppe · 2023-04-23T00:58:55Z

1.24.3 is out

mkoeppe · 2023-06-20T01:08:09Z

numpy 1.25.0 is out, which supports Python 3.9–3.11, but not the upcoming 3.12. https://numpy.org/devdocs/release/1.25.0-notes.html
A version 1.26 is promised to provide Python 3.12 support.

### 📚 Description Mostly due to a deprecation warning: `Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)`. Also fix: - a change of output in `numpy.linalg.eig()` - a change in an exception class See: #35081        ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion.   URL: #35826 Reported by: Gonzalo Tornaría Reviewer(s):

github-actions · 2023-07-09T03:18:48Z

Documentation preview for this PR (built with commit aee02c6; changes) is ready! 🎉

mkoeppe · 2023-08-21T16:45:26Z

v1.26.0b1 is out, with Python 3.12 support and Cython 3 compatibility (see #36110).

Let's skip this update and do 1.26

mkoeppe added the c: packages: standard label Feb 12, 2023

mkoeppe added the s: needs work label Feb 12, 2023

mkoeppe added this to the sage-9.9 milestone Feb 12, 2023

mkoeppe added s: needs review and removed s: needs work labels Feb 15, 2023

mkoeppe self-assigned this Feb 18, 2023

mkoeppe force-pushed the t/34816/update_numpy_to_1_24 branch from 6a2aeb4 to 4430324 Compare February 22, 2023 01:33

mkoeppe force-pushed the t/34816/update_numpy_to_1_24 branch from 4430324 to 7830cae Compare March 28, 2023 02:10

kiwifb approved these changes Apr 4, 2023

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mkoeppe force-pushed the t/34816/update_numpy_to_1_24 branch from 7830cae to ffd9ee9 Compare April 4, 2023 21:13

Matthias Koeppe added 5 commits April 22, 2023 22:12

build/pkgs/numpy: Update to 1.24.0rc1

dea2948

build/pkgs/numpy: Update to 1.24.0rc2

1a5b9ed

build/pkgs/numpy: Update to 1.24.0

60fc486

build/pkgs/numpy: Update to 1.24.2

d7acfb6

build/pkgs/numpy: Update to 1.24.3

0442126

mkoeppe force-pushed the t/34816/update_numpy_to_1_24 branch from ffd9ee9 to 0442126 Compare April 23, 2023 05:13

mkoeppe changed the title ~~Update numpy to 1.24.2~~ Update numpy to 1.24.3 Apr 23, 2023

mkoeppe modified the milestones: sage-10.0, sage-10.1 Apr 30, 2023

tornaria mentioned this pull request Jun 24, 2023

Fixes to support numpy 1.25.0 #35826

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Merge branch 'develop' into t/34816/update_numpy_to_1_24

aee02c6

mkoeppe removed this from the sage-10.1 milestone Aug 7, 2023

mkoeppe closed this Aug 21, 2023

github-actions bot removed the s: needs review label Aug 21, 2023

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Update numpy to 1.24.3 #35081

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Update numpy to 1.24.3 #35081

Update numpy to 1.24.3 #35081

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