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Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x #32423

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mkoeppe opened this issue Aug 25, 2021 · 81 comments
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Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x #32423

mkoeppe opened this issue Aug 25, 2021 · 81 comments
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c: packages: standard p: major / 3 t: enhancement
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sage-9.7

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@mkoeppe
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mkoeppe commented Aug 25, 2021

These updates:

SciPy also has stricter compiler requirements: C++14 support. According to https://scipy.github.io/devdocs/dev/toolchain.html, GCC >= 6.3.

Related:

Next updates:

Depends on #32937
Depends on #33316
Depends on #33782
Depends on #34017

CC: @dimpase @kiwifb @sagetrac-tmonteil

Component: packages: standard

Author: Matthias Koeppe

Branch/Commit: 2534f5a

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/32423
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slel commented Nov 25, 2021

Changed dependencies from #32105 to #32105, #32937

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mkoeppe commented Dec 20, 2021

Changed dependencies from #32105, #32937 to #32937, #33049

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Branch: u/arojas/update_numpy_to_1_22_x__scipy_1_8_x___requires_dropping_python_3_7

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comment:7

Untested on sage-the-distro, this works on Arch. Should be rebased after #33049 is merged I guess.

New commits:

46ff9f1Update numpy to 1.22.2
039c5e4Update scipy to 1.8.0
cab17dcFix deprecation warning with scipy 1.8

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Author: Antonio Rojas

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Commit: cab17dc

@mkoeppe
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mkoeppe commented Feb 6, 2022

comment:8

Is the fix for the deprecation warning also OK for early scipy?
Then it's better to put it on a separate ticket that can be merged earlier.

(I think I would want to hold off on the scipy 1.8 upgrade for a little while - maybe it should go into Sage 9.7, not 9.6)

@mkoeppe mkoeppe changed the title Update numpy to 1.22.x, scipy 1.8.x - requires dropping python 3.7 Update numpy to 1.22.x, scipy 1.8.x - requires dropping python 3.7 and dropping systems GCC < 6.3 Feb 6, 2022
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mkoeppe commented Feb 8, 2022

Changed dependencies from #32937, #33049 to #32937, #33049, #33316

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comment:12

Replying to @mkoeppe:

Is the fix for the deprecation warning also OK for early scipy?
Then it's better to put it on a separate ticket that can be merged earlier.

Done #33336

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sagetrac-git mannequin commented Feb 13, 2022

Branch pushed to git repo; I updated commit sha1. New commits:

02d017fMove deprecation warning fix to another ticket

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sagetrac-git mannequin commented Feb 13, 2022

Changed commit from cab17dc to 02d017f

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@mkoeppe mkoeppe changed the title Update numpy to 1.22.x, scipy 1.8.x - requires dropping python 3.7 and dropping systems GCC < 6.3 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.7.x - requires dropping python 3.7 and dropping systems GCC < 6.3 Mar 3, 2022
@mkoeppe mkoeppe added this to the sage-9.7 milestone Mar 3, 2022
@mkoeppe mkoeppe removed the pending label Mar 3, 2022
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comment:15

Opened #33495 to fix test regressions with networkx 2.7

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Changed dependencies from #32937, #33049, #33316 to #32937, #33049, #33316, #33495

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@mkoeppe mkoeppe changed the title Update numpy to 1.22.x, scipy 1.8.x, networkx 2.7.x - requires dropping python 3.7 and dropping systems GCC < 6.3 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x - requires dropping python 3.7 and dropping systems GCC < 6.3 Apr 10, 2022
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mkoeppe commented Apr 21, 2022

Changed branch from u/arojas/update_numpy_to_1_22_x__scipy_1_8_x___requires_dropping_python_3_7 to u/mkoeppe/update_numpy_to_1_22_x__scipy_1_8_x___requires_dropping_python_3_7

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mkoeppe commented Apr 21, 2022

Changed commit from 02d017f to 1a46a28

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mkoeppe commented Jun 29, 2022

Changed dependencies from #32937, #33316, #33782 to #32937, #33316, #33782, #34017

@mkoeppe mkoeppe changed the title Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x - requires dropping python 3.7 and dropping system GCC < 6.3 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x Jun 29, 2022
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mkoeppe commented Jun 29, 2022

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/2359587924, https://github.com/mkoeppe/sage/actions/runs/2359587917 to https://github.com/mkoeppe/sage/actions/runs/2586202083

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mkoeppe commented Jun 30, 2022

comment:53

Fails on local-macos (2, homebrew-macos-usrlocal-standard, default, macos-latest) https://github.com/mkoeppe/sage/runs/7121386623
(tested with #33530, thus with the setuptools upgrade!)

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mkoeppe commented Jun 30, 2022

comment:54

from the log:

Processing /Users/runner/work/sage/sage/.tox/local-homebrew-macos-usrlocal-standard/local/var/tmp/sage/build/numpy-1.22.4/src
  Preparing metadata (setup.py): started
  Running command python setup.py egg_info
  Running from numpy source directory.
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/Users/runner/work/sage/sage/.tox/local-homebrew-macos-usrlocal-standard/local/var/tmp/sage/build/numpy-1.22.4/src/setup.py", line 92, in <module>
      raise RuntimeError("setuptools versions >= '60.0.0' require "
  RuntimeError: setuptools versions >= '60.0.0' require SETUPTOOLS_USE_DISTUTILS=stdlib in the environment
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.

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mkoeppe commented Jun 30, 2022

comment:55

That's from https://github.com/numpy/numpy/blob/main/setup.py#L86

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mkoeppe commented Jun 30, 2022

comment:56

We are setting SETUPTOOLS_USE_DISTUTILS=local on homebrew to avoid homebrew's distutils.cfg, which is still present (and broken) in pre-3.10 versions:

$ find /usr/local/opt/python@3.7/ -name distutils.cfg
/usr/local/opt/python@3.7//Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/distutils.cfg
$ find /usr/local/opt/python@3.8/ -name distutils.cfg
/usr/local/opt/python@3.8//Frameworks/Python.framework/Versions/3.8/lib/python3.8/distutils/distutils.cfg
$ find /usr/local/opt/python@3.9/ -name distutils.cfg
/usr/local/opt/python@3.9//Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/distutils.cfg
$ find /usr/local/opt/python@3.10/ -name distutils.cfg
$ cat /usr/local/opt/python@3.9//Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/distutils.cfg
[install]
prefix=/usr/local
[build_ext]
include_dirs=/usr/local/include:/usr/local/opt/openssl@1.1/include:/usr/local/opt/sqlite/include
library_dirs=/usr/local/lib:/usr/local/opt/openssl@1.1/lib:/usr/local/opt/sqlite/lib

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mkoeppe commented Jun 30, 2022

comment:57

This code is from numpy/numpy#20963. I'll just patch it out.

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mkoeppe commented Jun 30, 2022

comment:58

That's now numpy/numpy#21891

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sagetrac-git mannequin commented Jun 30, 2022

Changed commit from ee79c2e to 2534f5a

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sagetrac-git mannequin commented Jun 30, 2022

Branch pushed to git repo; I updated commit sha1. New commits:

2534f5abuild/pkgs/numpy/patches/21891.patch: New

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mkoeppe commented Jun 30, 2022

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/2586202083 to https://github.com/mkoeppe/sage/actions/runs/2593290132

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mkoeppe commented Jul 1, 2022

comment:61

Replying to @mkoeppe:

The workaround export NPY_DISABLE_SVML=1 works

Upstream PR to make this workaround unnecessary (for i386 on x86_64): numpy/numpy#21896

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mkoeppe commented Jul 3, 2022

comment:62

Let's get this upgrade in please

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dimpase commented Jul 4, 2022

comment:64

lgtm

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dimpase commented Jul 4, 2022

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/2593290132 to Dima Pasechnik

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mkoeppe commented Jul 4, 2022

comment:65

Thanks!

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vbraun commented Jul 9, 2022

Changed branch from u/mkoeppe/update_numpy_to_1_22_x__scipy_1_8_x___requires_dropping_python_3_7 to 2534f5a

@vbraun vbraun closed this as completed in 662aaf2 Jul 9, 2022
@dimpase dimpase mentioned this issue Jan 6, 2023
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@slel slel mentioned this issue May 29, 2022
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kryzar pushed a commit to kryzar/sage that referenced this issue Feb 6, 2023
Trac sagemath#34081: Upgrade scipy to 1.9.x, add meson toolchain
5048fd4 
- https://scipy.github.io/devdocs/release.1.9.0.html (released)
  - scipy.optimize.milp (HiGHS MIP solver)
  - https://scipy.github.io/devdocs/release.1.9.0.html#scipy-switched-
to-meson-as-its-build-system

This ticket is also the target ticket for https://github.com/FFY00
/meson-python/blob/main/.github/workflows/ci-sage.yml

Previous update:
- sagemath#32423 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x

See also:
- sagemath#34110 numpy 1.23.x

URL: https://trac.sagemath.org/34081
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik
dimpase pushed a commit to tornaria/sage that referenced this issue Feb 7, 2023
@mkoeppe
Merge sagemath#32423
fd31566
mkoeppe added a commit to mkoeppe/sage that referenced this issue Aug 22, 2023
@mkoeppe
build/pkgs/numpy: Switch build system to meson_python, back out worka…
2e652c0 
…rounds from sagemath#34110, sagemath#32746, sagemath#32423
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