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

[mkoeppe]

These updates:

• numpy 1.22.0 https://numpy.org/devdocs/release/1.22.0-notes.html, https://github.com/numpy/numpy/releases
• scipy 1.8.0 https://scipy.github.io/devdocs/release.1.8.0.html
  will require us to drop python 3.7 support.
• networkx 2.8.0 https://github.com/networkx/networkx/blob/main/doc/release/release_2.7.rst requires us to drop python 3.7 support too

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

Related:

• Update scipy 1.7.x; add pythran package (scipy prerequisite) #32105 Update numpy 1.21.x, scipy 1.7.x;
• Adopt the “time window-based” policy for support of Python versions from NEP 29 #30384 NEP 29
• Meta-ticket: Review of Python 3 features that sagelib should use systematically #29756 Meta-ticket: Review of Python 3 features that sagelib should use systematically

Next updates:

• numpy 1.23.x #34110 numpy 1.23.x
• Upgrade scipy to 1.9.x, add meson toolchain #34081 scipy 1.9.x

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

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,9 +1,10 @@
 These updates:
 - `numpy` 1.22.0 https://numpy.org/devdocs/release/1.22.0-notes.html
-- `scipy` 1.8.0 
+- `scipy` 1.8.0 https://scipy.github.io/devdocs/release.1.8.0.html
 will require us to drop python 3.7 support.
 
 Related: 
+- #32105 Update numpy 1.21.x, scipy 1.7.x;
 - #30384 NEP 29
 - #29756 Meta-ticket: Review of Python 3 features that sagelib should use systematically
 

[slel]

Changed dependencies from #32105 to #32105, #32937

[mkoeppe]

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

[mkoeppe]

Description changed:

--- 
+++ 
@@ -2,6 +2,8 @@
 - `numpy` 1.22.0 https://numpy.org/devdocs/release/1.22.0-notes.html
 - `scipy` 1.8.0 https://scipy.github.io/devdocs/release.1.8.0.html
 will require us to drop python 3.7 support.
+
+SciPy also has stricter compiler requirements: C++14 support. According to https://docs.scipy.org/doc/scipy/reference/dev/toolchain.html#c-and-c-language-standards, GCC >= 5.x and according to https://github.com/scipy/scipy/releases, GCC >= 6.3.
 
 Related: 
 - #32105 Update numpy 1.21.x, scipy 1.7.x;

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,5 +1,5 @@
 These updates:
-- `numpy` 1.22.0 https://numpy.org/devdocs/release/1.22.0-notes.html
+- `numpy` 1.22.0 https://numpy.org/devdocs/release/1.22.0-notes.html, https://github.com/numpy/numpy/releases
 - `scipy` 1.8.0 https://scipy.github.io/devdocs/release.1.8.0.html
 will require us to drop python 3.7 support.
 

[antonio-rojas]

Branch: u/arojas/update_numpy_to_1_22_x__scipy_1_8_x___requires_dropping_python_3_7

[antonio-rojas]

comment:7

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

---

New commits:

46ff9f1	Update numpy to 1.22.2
039c5e4	Update scipy to 1.8.0
cab17dc	Fix deprecation warning with scipy 1.8

[antonio-rojas]

Author: Antonio Rojas

[antonio-rojas]

Commit: cab17dc

[mkoeppe]

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]

Description changed:

--- 
+++ 
@@ -3,7 +3,7 @@
 - `scipy` 1.8.0 https://scipy.github.io/devdocs/release.1.8.0.html
 will require us to drop python 3.7 support.
 
-SciPy also has stricter compiler requirements: C++14 support. According to https://docs.scipy.org/doc/scipy/reference/dev/toolchain.html#c-and-c-language-standards, GCC >= 5.x and according to https://github.com/scipy/scipy/releases, GCC >= 6.3.
+SciPy also has stricter compiler requirements: C++14 support. According to https://scipy.github.io/devdocs/dev/toolchain.html, GCC >= 6.3.
 
 Related: 
 - #32105 Update numpy 1.21.x, scipy 1.7.x;

[mkoeppe]

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

[antonio-rojas]

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

[sagetrac-git]

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

02d017f

Move deprecation warning fix to another ticket

[sagetrac-git]

Changed commit from cab17dc to 02d017f