Upgrade various Python packages for Sage 9.3

[mkoeppe]

• numpy: https://pypi.org/project/numpy/#history, https://numpy.org/devdocs/release/1.19.4-notes.html
• scipy 1.5.4
• networkx 2.5
• remove path.py, added in Upgrade to IPython 4.0.0 + Jupyter #19128, as pickleshare no longer uses it
• and many more - everything that is not exclusively needed for Sphinx or IPython/Jupyter

On separate tickets:

• Sphinx and friends
• IPython/Jupyter
• Upgrade kiwisolver to 1.3.x #30898 kiwisolver
• Upgrade: psutil 5.8.0 #26253 psutil
• igraph, python-igraph: Update to 0.8.3 #30899 igraph, python-igraph

CC: @kiwifb @slel

Component: packages: standard

Keywords: upgrade

Author: Matthias Koeppe

Branch/Commit: 13af6c6

Reviewer: François Bissey

Issue created by migration from https://trac.sagemath.org/ticket/30611

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,6 +1,3 @@
-released 2020-09-10
 
-https://pypi.org/project/numpy/#history
+- numpy: https://pypi.org/project/numpy/#history, https://numpy.org/devdocs/release/1.19.4-notes.html
 
-https://numpy.org/devdocs/release/1.19.2-notes.html
-

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,3 +1,5 @@
 
 - numpy: https://pypi.org/project/numpy/#history, https://numpy.org/devdocs/release/1.19.4-notes.html
+- scipy 1.5.4
+- networkx 2.5
 

[kiwifb]

comment:4

sphinx and friends?

[mkoeppe]

Branch: u/mkoeppe/upgrade_numpy_to_1_19_2

[mkoeppe]

Last 10 new commits:

a368bb7	build/pkgs/fpylll: Update to 0.5.2dev
be49932	build/pkgs/kiwisolver: Update to 1.3.1
2b45418	build/pkgs/markupsafe: Update to 1.1.1
25e7fb2	build/pkgs/matplotlib: Update to 3.3.2
4bfae6e	build/pkgs/packaging: Update to 20.4
1b3c2f0	build/pkgs/pathpy: No longer required by pickleshare, remove
2e2e98b	build/pkgs/pyparsing: Update to 2.4.7
f37753f	build/pkgs/python_igraph: Update to 0.8.3
6c159bc	build/pkgs/pytz: Update to 2020.4
514acf4	build/pkgs/rpy2: Update to 3.3.6

[mkoeppe]

Description changed:

--- 
+++ 
@@ -2,4 +2,6 @@
 - numpy: https://pypi.org/project/numpy/#history, https://numpy.org/devdocs/release/1.19.4-notes.html
 - scipy 1.5.4
 - networkx 2.5
+- and many more - everything that is not exclusively needed for Sphinx or IPython/Jupyter
 
+

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Commit: 514acf4

[mkoeppe]

comment:7

Replying to @kiwifb:

sphinx and friends?

Separate ticket please

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

b5fe879	build/pkgs/markupsafe: Update to 1.1.1
e906ede	build/pkgs/matplotlib: Update to 3.3.2
d365707	build/pkgs/packaging: Update to 20.4
248c84a	build/pkgs/pathpy: No longer required by pickleshare, remove
be5bdf2	build/pkgs/pyparsing: Update to 2.4.7
51a45c0	build/pkgs/python_igraph: Update to 0.8.3
014d4a6	build/pkgs/pytz: Update to 2020.4
e1772fd	build/pkgs/rpy2: Update to 3.3.6

[sagetrac-git]

Changed commit from 514acf4 to e1772fd

[mkoeppe]

Description changed:

--- 
+++ 
@@ -4,4 +4,8 @@
 - networkx 2.5
 - and many more - everything that is not exclusively needed for Sphinx or IPython/Jupyter
 
-
+On separate tickets:
+- sphinx and friends
+- IPython/Jupyter
+- #30898 kiwisolver
+- #26253 psutil

[kiwifb]

comment:10

Is there already a separate ticket for rpy2 somewhere? I seem to remember there was an issue (apart from py27 compatibility which we don't care about anymore).

python_igraph, can this be done without also upgrading igraph? I am expecting (gut feelings) issues.

[sagetrac-git]

Changed commit from e1772fd to 6314ba9

[sagetrac-git]

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

6314ba9

build/pkgs/scipy/patches/extern_decls.patch: Remove