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

[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]

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

[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

[kiwifb]

comment:12

Replying to @kiwifb:

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).

Looks like I was thinking of 3.3.5 at #29441 but it is all fixed. I had an issue with it in Gentoo especially during testing that has been solved upstream in 3.3.6. So it is all good.

[mkoeppe]

comment:13

Replying to @kiwifb:

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

No idea; I'll push it to a separate ticket.

[sagetrac-git]

Changed commit from 6314ba9 to 7cd96b2

[sagetrac-git]

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

88b8427	build/pkgs/pytz: Update to 2020.4
df7972c	build/pkgs/rpy2: Update to 3.3.6
7cd96b2	build/pkgs/scipy/patches/extern_decls.patch: Remove

[kiwifb]

Reviewer: François Bissey

[kiwifb]

comment:17

I am quite happy with the ticket as it is. With a few exceptions (rpy2, certifi) we are at those levels in Gentoo and I don't expect issues.

[mkoeppe]

comment:18

Thanks!

[slel]

Changed keywords from none to upgrade

[slel]

comment:19

Thanks for the upgrades!

Just to verbalise the removal of pathpy (our name for path.py).

The commit message for the removal commit says it all:

build/pkgs/pathpy: No longer required by pickleshare, remove

Indeed: ipython/pickleshare@2141463

Side note: on PyPI, path.py (which used to provide os.path
before the standard library included pathlib), is now path,
and there's a different unrelated pathpy for "analysis and
visualisation of time series data on complex networks with
higher- and multi-order graphical models".

• https://pypi.org/project/path.py (which we used to ship)
• https://pypi.org/project/path (its new name for newer versions)
• https://pypi.org/project/pathpy (unrelated)

Bye path.py. Sorry everyone for the noise.

[vbraun]

comment:20

Can't find a networkx file with the right checksum, url is wrong

[kiwifb]

comment:21

It is indeed

upstream_url=https://github.com/networkx/networkx/archive/networkx-2.4.zip

[kiwifb]

comment:22

It looks like that is the only source not from pypi in the lot. Fixing.

[kiwifb]

Changed commit from 7cd96b2 to 84d778c

[kiwifb]

Changed branch from u/mkoeppe/upgrade_numpy_to_1_19_2 to u/fbissey/upgrade_numpy_to_1_19_2

[kiwifb]

New commits:

84d778c

Fixing upstream url for networkx

[kiwifb]

comment:24

Back to positive review.

[kiwifb]

comment:25

Forgot to change stuff has I have gone from zip to tar.gz.

[sagetrac-git]

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

13af6c6

fix tarball name

[sagetrac-git]

Changed commit from 84d778c to 13af6c6

[kiwifb]

comment:27

Surprisingly, the checksum did not change.

[vbraun]

Changed branch from u/fbissey/upgrade_numpy_to_1_19_2 to 13af6c6