Opened 2 years ago

Closed 23 months ago

#30611 closed enhancement (fixed)

Upgrade various Python packages for Sage 9.3

Reported by: Matthias Köppe Owned by:
Priority: major Milestone: sage-9.3
Component: packages: standard Keywords: upgrade
Cc: François Bissey, Samuel Lelièvre Merged in:
Authors: Matthias Koeppe Reviewers: François Bissey
Report Upstream: N/A Work issues:
Branch: 13af6c6 (Commits, GitHub, GitLab) Commit: 13af6c6b8c1533ba9d1b45b127e1a7b7d30000c6
Dependencies: Stopgaps:

Status badges

Description (last modified by Samuel Lelièvre)

On separate tickets:

  • Sphinx and friends
  • IPython/Jupyter
  • #30898 kiwisolver
  • #26253 psutil
  • #30899 igraph, python-igraph

Change History (28)

comment:1 Changed 2 years ago by Matthias Köppe

Milestone: sage-9.2sage-9.3

comment:2 Changed 23 months ago by Matthias Köppe

Cc: François Bissey added
Description: modified (diff)
Summary: Upgrade numpy to 1.19.2Upgrade various Python packages

comment:3 Changed 23 months ago by Matthias Köppe

Cc: Samuel Lelièvre added
Description: modified (diff)
Summary: Upgrade various Python packagesUpgrade various Python packages for Sage 9.3

comment:4 Changed 23 months ago by François Bissey

sphinx and friends?

comment:5 Changed 23 months ago by Matthias Köppe

Branch: u/mkoeppe/upgrade_numpy_to_1_19_2

comment:6 Changed 23 months ago by Matthias Köppe

Authors: Matthias Koeppe
Commit: 514acf4cd70fa536e986555a4df0358f28c62134
Description: modified (diff)

Last 10 new commits:

a368bb7build/pkgs/fpylll: Update to 0.5.2dev
be49932build/pkgs/kiwisolver: Update to 1.3.1
2b45418build/pkgs/markupsafe: Update to 1.1.1
25e7fb2build/pkgs/matplotlib: Update to 3.3.2
4bfae6ebuild/pkgs/packaging: Update to 20.4
1b3c2f0build/pkgs/pathpy: No longer required by pickleshare, remove
2e2e98bbuild/pkgs/pyparsing: Update to 2.4.7
f37753fbuild/pkgs/python_igraph: Update to 0.8.3
6c159bcbuild/pkgs/pytz: Update to 2020.4
514acf4build/pkgs/rpy2: Update to 3.3.6

comment:7 in reply to:  4 Changed 23 months ago by Matthias Köppe

Replying to fbissey:

sphinx and friends?

Separate ticket please

comment:8 Changed 23 months ago by git

Commit: 514acf4cd70fa536e986555a4df0358f28c62134e1772fd5275629dcb0cb1a9d013c6018a5e36102

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

b5fe879build/pkgs/markupsafe: Update to 1.1.1
e906edebuild/pkgs/matplotlib: Update to 3.3.2
d365707build/pkgs/packaging: Update to 20.4
248c84abuild/pkgs/pathpy: No longer required by pickleshare, remove
be5bdf2build/pkgs/pyparsing: Update to 2.4.7
51a45c0build/pkgs/python_igraph: Update to 0.8.3
014d4a6build/pkgs/pytz: Update to 2020.4
e1772fdbuild/pkgs/rpy2: Update to 3.3.6

comment:9 Changed 23 months ago by Matthias Köppe

Description: modified (diff)

comment:10 Changed 23 months ago by François Bissey

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.

comment:11 Changed 23 months ago by git

Commit: e1772fd5275629dcb0cb1a9d013c6018a5e361026314ba9b870f61d922d376bc0ede2a0dac736c93

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

6314ba9build/pkgs/scipy/patches/extern_decls.patch: Remove

comment:12 Changed 23 months ago by François Bissey

Replying to fbissey:

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.

comment:13 in reply to:  10 Changed 23 months ago by Matthias Köppe

Replying to fbissey:

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.

comment:14 Changed 23 months ago by Matthias Köppe

Description: modified (diff)

comment:15 Changed 23 months ago by git

Commit: 6314ba9b870f61d922d376bc0ede2a0dac736c937cd96b2efb72094abaf6c5c5016a4496ff5111b5

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

88b8427build/pkgs/pytz: Update to 2020.4
df7972cbuild/pkgs/rpy2: Update to 3.3.6
7cd96b2build/pkgs/scipy/patches/extern_decls.patch: Remove

comment:16 Changed 23 months ago by Matthias Köppe

Status: newneeds_review

comment:17 Changed 23 months ago by François Bissey

Reviewers: François Bissey
Status: needs_reviewpositive_review

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.

comment:18 Changed 23 months ago by Matthias Köppe

Thanks!

comment:19 Changed 23 months ago by Samuel Lelièvre

Description: modified (diff)
Keywords: upgrade added

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: https://github.com/pickleshare/pickleshare/commit/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".

Bye path.py. Sorry everyone for the noise.

comment:20 Changed 23 months ago by Volker Braun

Status: positive_reviewneeds_work

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

comment:21 Changed 23 months ago by François Bissey

It is indeed

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

comment:22 Changed 23 months ago by François Bissey

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

comment:23 Changed 23 months ago by François Bissey

Branch: u/mkoeppe/upgrade_numpy_to_1_19_2u/fbissey/upgrade_numpy_to_1_19_2
Commit: 7cd96b2efb72094abaf6c5c5016a4496ff5111b584d778c219151e6b179b75c1f50c19bf801207fc

New commits:

84d778cFixing upstream url for networkx

comment:24 Changed 23 months ago by François Bissey

Status: needs_workpositive_review

Back to positive review.

comment:25 Changed 23 months ago by François Bissey

Status: positive_reviewneeds_work

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

comment:26 Changed 23 months ago by git

Commit: 84d778c219151e6b179b75c1f50c19bf801207fc13af6c6b8c1533ba9d1b45b127e1a7b7d30000c6

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

13af6c6fix tarball name

comment:27 Changed 23 months ago by François Bissey

Status: needs_workpositive_review

Surprisingly, the checksum did not change.

comment:28 Changed 23 months ago by Volker Braun

Branch: u/fbissey/upgrade_numpy_to_1_19_213af6c6b8c1533ba9d1b45b127e1a7b7d30000c6
Resolution: fixed
Status: positive_reviewclosed
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