Upgrade to Cython 0.29.1

[jdemeyer]

Tarball: https://files.pythonhosted.org/packages/f0/f8/7f406aac4c6919d5a4ce16509bbe059cd256e9ad94bae5ccac14094b7c51/Cython-0.29.1.tar.gz

Follow-up tickets:

• Enable Cython caching again #25288: Enable Cython caching again
• Compile Sage with Cython language_level=3str #26403: Compile Sage with Cython language_level=3str

Upstream: Fixed upstream, but not in a stable release.

CC: @kiwifb @embray @saraedum

Component: packages: standard

Author: Jeroen Demeyer

Branch/Commit: 4c3e314

Reviewer: Timo Kaufmann

Issue created by migration from https://trac.sagemath.org/ticket/25292

[videlec]

comment:1

update milestone 8.3 -> 8.4

[jdemeyer]

Author: Jeroen Demeyer

[jdemeyer]

Dependencies: #26396

[jdemeyer]

Branch: u/jdemeyer/upgrade_to_cython_0_29

[sagetrac-git]

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

3275637

Explicitly set Cython language level to current Python version

[sagetrac-git]

Commit: 3275637

[jdemeyer]

Changed dependencies from #26396 to #26396, #26402

[jdemeyer]

Changed dependencies from #26396, #26402 to #26396

[sagetrac-git]

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

bcba4f1	Upgrade to cypari2-1.3.1
f77de1d	Upgrade to Cython 0.29

[sagetrac-git]

Changed commit from 3275637 to f77de1d

[Konrad127123]

comment:13

Attachment: cython-0.29.log

Running make distclean && make cython with SAGE_CHECK=yes, I'm reproducibly getting one test failing (see log).

(The two failing tests in #26450 don't seem to be an issue anymore in 0.29.)

[sagetrac-git]

Changed commit from f77de1d to 7ffa946

[sagetrac-git]

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

7ffa946

Upgrade to Cython 0.29

[jdemeyer]

Upstream: Fixed upstream, but not in a stable release.

[jdemeyer]

comment:16

Replying to @Konrad127123:

Running make distclean && make cython with SAGE_CHECK=yes, I'm reproducibly getting one test failing (see log).

Fixed by cython/cython#2674

[jdemeyer]

Changed dependencies from #26396 to none

[Konrad127123]

comment:18

Replying to @jdemeyer:

Replying to @Konrad127123:

Running make distclean && make cython with SAGE_CHECK=yes, I'm reproducibly getting one test failing (see log).

Fixed by cython/cython#2674

I can confirm that cython now builds with SAGE_CHECK=yes. I've not tested it apart from that.

[jdemeyer]

comment:19

Can somebody review this please? There are follow-up tickets depending on this one.

[embray]

comment:20

Does this mean Cython 0.29 will become a hard dependency of Sage? I don't mind that ofc, but maybe the tickets that depend on it can be done in such a way that checks this (e.g., checks the Cython version before enabling those features).

I'm going to give this a quick check on Cygwin, but I doubt there will be any problem, so positive_review from me if it that works.

[timokau]

comment:29

For what its worth, here is the status of cython on various distros and these are the distros that package sage. Debian Unstable hasn't upgraded yet. Arch and Nix have. Gentoo isn't listed for some reason.

[kiwifb]

comment:30

Replying to @timokau:

For what its worth, here is the status of cython on various distros and these are the distros that package sage. Debian Unstable hasn't upgraded yet. Arch and Nix have. Gentoo isn't listed for some reason.

Gentoo main tree, doesn't have it yet. But the sage-on-gentoo repo does have a package ready for when this ticket makes it regardless of the main tree.

[Konrad127123]

comment:31

Note that Cython 0.29.1 has now been released.

[kiwifb]

comment:32

Actually the Gentoo main tree caught up to me yesterday and 0.29.1 is in the main tree.

[sagetrac-git]

Changed commit from 7ffa946 to 4c3e314

[sagetrac-git]

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

4c3e314

Upgrade to Cython 0.29.1

[jdemeyer]

comment:35

Not tested yet...

[embray]

comment:36

Replying to @timokau:

For what its worth, here is the status of cython on various distros and these are the distros that package sage. Debian Unstable hasn't upgraded yet. Arch and Nix have. Gentoo isn't listed for some reason.

That's a cool site--I was not aware of it before. It doesn't look like it tracks conda-forge or cygwin packages either. I wonder how hard it would be to add trackers for new repositories to the site...

[timokau]

comment:37

Replying to @embray:

Replying to @timokau:

For what its worth, here is the status of cython on various distros and these are the distros that package sage. Debian Unstable hasn't upgraded yet. Arch and Nix have. Gentoo isn't listed for some reason.

That's a cool site--I was not aware of it before. It doesn't look like it tracks conda-forge or cygwin packages either. I wonder how hard it would be to add trackers for new repositories to the site...

Yeah its pretty neat. Nix uses a bot that automatically generates trivial package update PRs based on repology data. I think adding support for another repo would basically sonsist of (1) finding a relibale data source that gives current metadata about all packages and (2) converting that datasource into the format repology expects. There are already issues for conda-forge and cygwin.

[timokau]

comment:38

Replying to @jdemeyer:

With only this ticket applied (not the follow-up tickets), it requires only minor adjustments to support both Cython 0.28 and Cython 0.29.

So what you are saying is maybe more an argument to postpone the follow-up tickets until we know for sure that Debian is ready for Cython 0.29.

Back to topic: So in its current state this ticket is not backwards compatible?

[kiwifb]

comment:39

Replying to @timokau:

For what its worth, here is the status of cython on various distros and these are the distros that package sage. Debian Unstable hasn't upgraded yet. Arch and Nix have. Gentoo isn't listed for some reason.

The curating is imperfect and for some distros it is listed under "cython" and for other under "python:cython" https://repology.org/metapackage/python:cython/versions not much you can do about that.

[timokau]

comment:40

You can report it (I just did). Every time I've done that it has been resolved within a couple of hours.

[jdemeyer]

comment:41

Replying to @timokau:

Back to topic: So in its current state this ticket is not backwards compatible?

No, it is not. The difference is really small though, packagers that insist on Cython 0.28 can easily revert this patch.

[timokau]

comment:42

Okay since the majority have already switched (all but debian I think) and its very possible that debian will have switched by the time 8.5 is released, I think we can go forward. Any other opinions?

[embray]

comment:43

Replying to @jdemeyer:

Replying to @timokau:

Back to topic: So in its current state this ticket is not backwards compatible?

No, it is not. The difference is really small though, packagers that insist on Cython 0.28 can easily revert this patch.

I think that's a bit presumptuous. But I agree there's no reason for anyone to hold back up on updating Cython and that it should/will happen before long so I don't object to moving forward on this.

[timokau]

Reviewer: Timo Kaufmann

[vbraun]

Changed branch from u/jdemeyer/upgrade_to_cython_0_29 to 4c3e314