Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Please switch to Python3 #15

Closed
tillea opened this issue May 3, 2018 · 22 comments
Closed

Please switch to Python3 #15

tillea opened this issue May 3, 2018 · 22 comments

Comments

@tillea
Copy link

tillea commented May 3, 2018

Hi,
Debian is currently debating the support of Python2 which is marked end of life in 2020 (which is only one release cycle away. I'd recommend to switch to Python3 in the near future. I made some good experiences using 2to3 to port code from Python2 to Python3.
Kind regards, Andreas.
@tillea
Copy link
Author

tillea commented Aug 2, 2019

Any news about this? It becomes even more urgent after the release of Debian 10. Now Python2 code is actively removed from Debian.
Kind regards, Andreas.

@MikkelSchubert
Copy link
Owner

I am working on this now along with an overhaul of parts of the program.

I realize that you would probably prefer a smaller update that just adds Python 3 support, but that would not be efficient use of my time, as I would need to spend a lot of time testing and validating code that would then immediately be removed or rewritten following that release.

@tillea
Copy link
Author

tillea commented Sep 11, 2019

That's fine. BTW, I realised an old code copy of pyyaml. Do you think you could simply use official pyyaml (which is at version 5.1 now)? This would be really helpful as well.

@MikkelSchubert
Copy link
Owner

I've already replaced that copy with a dependency on ruamel.yaml in the development branch, based on your previous suggestions (see 433a33d). Is there a specific reason why you recommend PyYAML now?

@tillea
Copy link
Author

tillea commented Sep 11, 2019 via email

@tillea
Copy link
Author

tillea commented Dec 17, 2019

I am working on this now along with an overhaul of parts of the program.

I realize that you would probably prefer a smaller update that just adds Python 3 support, but that would not be efficient use of my time, as I would need to spend a lot of time testing and validating code that would then immediately be removed or rewritten following that release.

I wonder whether the just released version 1.2.14 should be that Python3 version you was talking about. At least 2to3 is marking quite some diff so probably not. Kind regards, Andreas.

@MikkelSchubert
Copy link
Owner

Python 3 development takes place in the py3x branch, but I've been too busy to work much on it recently. The releases I've made over the last few months have just been minor bug-fixes and such for the Python 2 branch.

Best,
Mikkel

@tillea
Copy link
Author

tillea commented Feb 8, 2020

Any news for the py3x branch. Is it somehow usable? We really want to get rid of all python2 pysam dependencies and Paleomix is one of the two remaining ones.

@sandrotosi
Copy link

looks like the py3k branch was merged a couple of months ago, so is Paleomix python3 fully-compatible now? thanks!

@tillea
Copy link
Author

tillea commented Apr 6, 2020

Unfortunately there is no newer release than 1.2.14 (which is Python2).

@sandrotosi
Copy link

@tillea you can just generate a tarball for the current master HEAD and use it for updating the Debian package, it's common practice to do so.

@MikkelSchubert
Copy link
Owner

MikkelSchubert commented Apr 7, 2020 via email

@frikiluser
Copy link

Please consider patching master branch using this patch:
https://salsa.debian.org/friki/paleomix/-/blob/73112c5a190e65ebdb369ca0a8ae3fdd8d0ebd15/debian/patches/2to3.patch

It would be also great to have a new paleomix release dedicated to Python3 migration as soon as possible.

Best regards

@tillea
Copy link
Author

tillea commented Jul 30, 2020

Hi Mikkel,
is there any progress with a Palemomix version that works with Python3? Debian is agressively removing Python2 code and once Paleomix might be removed from Debian it is harder to re-include it again. It would be very helpful if you could give some estimation of the time you expect to have a distributable Python3 release.
Thanks a lot, Andreas.

@MikkelSchubert
Copy link
Owner

Sorry for the lack of updates.
For personal reasons I have not been able to focus a lot of attention on this project.

My current goal is to have a python3 version of PALEOMIX ready before next month.
The other, larger changes I had planned will have to wait until after that is done.

Best regards,
Mikkel

@tillea
Copy link
Author

tillea commented Aug 17, 2020 via email

@MikkelSchubert
Copy link
Owner

I've released the first Python 3 version of PALEOMIX, v1.3.0. Sorry for the many delays.
There are still a lot of things to be done, but I'll be pushing those out in smaller increments as time permits.

Please let me know if there are any issues on your end.

@tillea
Copy link
Author

tillea commented Sep 1, 2020

Thanks a lot. That's really great news. I nearly finished the Debian package. When doing so I changed shebang lines in all scripts. Feel free to download and apply the patch in our packaging code.
Kind regards, Andreas.

@sandrotosi
Copy link

there's absolutely no need to write a patch to change shebang, dh_pyhton3 does that already:

override_dh_python3:
        dh_python3 --shebang /usr/bin/python3

@tillea
Copy link
Author

tillea commented Sep 1, 2020 via email

@MikkelSchubert
Copy link
Owner

Thanks, Andreas.
I've applied the patch and will include it in the next release.

Best,
Mikkel

@tillea
Copy link
Author

tillea commented Sep 1, 2020 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@sandrotosi @MikkelSchubert @tillea @frikiluser