Stable ete4 release

[Zethson]

Hi,

I have a package that is dependent on ete3 and I'm still getting lots of reports from people that have trouble installing my package because they can't install ete3. Be it Macs or even Intel/Amd based clusters.

I am hoping that more installation issues will be resolved with ete4 which, if I read correctly, no longer has pyqt dependencies. I was wondering what the timeline for a stable ete4 release is given that you put out a 4.1.0 pre-release already?

Thank you very much!

[jhcepas]

Hi Lukas,
thanks for contacting.
Yes, all our efforts are currently on ete4. Depending on how you are using ete3, you could consider migrating to ete4 now, as many things are already stable. But, some syntax has changed and a few modules are not fully migrated/tested yet. We could advise on the migration if that helps. May I ask what is your project and what ete3 features does it use?
thanks!

[Zethson]

Thanks!

We could advise on the migration if that helps. May I ask what is your project and what ete3 features does it use? thanks!

This is the project: https://github.com/theislab/pertpy and it's only used in here: https://github.com/theislab/pertpy/blob/main/pertpy/tools/_coda/_base_coda.py. It's probably fine if you just CTRL-F ete3 in that file. We're not using a lot of features.

I'd be very happy if you could help us migrate (maybe even with a quick PR?) but to be able to make releases of pertpy, we'd need an ete4 candidate on pypi.

Thanks again!

[Zethson]

@dengzq1234 I saw that you assigned yourself to this issue and I was wondering whether you'd be up for that? I'm happy to guide a bit on the general code etc if necessary. Thanks!

[dengzq1234]

Hi Lukas! yes, it would be me! Sorry for the delay cuz we are undergoing some minor updates and we don't want to effect your scripts. I would work on it and definately keep you updated! Let's use this thread for further discussion! Keep in touch! Best, Ziqi Lukas Heumos ***@***.***> 于 2024年5月20日周一 下午4:51写道：

…

@dengzq1234 <https://github.com/dengzq1234> I saw that you assigned yourself to this issue and I was wondering whether you'd be up for that? I'm happy to guide a bit on the general code etc if necessary. Thanks! — Reply to this email directly, view it on GitHub <#739 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDS2VYQ2MOXU26C3WXW56TZDIEVNAVCNFSM6AAAAABC34BMQSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRQGYYTSNJXGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[dengzq1234]

@Zethson PR in regards to this thread has been requested in scverse/pertpy#618, therefore I will close this issue and further discussion will be conduct in the PR