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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
768 stars 216 forks source link

Stable ete4 release #739

Closed Zethson closed 1 month ago

Zethson commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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 commented 1 month ago

@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 commented 1 month ago

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 https://github.com/etetoolkit/ete/issues/739#issuecomment-2120619576, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGDS2VYQ2MOXU26C3WXW56TZDIEVNAVCNFSM6AAAAABC34BMQSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRQGYYTSNJXGY . You are receiving this because you were mentioned.Message ID: @.***>

dengzq1234 commented 1 month ago

@Zethson PR in regards to this thread has been requested in https://github.com/theislab/pertpy/pull/618, therefore I will close this issue and further discussion will be conduct in the PR