chore: run CI with Python 3.13

[himkt]

🔗. #1162 (comment)

[ecederstrand]

Hi @himkt I see tests for 3.13 are failing in CI. Did you get this to run locally? Just wondering if I should attempt building the package locally for Python 3.13 until a new version lands on PyPI.

[himkt]

@ecederstrand

Did you get this to run locally?

Yeah, tests succeeded on the local environment with Python 3.13... Currently I do not have any problem in nglview with Python 3.13 but at the same time I still have no clue about this problem.

[himkt]

Identified the root cause and scope of this problem.

https://github.com/nglviewer/nglview/pull/1167/files#diff-e34f8e5ab1b296643878b9e10b83741dec325770b494027a5811fe57949b450eR257

Core dump happens on pytraj API call inside test_add_trajectory and I created the dev environment using normal Python (not conda), which skips this test since pytraj was not installed.

Therefore, users using nglview with Python 3.13 and pytraj will encounter the error (cc. @ecederstrand). And I think I'm not sure it is the nglview specific problem. Although I'll create an environment to prepare all packages using conda later, this is the report at this time.

@hainm Do you have any idea for this problem inside pytraj? I'm wondering how I should work on this problem (e.g. merge this PR with skipping pytraj call on Python 3.13, or keeping not to run CI on Python 3.13 until pytraj problem is fixed, ...)

[hai-schrodinger]

Hi @himkt

It's up to you. I am fine with either.

[himkt]

@hainm Since I think running other tests on Python 3.13 would have benefit for users, I added a workaround 26ee544 to skip pytraj in the widget test. Let me ask you review this PR.

I'll investigate pytraj on Python 3.13.

[hainm]

Thanks @himkt very much for all the work. I will make a release soon. may be today.

[hainm]

I'll investigate pytraj on Python 3.13.

@himkt no need. I will do this since I was the one making pytraj. Thanks.

[himkt]

I will do this since I was the one making pytraj

(I noticed that during pytest investigation, and I was so amazed by your contributions to computational chemistry) Thank you so much!

[hainm]

Thank you. Just felt/feel good when doing that.

[hainm]

@himkt I have made 4.0 release in pypi.
conda version will be available soon.