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awesome-panel / panel-chemistry

🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.
MIT License
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Adds Pbde Molstar #20

Closed MarcSkovMadsen closed 2 years ago

MarcSkovMadsen commented 2 years ago

Continuation of #19

A Panel Pane to wrap the PDBe implementation of the Mol* ('MolStar') viewer.

Check out

Cite Mol: David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.

Todo:

MarcSkovMadsen commented 2 years ago

panel serve 'panel_chemistry/pane/pdbe_molstar.py' --auto --show

https://user-images.githubusercontent.com/42288570/147883741-25b67e5b-afa6-4fbd-9e65-4fb9c34cb0dc.mp4

I will leave it here for now @Jhsmit . Could you give it a spin and make a PR into this branch? Feel free to tell me if I should work on something to help.

MarcSkovMadsen commented 2 years ago

FYI. I've added you as a member of this repo and to the gitter channel @Jhsmit

Jhsmit commented 2 years ago

Thanks Marc, I'll have a look.

"make a PR into this branch?" , What do you mean by this? add commits to this PR or should I start from here and commit to my own fork and PR from there?

MarcSkovMadsen commented 2 years ago

What I mean is that It would be nice for me to see and accept changes to this branch.

I would expect that has to be done via a separate pull request from your fork/ branch into this branch. But if there are other ways and you prefer them just use them.

If you know how to collaborate on a feature branch like this please let me know. Not so used to it :-) Normally I make all the code and finally make a PR into master.

Jhsmit commented 2 years ago

Ok yep I think i managed it in #21. Usually my workflow is just me in a lonely repo so I had to do some git-fu to figure it out.

MarcSkovMadsen commented 2 years ago

Another PR has been approved

MarcSkovMadsen commented 2 years ago

I was wrong :-)

MarcSkovMadsen commented 2 years ago

I will approve this one now @Jhsmit . I believe its in a good enough state to release, and then we can improve later.

I plan to publish package and market it on twitter later today. Hope its ok?

Jhsmit commented 2 years ago

Thanks Marc! Sounds good to me. Lets get it out and then we might solutions to the resizing / events later. I'll put it in PyHDX and also tweet about it later

MarcSkovMadsen commented 2 years ago

It will not be today. But ASAP. Something got in the way :-)

MarcSkovMadsen commented 2 years ago

I've tested. But for some reason the Panel jupyter-preview and Panel apps are not working on binder.

Jhsmit commented 2 years ago

Both work fine for me: I found your fix for binder now

I did have the issue where the resizing wasn't triggered correctly and only half of the viewer was showing. But re-executing the cell solved that.

On conda-forge, you should merge the PR yourself if all checks pass since you're the maintainer.

MarcSkovMadsen commented 2 years ago

Hmm. I don't have a merge button.

image

MarcSkovMadsen commented 2 years ago

Regarding Binder I still cannot get the Jupyter Panel Preview to work. It just throws a 404 error.

Jhsmit commented 2 years ago

I get this for the preview binding link you posted above: image

All seems to work fine.

Jhsmit commented 2 years ago

Regarding conda-forge, its strange you do not have write access

Are you in the conda-forge/panel-chemistry team? You should be able to find that on your github.com homepage in the bar on the left

This is what it looks like for me: image

Perhaps you could try this procedure here: https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-maintainer-list