napari integration

[kephale]

Hi Folks,

I was wondering if you all had looked into integrating tyssue and napari, since there is already a pretty major shared dependency of vispy. I am quite interested in this integration and was thinking about looking into it in the near future.

Cheers,
Kyle

[glyg]

Hi Kyle,
I for one have not, maybe @sophietheis has thought of something, but that could be fun to display tyssue meshes in napari indeed!
Please feel very welcome to look into it and report here what you found. The vispy viewer is not super tested because we have used ipyvolume instead, but hopefully it's a good basis!

Cheers,

Guillaume

[sophietheis]

Hi,

I just told myself that it will be nice if we integrate tyssue and napari, but I never take the time to look into it.
Recently I used ParaView to visualise, but I need to export sheet in vtk file. Clearly not the ideal solution...

Cheers,

Sophie

[kephale]

Okey doke, I'm still polishing it and the docs but it is getting there https://github.com/kephale/napari-tyssue

[kephale]

Would you all be willing to push https://github.com/DamCB/invagination to pypi? I have the apoptosis and invagination simulations working in napari-tyssue (some gifs are in https://github.com/kephale/napari-tyssue/blob/main/README.md now) but to make the plugin installable I can't use invagination @ git+https://github.com/DamCB/invagination.git when pushing the plugin to pypi (which is required for publishing to napari hub).

[sophietheis]

Can you use https://github.com/suzannelab/invagination instead ? I am not sure the version in DamCB is up to date.

@glyg maybe we should make the repo at suzannelab as the main repo (now, suzannelab is forked from mine-sophietheis, which is forked from yours-DamCB). It won't be a problem for the paper, since the link refers to suzannelab/invagination.

[glyg]

Hi
First: This is awesome :) — I am testing it asap (which is not right now because I have too much work)

Second, yes no problem to set suzannelab as the main repo, of course, and publishing to PiPy (@sophietheis can you do all that? I think you are still admin on Magali's repo?

G

[sophietheis]

Sure I update everything today (and transfer the ownership for other repo in the same time). I am still admin on Magali's repo.
I'll let you know when it is published on PiPy.

[sophietheis]

It is published now. You should be able to install via

pip install invagination==0.0.2

[kephale]

@sophietheis I'm having some issues using it (I've tried a handful of variations of this):

% pip install invagination==0.0.2
ERROR: Could not find a version that satisfies the requirement invagination==0.0.2 (from versions: none)
ERROR: No matching distribution found for invagination==0.0.2

It looks like the invagination package is published as a .egg while tyssue (which works fine) is published as a .whl on pypi.

[sophietheis]

Hum, this is the first time that I try to publish to PyPi. Seems that the tuto that I follow was not corect. I try to fix it this week.

[kephale]

Thank you! Yes, publishing artifacts frustrates me too because I generally have to read the instructions every time.

[sophietheis]

You can try now. It is published as .whl on pypi, and I don't have error when try to install via pypi. 🤞

[kephale]

@sophietheis thank you! It works for me now.