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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.
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!
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...
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).
@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.
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?
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 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.
Activity
glyg commentedon Oct 3, 2022
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 commentedon Oct 3, 2022
Hi,
I just told myself that it will be nice if we integrate
tyssueandnapari, 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 commentedon Oct 14, 2022
Okey doke, I'm still polishing it and the docs but it is getting there https://github.com/kephale/napari-tyssue
kephale commentedon Oct 14, 2022
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 useinvagination @ git+https://github.com/DamCB/invagination.gitwhen pushing the plugin to pypi (which is required for publishing to napari hub).sophietheis commentedon Oct 17, 2022
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 commentedon Oct 17, 2022
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 commentedon Oct 17, 2022
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 commentedon Oct 17, 2022
It is published now. You should be able to install via
kephale commentedon Oct 17, 2022
@sophietheis I'm having some issues using it (I've tried a handful of variations of this):
It looks like the
invaginationpackage is published as a.eggwhiletyssue(which works fine) is published as a.whlon pypi.sophietheis commentedon Oct 17, 2022
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 commentedon Oct 17, 2022
Thank you! Yes, publishing artifacts frustrates me too because I generally have to read the instructions every time.
sophietheis commentedon Oct 20, 2022
You can try now. It is published as
.whlon pypi, and I don't have error when try to install via pypi. 🤞kephale commentedon Oct 20, 2022
@sophietheis thank you! It works for me now.