Switch to colab #69
Merged
Switch to colab #69
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
|
Contributor
Author
|
Once we get this merged I will add a badge to the readme |
Contributor
Author
Contributor
Author
|
Also you can view this without logging into google |
This was referenced Jun 5, 2023
Contributor
Author
|
Resolves issue #70 |
Member
|
NGLView widget isn't showing. I'm not sure if that's an inherent limitation of Colab, or maybe if that needs the old |
Member
|
it needs enabling using: |
Contributor
Author
|
@IAlibay I tried that but wasn't able to get it to work, did it work for you? |
Contributor
Author
|
I tried a bunch of things and nothing seemed to work, which is why I added the comment |
Member
|
it worked in MDA, I'll try to have a stab tomorrow |
Contributor
Author
|
Thanks and just in case it helps, this is what packages we have installed (maybe we need the right nglview version or something)
|
Contributor
|
I don't think nglview is worth fighting for here, we use it once in a cell up top for a nice vis, but I think later vis we might use one day are py3dmol |
richardjgowers
approved these changes
Jun 7, 2023
Contributor
richardjgowers
left a comment
richardjgowers
left a comment
There was a problem hiding this comment.
possibly yank the ngl cell or annotate it as flakey within colab
I had the second colab check cell fail and had to rerun (as commented).. possible this could be put inside a retry loop:
for _ in range(3):
try:
colab stuff
except:
pass
else:
break
Member
|
If we remove nglview, can we put in a static image of the system please? there's nothing worse than being shown a notebook about a system and not actually seeing it |
Member
Looping on a set of bash calls might not go so well? You probably will need to switch to some kind of subprocess call to properly capture outputs. |
Contributor
Author
|
@IAlibay Let me know if you get the nglview working/can point me towards one working on colab |
Member
nah there's a deeper ipywidgets issue but I don't have the time to work it out. If you can replace it with a static image (essentially the text is just "here's the system"), then it'll do for now. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.