Sisl files not available in readthedocs documentation

[pfebrer]

The SISL_FILES_TESTS variable is not set in readthedocs and it causes errors for some notebooks that plot files: https://sisl.readthedocs.io/en/latest/visualization/viz_module/index.html

This doesn't happen in the other documentation site:
https://zerothi.github.io/sisl/visualization/viz_module/index.html

[zerothi]

Yes, I seem to recall I disabled it on rtd because of time-outs, RTD has a limitation on the amount of time it allowed to run. We can try and re-enable it to see if will actually work.

[pfebrer]

Maybe I can try to change the tutorials so that they don't use files. But I think plotting bands files is what most people would want to do so it is nice to have it in the tutorial.

[zerothi]

Lets first see if we can get it up and running

[zerothi]

Can you see the build log here: https://readthedocs.org/projects/sisl/builds/24039054/
I can't understand why this fails, same sphinx version locally, and here all works...

[pfebrer]

If I install sisl in development mode I can't import sisl_toolbox, but it seems like it installs sisl normally, right?

[zerothi]

Hmm, what are you doing? I don't have any issues? Are you doing an editable intsall?

[pfebrer]

Yes, I meant editable install

[pfebrer]

Sorry, I can import it, but running stoolbox --help gives:

Traceback (most recent call last):
  File "/home/pfebrer/miniconda3/envs/simulations/bin/stoolbox", line 5, in <module>
    from sisl_toolbox.cli import stoolbox_cli
  File "/home/pfebrer/webDevelopement/sislGUI/sisl/src/sisl_toolbox/cli/__init__.py", line 11, in <module>
    from ._cli import *
ModuleNotFoundError: No module named 'sisl_toolbox.cli._cli'

[pfebrer]

import sisl_toolbox.siesta.atom

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/pfebrer/webDevelopement/sislGUI/sisl/src/sisl_toolbox/siesta/atom/__init__.py", line 6, in <module>
    from ._atom import AtomInput
  File "/home/pfebrer/webDevelopement/sislGUI/sisl/src/sisl_toolbox/siesta/atom/_atom.py", line 847, in <module>
    from sisl_toolbox.cli import register_toolbox_cli
  File "/home/pfebrer/webDevelopement/sislGUI/sisl/src/sisl_toolbox/cli/__init__.py", line 11, in <module>
    from ._cli import *
ModuleNotFoundError: No module named 'sisl_toolbox.cli._cli'

[zerothi]

Ah, I see now, I had completely forgotton to add this one in a prior PR... 2 secs

[zerothi]

try now ;)

[pfebrer]

Yes, now it works, so maybe it is the same problem that RTD had when importing sisl_toolbox.siesta.atom ?

[zerothi]

I think so, it is running just now ;)

[zerothi]

On another related note:

This goes fine:
https://readthedocs.org/projects/sisl/builds/24047173/

Yet, this one doesn't:
https://github.com/zerothi/sisl/actions/runs/8662894836/job/23755808712

You can even see it on the RTD page: https://sisl.readthedocs.io/en/latest/visualization/viz_module/index.html
There you can see broken thumbnails, and for some it works, for others it doesn't?

I also sometimes see this locally, the plot object not having a show method, why is that?

[pfebrer]

Hmm ok this is because the plot is not computed yet. I don't know how to handle this, because if the plot is not computed this kind of methods will fail, but if the plot has been computed it will work.

I could call .get() on the plot when some attribute is requested, but I don't know if I should do it only when the plot hasn't been computed yet, or in all cases. If I do it in all cases this means that the plot will get updated if inputs have been updated (it would trigger a computation of the plot). I don't know if this would be fine or not 😅

[zerothi]

But how could the plot not be computed yet? I mean it is a function call ;)
And the cells are executed?

[pfebrer]

No, it is not a function call, it is a Node call 😅 And nodes are lazy by default :)

So the question then is if by calling .show() the user wants to see the latest updated plot or just the current state of the plot.

[zerothi]

Hmm, I see. But how was it then working previously? There you also used 'show' for the thumbnails, are the png even necessary for the thumbnails?

It was because of my clean-up of the thumbnails in the docs.