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update aiida project template #4
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* update to latest renkulab dockerfile * update aiida-core python requirement
Add jupyter notebook that allows to * import the dataset * explore it
when run locally, project name may be empty (and path may be different).
aiida-activate check for profile existence is fragile
Hi @ltalirz thanks for this update! Regarding your first question have you tried adding an |
Thanks - for some reason I didn't think of trying this. I've modified the post-init.sh here: But it turns out that doesn't propagate to the environment in the terminal (same in the jupyter notebook) |
Ah you're right of course - I thought the script was sourced but it's actually executed with |
It would be quite useful to be able to set environment variables, so I would support this. |
Ok I will make an issue for it - I won't be able to get to it today, most likely... |
@rokroskar this should be ready for review now. I tested it and it seems to work fine. P.S. By the way, I again get the warning about an outdated renku version, but it displays the same version for the new one and the one of the repo |
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Thanks for the PR!
A minor note: we have a new renku-python release, you should probably include it in the template (see inline).
I tried to run the code on the notebook but I got an error, and I noticed the daemon is not running. Is this expected (i.e. I need to configure something first) or should it be running anyway?
thanks for the review @lorenzo-cavazzi !
Would you mind sharing the error you saw? I remember trying it and it did work fine for me. It may have been that you did not specify a path to an AiiDA archive file (although that field was optional, part of the template did assume that a valid URL was provided). For an example URL see #4 (comment) The archive URL will be prefilled for users that enter via the Materials Cloud Archive, but of course the template should still work if someone creates a project from it manually and does not specify the url. I've now put in some extra guards to also cover that use case. |
P.S. Yes, it is expected that the daemon is not running - I forgot to update the expected output in the README (now fixed). |
After your commits, I don't get the exception anymore. Currently, if I don't provide the initial URL, it fails gracefully 👍 There is another minor detail on the README.md to possibly adjust, I'll provide the details in a commit suggestion. Fell free to include or discard it, then we are ready to merge this PR. I have one final question: I noticed the repository contains uncommitted changes when I access a pristine environment. I assume a post initialization script runs something that creates those files. |
Thanks! The Will adding it to the |
The code won't be preserved when starting a new environment from a new commit. |
Ok! I'm sure there will be further changes once people start using it, and we'll try to make it as user-friendly as possible. |
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Let's merge this!
I've tagged a new version here and included the reference in the main renku repository, so that the new templates will be included in renkulab.io on the next release SwissDataScienceCenter/renku#2114 . If this is urgent, let us know and we can speed up the process |
Updates to the AiiDA project template
(with instructions on how to import & work with the data)
Questions:
AIIDA_PATH
) in the.bashrc
and it is available in the terminal, but not in the jupyter notebook.Todo: