Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Replace container support with conda-forge distribution #285

Open
tsalo opened this issue Jan 29, 2024 · 4 comments · May be fixed by #289
Open

Replace container support with conda-forge distribution #285

tsalo opened this issue Jan 29, 2024 · 4 comments · May be fixed by #289
Assignees
Labels
breaking-change question Further information is requested

Comments

@tsalo
Copy link
Member

tsalo commented Jan 29, 2024

Per @mattcieslak, it may not be worth it to retain container support.

Stems from #282 (comment).

We should try to get CuBIDS into conda-forge (https://conda-forge.org/), so that we can install it with its requirements (at least datalad, git, git-annex- not sure about bids-validator).

@tsalo tsalo added question Further information is requested breaking-change labels Jan 29, 2024
@tsalo
Copy link
Member Author

tsalo commented Jan 29, 2024

What does container support give us? The main dependencies seem to be pyBIDS and scikit-learn (per @mattcieslak in a comment in #282), so the only thing I can think of is Datalad. Basically, do we need extra container support in order to work with Datalad in certain environments (e.g., HPCs). Also, what do the extra steps implemented within CuBIDS do? Can we just have a Dockerfile with datalad included instead?

EDIT: It looks like the extra steps implemented in CuBIDS are specifically for using CuBIDS outside of a container and then submitting the calls to a container. What container would people use? Just the BIDS Validator?

@mattcieslak
Copy link
Contributor

The containers were useful for datalad and the bids validator. But Datalad and node are available via conda, so I think us supporting containerized datalad and bids-validator might be a bad use of our time. I can't think of a time recently that I've struggled to install datalad or bids-validator on a new computer, have you?

@tsalo
Copy link
Member Author

tsalo commented Jan 29, 2024

The only times I had to use containerized versions of Datalad and the validator were on FIU's HPC, where downloading anything was a lot of trouble. I agree that dropping container support seems reasonable.

I wonder if we could include datalad and the validator in the pyproject.toml somehow? Datalad seems doable. Not sure about the validator though.

@tsalo tsalo linked a pull request Jan 30, 2024 that will close this issue
2 tasks
@tsalo tsalo changed the title Consider dropping container support Replace container support with conda-forge distribution Jan 31, 2024
@tsalo
Copy link
Member Author

tsalo commented Feb 1, 2024

According to Chris M (not going to drag him into the thread), it should be possible to include the BIDS validator as a dependency, but the bare bones Python-based validator is already on conda-forge as bids-validator, so the validator devs may need to add the JS version to conda-forge before we can include it as a dependency in CuBIDS.

@tsalo tsalo self-assigned this Feb 5, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
breaking-change question Further information is requested
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants