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

Migrate ome_model Python package to its own repository #194

Open
sbesson opened this issue Nov 25, 2024 · 2 comments
Open

Migrate ome_model Python package to its own repository #194

sbesson opened this issue Nov 25, 2024 · 2 comments

Comments

@sbesson
Copy link
Member

sbesson commented Nov 25, 2024

The code under https://github.com/ome/ome-model/tree/v6.3.6/ome_model has had little maintenance/development over the last 4 years.
Functionally, its content is also very different from the rest of this code base which contains:

1- the source XSD files for the OME data model
2- sample XML files for the different schema versions
3- the code-generated Java implementation of the OME model objects

Following the extraction to a separate repository, a decision should likely be made with regard to maintaining it vs archiving it in favor of other community Python projects like https://pypi.org/project/ome-types/.

Originally posted by @sbesson in #193 (review)

@joshmoore
Copy link
Member

Especially if we feel comfortable that our existing scripts could be re-written on top of ome-types, I'd be 👍 trying to unify on it.

@sbesson
Copy link
Member Author

sbesson commented Dec 11, 2024

Agreed, as a proof of concept, I worked on a minimal example upgrading a IDR script generating an HCS companion file using this package to ome-types.

The code difference is very reasonable - see IDR/idr0092-ostrop-organoid#2 and the generated OME-XML is consistent with the original one with the only differences being related to attribute ordering and UUIDs.

Based on this minimal investigation, I am further inclined to remove this project and deprecate it in favor of ome-types. At the API level, I cannot see anything that I would care about maintaining. If any was raised as valuable, I would propose to discuss how to open it as a contribution against ome-types directly. Any valuable experience gained from this project could be also be converted into documentation https://ome-types.readthedocs.io/.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants