-
Notifications
You must be signed in to change notification settings - Fork 40
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
InSTAnT #150
base: main
Are you sure you want to change the base?
InSTAnT #150
Conversation
Hi @bhavaygg, thanks for submitting the package. I have a couple of comments:
I can't find automated tests, nor continuous integration setup in your repository. At the very least, you should have end-to-end tests that ensure that the main functions of your package can be successfully executed. Better would be to additionally have unit tests that check the correctness of the results. You can find more information about tests in the pyopensci guidebook and find an example in our cookiecutter template.
By API documentation, we mean a listing of all functions/classes/class methods that your package provides, including their arguments, e.g. scirpy API docs. If you have only a few of them, it's fine to do it in the README, otherwise, I strongly recommend checking out tools such as sphinx autodoc. You README shows some of the functions available, but there are some additional Classes exported from your namespace, e.g.
You should consider supporting SpatialData which is the new scverse data structure for spatial datasets which readily supports subcellular resolution. @LucaMarconato can tell you more about it if you have any questions. AnnData for spatial datasets is a legacy format that has no future in scverse. Finally, we are starting a partnership with pyopensci - If you want you can also get a more comprehensive package review through them. This is optional for now, but will eventually become the standard for adding scverse ecosystem packages. |
@bhavaygg great work and thanks for contributing to the scverse ecosystem! As Gregor said feel free to reach out to me here in GitHub or via the scverse Zulip chat for any question. https://scverse.zulipchat.com/#narrow/stream/315824-spatial |
Mandatory
Name of the tool: InSTAnT
Short description: InSTAnT is a toolkit to identify gene pairs which are d-colocalized from single molecule measurement data e.g. MERFISH or SeqFISH. A gene pair is d-colocalized when their transcripts are within distance d across many cells.
How does the package use scverse data structures (please describe in a few sentences): The package offers support for
anndata
input/output.