Skip to content

Load visium as SPE#16

Merged
keviny2 merged 11 commits intomainfrom
visium
Feb 28, 2025
Merged

Load visium as SPE#16
keviny2 merged 11 commits intomainfrom
visium

Conversation

@keviny2
Copy link
Collaborator

@keviny2 keviny2 commented Feb 4, 2025

#7

@keviny2
Copy link
Collaborator Author

keviny2 commented Feb 17, 2025

read_10x_visium requires combine ops for SpatialExperiment objects. Wait for combine ops to be implemented.

#22

@keviny2 keviny2 linked an issue Feb 17, 2025 that may be closed by this pull request
@keviny2 keviny2 requested a review from jkanche February 28, 2025 21:36
@keviny2 keviny2 self-assigned this Feb 28, 2025
Copy link
Member

@jkanche jkanche left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Additionally, I would add optional dependencies on L70 here https://github.com/BiocPy/SpatialExperiment/blob/main/setup.cfg#L70

This lists additional dependencies the package has

optional =
pandas
requests

Then folks can install these by pip install spatialexperiment[optional]

@keviny2 keviny2 merged commit 10e93d5 into main Feb 28, 2025
7 checks passed
@keviny2 keviny2 deleted the visium branch February 28, 2025 23:42
setuptools
pytest
pytest-cov
%(optional)s
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is cool, wish i knew we can do this

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

Status: No status

Development

Successfully merging this pull request may close these issues.

Load visium (& may be others) as SPE objects

2 participants