Skip to content

Dataset cannot be opened when underlying zarr arrays have fill_value set. #960

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.

Sign up for GitHub

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

Jump to bottom
Open
benjeffery opened this issue Nov 21, 2022 · 0 comments
Open

Dataset cannot be opened when underlying zarr arrays have fill_value set. #960

benjeffery opened this issue Nov 21, 2022 · 0 comments
Labels
upstream Used when our build breaks due to upstream changes

Comments

@benjeffery
Copy link
Collaborator

Due to pydata/xarray#7292 zarr arrays with fill_value set get their dtype changed to float32. This causes the dataset to fail when opened with sgkit.

fill_value is used in zarr to set a default value for arrays, this can be useful as it allows chunks that only contain the default value to not be written to disk at all. I was investigating using this for tskit-dev/tsinfer#729 where we are storing many short haplotypes.
@hammer hammer added the upstream Used when our build breaks due to upstream changes label Nov 22, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
upstream Used when our build breaks due to upstream changes
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@benjeffery @hammer