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

Speed up clonotype distance calculation #470

Open
wants to merge 3 commits into
base: main
Choose a base branch
from

Conversation

felixpetschko
Copy link
Collaborator

@felixpetschko felixpetschko commented Jan 7, 2024

Close #368

compute_distances new version added

@grst grst changed the title compute_distances new version added Speed up clonotype distance calculation Jan 9, 2024
@grst
Copy link
Collaborator

grst commented Jan 9, 2024

Hi @felixpetschko,

I just had a look at the failing tests. Most of them are indeed direct or indirect failures due to the new distance calculator. Some of them are testing the API of the DoubleLookupNeighborFinder and are expected to fail because you changed the API (for good reasons). Those we'll have to adapt or remove eventually.

At first, I suggest you take a look at the tests in test_clonotypes -- it seems they cover some edge cases where your implementation throws an error.

image

LMK if anything is unclear!

Gregor

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

Successfully merging this pull request may close these issues.

speed up define_clonotypes
2 participants