Anndata concatentation + mapping integration #257
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Collaborator
noahbruderer
commented
Dec 12, 2024
noahbruderer
commented
- added support for anndata IO operations: concatenation and mapping
- developed tests for create_runnable and parameterize_query
- developed test cases for benchmarking for all prompts and expected answer for reading, concat and mapping
- fixed the serializing issue by importing Field from pydantic. - instead of Add defaults for optional fields, ensure consistency and clean serialization.
…om/biocypher/biochatter into anndata-concatentation-integration
… into anndata-concatentation-integration
…om/biocypher/biochatter into anndata-concatentation-integration
… into anndata-concatentation-integration
…om/biocypher/biochatter into anndata-concatentation-integration
…om/biocypher/biochatter into anndata-concatentation-integration
…red" Co-authored-by: Anis Ismail <anisdismail@users.noreply.github.com>
…om/biocypher/biochatter into anndata-concatentation-integration
Now the anndata is able to return code lines to concatenate anndata objs Co-authored-by: Anis Ismail <anisdismail@users.noreply.github.com>
Created MapAnnData class.
… into anndata-concatentation-integration
…yTlQueryBuilder and ConcatenateAnnData test -Minor fixes in the ScanpyTlQueryBuilder test
Added create runnable test for Anndata
…om/biocypher/biochatter into anndata-concatentation-integration
noahbruderer
had a problem deploying
to
Test CI
GitHub Actions
Failure
slobentanzer
had a problem deploying
to
Test CI
GitHub Actions
Failure
slobentanzer
had a problem deploying
to
Test CI
GitHub Actions
Failure
This was referenced Dec 12, 2024
slobentanzer
had a problem deploying
to
Test CI
GitHub Actions
Failure
slobentanzer
requested changes
Dec 13, 2024
There was a problem hiding this comment.
@noahbruderer @anisdismail you tried to merge into main; I changed it to biohackathon3, but now there are conflicts.
… into anndata-concatentation-integration
…om/biocypher/biochatter into anndata-concatentation-integration
slobentanzer
approved these changes
Dec 13, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.