Anndata concatentation + mapping integration#257

Merged

slobentanzer merged 37 commits intobiohackathon3from anndata-concatentation-integration

Dec 13, 2024

+1,307-310

Commits on Dec 12, 2024

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
anisdismail
committed
fixed the pydantic Optional syntax
noahbruderer
committed
Merge branch 'anndata-concatentation-integration' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
noahbruderer
committed
updated the method_name to title in the BaseAPIModel
noahbruderer
committed
added tools choice argument
anisdismail
committed
Merge branch 'anndata-concatentation-integration' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
anisdismail
committed
In create_runnable updated bind_tools by setting tool_choice="required"

noahbruderer
and
anisdismail
committed
Merge branch 'anndata-concatentation-integration' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
noahbruderer
committed
Added the ConcatenateAnnData BaseAPIModel class.

noahbruderer
and
anisdismail
committed
Changed 'title' field back to 'method_name'
noahbruderer
committed
fixed ':'
noahbruderer
committed
Added Map functionality
noahbruderer
committed
Added support for MapAnnData formatting
noahbruderer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
noahbruderer
committed
-Updated the system prompt, human prompt test assertions in the ScanpyTlQueryBuilder and ConcatenateAnnData test
noahbruderer
committed
Fixed the TestScanpyTlQueryBuilder test
noahbruderer
committed
Added create runnable test for Anndata
vd-dragan21
committed
Merge pull request #254 from bastienchassagnol/anndata_runnable_test
noahbruderer
authored
added use cases to the benchmark
anisdismail
committed
Merge branch 'anndata-concatentation-integration' of https://github.com/biocypher/biochatter into anndata-concatentation-integration
anisdismail
committed
Merging changes from biohackthon3 and anndata classes remain pydantic forms for now
noahbruderer
committed
Merge changes from biohackathon3; anndata changed to pydantic classes for now
noahbruderer
committed
fracture test regex
slobentanzer
committed
add openai models, run 3 times
slobentanzer
committed
deactivate non-scanpy
slobentanzer
committed