Refactor manual pydantics for scanpy pl agents#255

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mengerj wants to merge 173 commits intomainfrom refactor_manual_pydantics

+6,377-2,249

Commits on Dec 10, 2024

Commits on Dec 11, 2024

Change pymilvus dependency in the pyproject.toml from the fixed version 2.2.8 to superior or equal to 2.2.8. Indeed, it appears that the grpcio 1.53.0 external dependency of pymilvus version 2.2.8 …
bastienchassagnol
committed
api agent for scnapy tl using the generate_pydantic_class_from_module
mengerj
committed
generic method to generate pydantic classes for functions in a module.
mengerj
committed
working progress on QueryBuilder and its unit tests
mengerj
committed
Merge pull request #1 from mengerj/just_the_generic_function
bastienchassagnol
authored
Merge branch 'main' into dev/tl-bastien
bastienchassagnol
authored
Merge pull request #2 from bastienchassagnol/dev/tl-bastien
bastienchassagnol
authored
Scanpy-pl (#226 )

slobentanzer
and
daniele-lucarelli
authored
Anndata api integration (#229 )

noahbruderer
and
anisdismail
authored
switch scanpy pl to langchain bind_tools
daniele-lucarelli
committed
Fixed the prompt issue in the AnnDataIOQueryBuilder, but now no system prompt is updated for the anndata query
noahbruderer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
noahbruderer
committed
add in the benchmark a call to scanpy.pp to carry on a PCA with a given number of latent dimensions
bastienchassagnol
committed
fix schema issue with fixed length tuples
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
slobentanzer
committed
remove nested list in benchmark
slobentanzer
committed
remove unnecessary variable
slobentanzer
committed
remove dual httpx definition
slobentanzer
committed
update ABC to return list from parameterise_query
slobentanzer
committed
add umap pydantic class
daniele-lucarelli
committed
migrate legacy query builder and fetcher to work with list of pydantic classes
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
slobentanzer
committed
add draw_graph pydantic class
daniele-lucarelli
committed
assume list of classes as return
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
slobentanzer
committed
add draw_graph to tool list
daniele-lucarelli
committed
return variable instead of call
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
slobentanzer
committed
add spatial pydantic class
daniele-lucarelli
committed
Merge branch 'biohackathon3' into main
bastienchassagnol
authored
add anndata benchmark
slobentanzer
committed
add anndata benchmark test case
slobentanzer
committed
change from langchain pydantic to original pydantic
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter into biohackathon3
slobentanzer
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Added mock test for ScanpyTLQueryBuilder (without module specification)
vd-dragan21
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Merge branch 'main' into mock_test
bastienchassagnol
authored
Merge pull request #3 from bastienchassagnol/mock_test
bastienchassagnol
authored
remove irrelevant imports in scanpy.tl module
bastienchassagnol
committed
Merge branch 'main' of https://github.com/bastienchassagnol/biochatter
bastienchassagnol
committed
Merge branch 'biohackathon3' into main
bastienchassagnol
authored
move method_name to title
slobentanzer
committed
add test script to gitignore
slobentanzer
committed
Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter
bastienchassagnol
committed

Commits on Dec 12, 2024

Commits on Dec 19, 2024

Commits on Jan 2, 2025

Commits on Jan 16, 2025

work in progress to fix formatting of python calls for new classes
menger
committed

Commits on Jan 24, 2025

move example into description

menger
authored and
menger
committed
add the tools tl modules to API agent __init__.py

bastienchassagnol
authored and
menger
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add scanpy_tl module with general description

bastienchassagnol
authored and
menger
committed
Change pymilvus dependency in the pyproject.toml from the fixed version 2.2.8 to superior or equal to 2.2.8. Indeed, it appears that the grpcio 1.53.0 external dependency of pymilvus version 2.2.8 …

bastienchassagnol
authored and
menger
committed
api agent for scnapy tl using the generate_pydantic_class_from_module

mengerj
authored and
menger
committed
generic method to generate pydantic classes for functions in a module.

mengerj
authored and
menger
committed
working progress on QueryBuilder and its unit tests

mengerj
authored and
menger
committed
add in the benchmark a call to scanpy.pp to carry on a PCA with a given number of latent dimensions

bastienchassagnol
authored and
menger
committed
Scanpy-pl (#226 )

authored and
menger
committed
Anndata api integration (#229 )

authored and
menger
committed
switch scanpy pl to langchain bind_tools

daniele-lucarelli
authored and
menger
committed
fix schema issue with fixed length tuples

slobentanzer
authored and
menger
committed
Fixed the prompt issue in the AnnDataIOQueryBuilder, but now no system prompt is updated for the anndata query

noahbruderer
authored and
menger
committed
remove nested list in benchmark

slobentanzer
authored and
menger
committed
remove unnecessary variable

slobentanzer
authored and
menger
committed
remove dual httpx definition

slobentanzer
authored and
menger
committed
update ABC to return list from parameterise_query

slobentanzer
authored and
menger
committed
migrate legacy query builder and fetcher to work with list of pydantic classes

slobentanzer
authored and
menger
committed
add umap pydantic class

daniele-lucarelli
authored and
menger
committed
assume list of classes as return

slobentanzer
authored and
menger
committed
add draw_graph pydantic class

daniele-lucarelli
authored and
menger
committed
return variable instead of call

slobentanzer
authored and
menger
committed
add draw_graph to tool list

daniele-lucarelli
authored and
menger
committed
add spatial pydantic class

daniele-lucarelli
authored and
menger
committed
remove irrelevant imports in scanpy.tl module

bastienchassagnol
authored and
menger
committed
Added mock test for ScanpyTLQueryBuilder (without module specification)

vd-dragan21
authored and
menger
committed
add anndata benchmark

slobentanzer
authored and
menger
committed
add anndata benchmark test case

slobentanzer
authored and
menger
committed
change from langchain pydantic to original pydantic

slobentanzer
authored and
menger
committed
move method_name to title

slobentanzer
authored and
menger
committed
add test script to gitignore

slobentanzer
authored and
menger
committed
Resolve merge conflicts (#239 )

authored and
menger
committed
add pl reduced args

daniele-lucarelli
authored and
menger
committed
first version of a function to build pydantic classes for all functions (#234 )

authored and
menger
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Generic function pydantic classes (#241 )

authored and
menger
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revert title to method_name

slobentanzer
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menger
committed
include BaseAPIModel

mengerj
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menger
committed
renamed anndata module to anndata_agent due to conflicts

mengerj
authored and
menger
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changing how pydantic classes are defined manually, alinging with

mengerj
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menger
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resolve import issue

slobentanzer
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menger
committed
Add the scanpy tool tl modules to API agent, next and closing steps. (#238 )

authored and
menger
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uuid to question_uuid in BaseAPIModule

mengerj
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menger
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refactored scanpy_pl and scanpy_pl_reduced according to new structure

mengerj
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menger
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fixed mock import error

mengerj
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menger
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formatting

slobentanzer
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menger
committed
format

slobentanzer
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menger
committed
Fix_benchmark_sc_plot (#244 )

authored and
menger
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add reduced builder class

slobentanzer
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menger
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add file ignores for test and benchmark

slobentanzer
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menger
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Modify the benchmark to test querybuilders for scanpy tool operations (#253 )

authored and
menger
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Create pydantic classes for the scanpy pp (#256 )

authored and
menger
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Include function description including to which module a tool belongs. Added function name to be interpretable by bind_tools

mengerj
authored and
menger
committed
Anndata concatentation + mapping integration (#257 )

authored and
menger
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adapt python call formatter to work with 'title' containing method key

mengerj
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menger
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figure params

slobentanzer
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menger
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refactor hooks to be more modular

slobentanzer
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menger
committed
some ruff complaints

slobentanzer
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menger
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docstrings

slobentanzer
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menger
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make more readable, fix ruff warnings

slobentanzer
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menger
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fix return value

slobentanzer
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menger
committed
comment cases for testing

slobentanzer
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menger
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move tool definitions to global module-level dictionary

slobentanzer
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menger
committed
ignore long lines

slobentanzer
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menger
committed
ruff demands

slobentanzer
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menger
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fix test

slobentanzer
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menger
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fix double plural

slobentanzer
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menger
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ruff warning

slobentanzer
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menger
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replace BaseModel with BaseAPIModel

slobentanzer
authored and
menger
committed
work in progress to fix formatting of python calls for new classes

menger
authored and
menger
committed
move example into description

menger
authored and
menger
committed
Merge branch 'refactor_manual_pydantics' of https://github.com/biocypher/biochatter into refactor_manual_pydantics

menger
authored and
menger
committed

Commits on Jan 27, 2025

changed autogeneration function to only collecting tool info, similar to how they are defined manually. Pydantic classes are then created through the BaseTools derived classes.

menger
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menger
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removed old approach of using autogeneration function. Use AutoModuleQueryBuilder(scanpy.tl) to build a agent for scanpy.tl

menger
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menger
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safe pydantic tools as at

menger
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menger
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save pydantic tools as attribute

menger
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menger
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save pydantic classes as attirbute

menger
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menger
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remove scanpy tl query builderemove scanpy tl query builder, because the automated approach can be applied

menger
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menger
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revert formatter changes to be confirm with previous code. I don't think a format as python call should be needed, as structued LLM output takes care of this.

menger
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menger
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go back to using method_name for testing purposes

menger
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menger
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latest version of anndata agent

menger
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menger
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a file that is not used, due to other, newer version of anndata_agent

menger
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menger
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remove the Tl query builder

menger
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menger
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remove ScanpyTlQueryBuilder

menger
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menger
committed