feat: add support for python API calling and scverse packages #263

slobentanzer · 2025-01-15T17:27:20Z

This PR is to extend API calling functionality towards Python functions, specifically from scverse packages. It is mainly derived from work done in the German BioHackathon 3, 2024.

Added:

concrete scverse module parameterisation classes
abstract API parameterisation by injection of a Python module and parsing
parsing of the structured LLM return into a callable Python function
benchmark to test LLM capabilities with regard to Python and scverse, specifically

Refactored:

API agent module now is structured into submodules
API agent documentation updated to reflect the changes

Further information can be found in the hackathon repo https://github.com/biocypher/scverse-x-biochatter and in a discussion https://github.com/orgs/biocypher/discussions/3

Not all features are fully functional yet, but the existing functionality integrates with the framework and does not harm existing processes. Recommending bump of minor.

This PR also already merged a fix proposed to improve the generic chat functionality handling and documentation, #262. Will merge simultaneously.

…on 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 is not compatible with Windows OS 11 and Python version 2.12.3, whatever it is the wheel or source version. Running pytest does not yield any errors, beyond raising deprecated warnings

method. Currently scanpy is imported when ScanpyTLQueryBuilder.parametrise_query is called.

Only includes functions which dont start with "_"

Just the generic function

Merge Dev/tl into main to avoid plenty of branches

* add scanpy_pl module with initial fields * add mocked test for module * add module to API agent __init__.py * add benchmark case * add conditional for module benchmark * downgrade httpx due to conflict 0.28 removed the proxy keyword, but openai is not aware * add back default `question_uuid` field into pydantic class * add scatter pydantic class * add sc.pl.pca * add pca benchmark case * distinguish web api and python api benchmark * change case to scatter * add tsne class * add tsne case * fix typing * add generic formatter (#233) * add formatter functions for REST and Python * make discoverable on module level * add required field * test the formatting functions * `scanpy` to `sc` to fit common usage * adjust benchmark to use the formatter --------- Co-authored-by: daniele-lucarelli <[email protected]>

* pushed starter anndata file * removed the tester * Aim of the anndata api module * Draft of the AnnDataIOParameters * added a prompt * updated the prompt * started to implement the AnndataIOQueryBuilder * added test for anndata api * pushed pydantic reader classes * Updated the anndata tool with integrated test: -> returns dict with method & args Co-authored-by: Anis Ismail <[email protected]> * added query builder * added querybuilder for anndata and its test * updated query builder * added exclude none * feat(BaseAPIModel): Add reusable base class for structured outputs • Introduced BaseAPIModel, a reusable base class to streamline the creation of Pydantic models for structured outputs. • The class includes: • uuid: An optional field (str | None) for unique identification of model instances. • method_name: A required field (str) to specify the associated function or method, ensuring consistency across models. • Configured with arbitrary_types_allowed to support flexible extensions. • Designed for use in structured output generation. This addition lays the groundwork for standardized, maintainable, and consistent API models. * update query builder to remove create_runnable * Updated the pydatic classes with the BaseAPIModel * Updated the system prompt in the runnable of the AnnDataIOQueryBuilder * fix in import of pydanticparser * added test for query builder parameterise_query * removed comments + redundant script --------- Co-authored-by: Anis Ismail <[email protected]> Co-authored-by: Anis Ismail <[email protected]>

…tem prompt is updated for the anndata query

… into biohackathon3

…en number of latent dimensions

replace with any length type (...)

… into biohackathon3

…c classes adjusts the ABC, the individual legacy classes (builder and fetcher), and the tests

… into biohackathon3

now has empty list in parameters

… into biohackathon3

rename modules, classes, and adjust the tests

mengerj · 2025-01-24T15:24:32Z

I will try to work on it on Monday. But I am also trying to get the automated approach working and finish the refactoring approach. It got a bit messy and I dont have a great overview of the package, so I hope I can get it done.

slobentanzer · 2025-01-27T12:49:04Z

@mengerj thanks, any feedback is welcome; the merge is also not urgent. if anybody needs a bit more time, just let me know. I am targeting end of this week as the deadline for the merge.

biochatter/api_agent/generate_pydantic_classes_from_module.py

MDLDan · 2025-01-27T14:18:41Z

@mengerj thanks, any feedback is welcome; the merge is also not urgent. if anybody needs a bit more time, just let me know. I am targeting end of this week as the deadline for the merge.

Looks good to me overall, just a bit weird we have pp and pl while tl is with the automated method

slobentanzer · 2025-01-30T17:29:41Z

Looks good to me overall, just a bit weird we have pp and pl while tl is with the automated method

@MDLDan true, but I would see this as a proof of concept / prototype, not a feature that we will prominently advertise. The main reason for the merge is that PRs shouldn't hang around forever, and we only need to make sure that nothing breaks (which CI should take care of for us).

bastienchassagnol and others added 30 commits December 10, 2024 13:52

add the tools tl modules to API agent __init__.py

db60467

add scanpy_tl module with general description

6abb3a9

api agent for scnapy tl using the generate_pydantic_class_from_module

a46df7a

method. Currently scanpy is imported when ScanpyTLQueryBuilder.parametrise_query is called.

generic method to generate pydantic classes for functions in a module.

d4f3184

Only includes functions which dont start with "_"

working progress on QueryBuilder and its unit tests

7b4df80

Merge pull request #1 from mengerj/just_the_generic_function

93be844

Just the generic function

Merge branch 'main' into dev/tl-bastien

0b5ea9d

Merge pull request #2 from bastienchassagnol/dev/tl-bastien

40a7751

Merge Dev/tl into main to avoid plenty of branches

switch scanpy pl to langchain bind_tools

4f885ae

Fixed the prompt issue in the AnnDataIOQueryBuilder, but now no sys…

835f096

…tem prompt is updated for the anndata query

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter…

ee0106b

… into biohackathon3

add in the benchmark a call to scanpy.pp to carry on a PCA with a giv…

f10839a

…en number of latent dimensions

fix schema issue with fixed length tuples

78b9a66

replace with any length type (...)

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter…

2010548

… into biohackathon3

remove nested list in benchmark

ee20735

remove unnecessary variable

0e003f9

remove dual httpx definition

f032635

update ABC to return list from parameterise_query

70d4a39

add umap pydantic class

e53bcbb

migrate legacy query builder and fetcher to work with list of pydanti…

799ba8a

…c classes adjusts the ABC, the individual legacy classes (builder and fetcher), and the tests

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter…

8f705d7

… into biohackathon3

add draw_graph pydantic class

993da5f

assume list of classes as return

0a3ab0c

now has empty list in parameters

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter…

c3f8e12

… into biohackathon3

add draw_graph to tool list

8c1b646

return variable instead of call

02c8d19

Merge branch 'biohackathon3' of https://github.com/biocypher/biochatter…

cc4d718

… into biohackathon3

slobentanzer added 10 commits January 15, 2025 11:22

remove debug

f4ae4a1

skip flaky test for now

d6579c6

update poetry

92ec961

name autogeneration of model and parameterisation adequately

c41fe89

rename modules, classes, and adjust the tests

rename abc.py because it shadowed Python ABC

521b123

refactor API agent into base, python, and web components

1976b9b

update docs

4f4c3ca

Merge branch 'make-user-optional' into biohackathon3

77f6007

update ruff config

bf584e7

run pre-commit

f22f9ec

slobentanzer temporarily deployed to Test CI January 15, 2025 17:27 — with GitHub Actions Inactive

slobentanzer requested review from bastienchassagnol, vd-dragan21, anisdismail, noahbruderer, MDLDan, mengerj and kvitoslava-yarish January 15, 2025 17:30

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slobentanzer added 3 commits January 30, 2025 18:36

Merge branch 'main' into biohackathon3

dfae5f5

doc format

b02a056

run pre-commit

aab9883

slobentanzer temporarily deployed to Test CI January 30, 2025 17:41 — with GitHub Actions Inactive

slobentanzer merged commit 15782fb into main Jan 30, 2025
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slobentanzer deleted the biohackathon3 branch January 30, 2025 17:44

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feat: add support for python API calling and scverse packages #263

feat: add support for python API calling and scverse packages #263

slobentanzer commented Jan 15, 2025

mengerj commented Jan 24, 2025

slobentanzer commented Jan 27, 2025

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MDLDan commented Jan 27, 2025

slobentanzer commented Jan 30, 2025

feat: add support for python API calling and scverse packages #263

feat: add support for python API calling and scverse packages #263

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slobentanzer commented Jan 15, 2025

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