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Merged
Josephrp merged 2 commits into from
Oct 6, 2025
Merged

fix: remove misleading @defer decorator comments #36

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cee9981
fix: remove misleading @defer decorator comments
MarioAderman Oct 6, 2025
54d599d
Merge branch 'dev' into fix/issue-2-remove-defer-decorator
MarioAderman Oct 6, 2025
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11 changes: 1 addition & 10 deletions DeepResearch/src/tools/bioinformatics_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,6 @@
from typing import Dict, List, Optional, Any
from pydantic import BaseModel, Field

# Note: defer decorator is not available in current pydantic-ai version

from .base import ToolSpec, ToolRunner, ExecutionResult, registry
from ..datatypes.bioinformatics import (
GOAnnotation,
Expand Down Expand Up @@ -55,8 +53,7 @@ def from_config(cls, config: Dict[str, Any], **kwargs) -> "BioinformaticsToolDep
)


# Deferred tool definitions for bioinformatics data processing
# @defer - not available in current pydantic-ai version
# Tool definitions for bioinformatics data processing
def go_annotation_processor(
annotations: List[Dict[str, Any]],
papers: List[Dict[str, Any]],
Expand All @@ -68,7 +65,6 @@ def go_annotation_processor(
return []


# @defer - not available in current pydantic-ai version
def pubmed_paper_retriever(
query: str, max_results: int = 100, year_min: Optional[int] = None
) -> List[PubMedPaper]:
Expand All @@ -78,7 +74,6 @@ def pubmed_paper_retriever(
return []


# @defer - not available in current pydantic-ai version
def geo_data_retriever(
series_ids: List[str], include_expression: bool = True
) -> List[GEOSeries]:
Expand All @@ -88,7 +83,6 @@ def geo_data_retriever(
return []


# @defer - not available in current pydantic-ai version
def drug_target_mapper(
drug_ids: List[str], target_types: Optional[List[str]] = None
) -> List[DrugTarget]:
Expand All @@ -98,7 +92,6 @@ def drug_target_mapper(
return []


# @defer - not available in current pydantic-ai version
def protein_structure_retriever(
pdb_ids: List[str], include_interactions: bool = True
) -> List[ProteinStructure]:
Expand All @@ -108,7 +101,6 @@ def protein_structure_retriever(
return []


# @defer - not available in current pydantic-ai version
def data_fusion_engine(
fusion_request: DataFusionRequest, deps: BioinformaticsToolDeps
) -> DataFusionResult:
Expand All @@ -127,7 +119,6 @@ def data_fusion_engine(
)


# @defer - not available in current pydantic-ai version
def reasoning_engine(
task: ReasoningTask, dataset: FusedDataset, deps: BioinformaticsToolDeps
) -> ReasoningResult:
Expand Down
8 changes: 0 additions & 8 deletions DeepResearch/src/tools/deep_agent_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,6 @@
from typing import Any, Dict
from pydantic_ai import RunContext

# Note: defer decorator is not available in current pydantic-ai version

# Import existing DeepCritical types
from ..datatypes.deep_agent_state import (
TaskStatus,
Expand All @@ -39,7 +37,6 @@


# Pydantic AI tool functions
# @defer - not available in current pydantic-ai version
def write_todos_tool(
request: WriteTodosRequest, ctx: RunContext[DeepAgentState]
) -> WriteTodosResponse:
Expand Down Expand Up @@ -81,7 +78,6 @@ def write_todos_tool(
)


# @defer - not available in current pydantic-ai version
def list_files_tool(ctx: RunContext[DeepAgentState]) -> ListFilesResponse:
"""Tool for listing files in the filesystem."""
try:
Expand All @@ -97,7 +93,6 @@ def list_files_tool(ctx: RunContext[DeepAgentState]) -> ListFilesResponse:
return ListFilesResponse(files=[], count=0)


# @defer - not available in current pydantic-ai version
def read_file_tool(
request: ReadFileRequest, ctx: RunContext[DeepAgentState]
) -> ReadFileResponse:
Expand Down Expand Up @@ -174,7 +169,6 @@ def read_file_tool(
)


# @defer - not available in current pydantic-ai version
def write_file_tool(
request: WriteFileRequest, ctx: RunContext[DeepAgentState]
) -> WriteFileResponse:
Expand Down Expand Up @@ -205,7 +199,6 @@ def write_file_tool(
)


# @defer - not available in current pydantic-ai version
def edit_file_tool(
request: EditFileRequest, ctx: RunContext[DeepAgentState]
) -> EditFileResponse:
Expand Down Expand Up @@ -287,7 +280,6 @@ def edit_file_tool(
)


# @defer - not available in current pydantic-ai version
def task_tool(
request: TaskRequestModel, ctx: RunContext[DeepAgentState]
) -> TaskResponse:
Expand Down
11 changes: 0 additions & 11 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,6 @@ python -m deepresearch.app flows.prime.params.adaptive_replanning=false

⚠️ **Known Issues:**
- Circular import issues in some tool modules (bioinformatics_tools, deep_agent_tools)
- Some pydantic-ai API compatibility issues (defer decorator not available in current version)
- These issues are being addressed and will be resolved in future updates

## 🏗️ Architecture
Expand Down Expand Up @@ -481,16 +480,6 @@ DeepCritical/
return AssessDataQuality()
```

4. **Register Deferred Tools**:
```python
from pydantic_ai.tools import defer

@defer
def go_annotation_processor(annotations, papers, evidence_codes):
# Processing logic
return processed_annotations
```

## 🚀 Advanced Usage

### Batch Processing
Expand Down