Run isort on src and tests

src/curategpt/adhoc/gocam_predictor.py

@@ -9,7 +9,6 @@
 
 import click
 import yaml
-
 from curate_gpt import BasicExtractor, DBAdapter
 from curate_gpt.store import get_store
 from curate_gpt.utils.eval_utils import Outcome, score_prediction

src/curategpt/agents/agent_utils.py

@@ -4,10 +4,9 @@
 from typing import Dict, List, Optional, Tuple
 
 import yaml
-from llm import Model
-
 from curate_gpt.store.db_adapter import SEARCH_RESULT
 from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from llm import Model
 
 logger = logging.getLogger(__name__)
 

src/curategpt/agents/bootstrap_agent.py

@@ -2,12 +2,11 @@
 from typing import Dict
 
 import yaml
-from jinja2 import Template
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.conf.prompts import PROMPTS_DIR
 from curate_gpt.extract import AnnotatedObject
+from jinja2 import Template
+from pydantic import BaseModel, ConfigDict
 
 
 class KnowledgeBaseSpecification(BaseModel):

src/curategpt/agents/chat_agent.py

@@ -6,12 +6,11 @@
 from typing import Any, Dict, Optional
 
 import yaml
-from llm import Conversation
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
 from curate_gpt.wrappers import BaseWrapper
+from llm import Conversation
+from pydantic import BaseModel, ConfigDict
 
 logger = logging.getLogger(__name__)
 

src/curategpt/agents/concept_recognition_agent.py

@@ -5,9 +5,8 @@
 from enum import Enum
 from typing import Dict, List, Optional, Tuple
 
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
+from pydantic import BaseModel, ConfigDict
 
 logger = logging.getLogger(__name__)
 

src/curategpt/agents/dase_agent.py

@@ -4,12 +4,11 @@
 from dataclasses import dataclass, field
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.agents.chat_agent import ChatResponse
 from curate_gpt.extract import AnnotatedObject
 from curate_gpt.store import DBAdapter
+from pydantic import BaseModel, ConfigDict
 
 logger = logging.getLogger(__name__)
 

src/curategpt/agents/dragon_agent.py

@@ -5,11 +5,10 @@
 from typing import Any, ClassVar, Dict, Iterable, List, Optional, Tuple, Union
 
 import yaml
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.extract import AnnotatedObject
 from curate_gpt.store import DBAdapter
+from pydantic import BaseModel, ConfigDict
 
 logger = logging.getLogger(__name__)
 

src/curategpt/agents/evidence_agent.py

@@ -4,7 +4,6 @@
 from typing import Dict, List, Optional, Union
 
 import yaml
-
 from curate_gpt import BasicExtractor
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse

src/curategpt/agents/mapping_agent.py

@@ -10,12 +10,11 @@
 
 import inflection
 import yaml
-from pydantic import BaseModel, ConfigDict
-
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.formatters.format_utils import remove_formatting
 from curate_gpt.store.db_adapter import SEARCH_RESULT
 from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
+from pydantic import BaseModel, ConfigDict
 
 logger = logging.getLogger(__name__)
 

src/curategpt/app/app.py

@@ -7,26 +7,22 @@
 import numpy as np
 import streamlit as st
 import yaml
-from scipy.spatial import distance_matrix
-
 from curate_gpt import BasicExtractor
 from curate_gpt.agents import MappingAgent
 from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
 from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.evidence_agent import EvidenceAgent
-from curate_gpt.app.components import (
-    DimensionalityReductionOptions,
-    limit_slider_component,
-    vectors_to_fig,
-)
+from curate_gpt.app.components import (DimensionalityReductionOptions,
+                                       limit_slider_component, vectors_to_fig)
 from curate_gpt.app.helper import get_applicable_examples, get_case_collection
 from curate_gpt.app.state import get_state
 from curate_gpt.extract import OpenAIExtractor, RecursiveExtractor
 from curate_gpt.wrappers import BaseWrapper
 from curate_gpt.wrappers.investigation.jgi_wrapper import JGIWrapper
 from curate_gpt.wrappers.literature import WikipediaWrapper
 from curate_gpt.wrappers.literature.pubmed_wrapper import PubmedWrapper
+from scipy.spatial import distance_matrix
 
 PUBMED = "PubMed (via API)"
 WIKIPEDIA = "Wikipedia (via API)"

src/curategpt/app/helper.py

@@ -3,7 +3,6 @@
 from typing import Dict, List, Optional
 
 import yaml
-
 from curate_gpt.conf import EXAMPLES_DIR
 
 HELP_CASES = EXAMPLES_DIR / "bio.yaml"

src/curategpt/cli.py

@@ -16,24 +16,21 @@
 import requests
 import yaml
 from click_default_group import DefaultGroup
-from linkml_runtime.dumpers import json_dumper
-from linkml_runtime.utils.yamlutils import YAMLRoot
-from llm import UnknownModelError, get_model, get_plugins
-from llm.cli import load_conversation
-from oaklib import get_adapter
-from pydantic import BaseModel
-
 from curate_gpt import ChromaDBAdapter, __version__
-from curate_gpt.agents.bootstrap_agent import BootstrapAgent, KnowledgeBaseSpecification
+from curate_gpt.agents.bootstrap_agent import (BootstrapAgent,
+                                               KnowledgeBaseSpecification)
 from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
-from curate_gpt.agents.concept_recognition_agent import AnnotationMethod, ConceptRecognitionAgent
+from curate_gpt.agents.concept_recognition_agent import (
+    AnnotationMethod, ConceptRecognitionAgent)
 from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.evidence_agent import EvidenceAgent
 from curate_gpt.agents.huggingface_agent import HuggingFaceAgent
 from curate_gpt.agents.summarization_agent import SummarizationAgent
-from curate_gpt.evaluation.dae_evaluator import DatabaseAugmentedCompletionEvaluator
-from curate_gpt.evaluation.evaluation_datamodel import StratifiedCollection, Task
+from curate_gpt.evaluation.dae_evaluator import \
+    DatabaseAugmentedCompletionEvaluator
+from curate_gpt.evaluation.evaluation_datamodel import (StratifiedCollection,
+                                                        Task)
 from curate_gpt.evaluation.runner import run_task
 from curate_gpt.evaluation.splitter import stratify_collection
 from curate_gpt.extract import AnnotatedObject
@@ -44,6 +41,12 @@
 from curate_gpt.wrappers import BaseWrapper, get_wrapper
 from curate_gpt.wrappers.literature.pubmed_wrapper import PubmedWrapper
 from curate_gpt.wrappers.ontology import OntologyWrapper
+from linkml_runtime.dumpers import json_dumper
+from linkml_runtime.utils.yamlutils import YAMLRoot
+from llm import UnknownModelError, get_model, get_plugins
+from llm.cli import load_conversation
+from oaklib import get_adapter
+from pydantic import BaseModel
 
 __all__ = [
     "main",

src/curategpt/evaluation/calc_statistics.py

@@ -1,12 +1,9 @@
 from typing import Any, Iterator, List, Tuple, Union
 
 import yaml
-
-from curate_gpt.evaluation.evaluation_datamodel import (
-    AggregationMethod,
-    ClassificationMetrics,
-    ClassificationOutcome,
-)
+from curate_gpt.evaluation.evaluation_datamodel import (AggregationMethod,
+                                                        ClassificationMetrics,
+                                                        ClassificationOutcome)
 
 
 def calculate_metrics(

src/curategpt/evaluation/dae_evaluator.py

@@ -4,15 +4,13 @@
 from typing import List, TextIO
 
 import yaml
-
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.evaluation.base_evaluator import BaseEvaluator
-from curate_gpt.evaluation.calc_statistics import (
-    aggregate_metrics,
-    calculate_metrics,
-    evaluate_predictions,
-)
-from curate_gpt.evaluation.evaluation_datamodel import ClassificationMetrics, ClassificationOutcome
+from curate_gpt.evaluation.calc_statistics import (aggregate_metrics,
+                                                   calculate_metrics,
+                                                   evaluate_predictions)
+from curate_gpt.evaluation.evaluation_datamodel import (ClassificationMetrics,
+                                                        ClassificationOutcome)
 
 logger = logging.getLogger(__name__)
 

src/curategpt/evaluation/runner.py

@@ -6,10 +6,10 @@
 from typing import TextIO
 
 import yaml
-
 from curate_gpt import BasicExtractor, ChromaDBAdapter
 from curate_gpt.agents.dragon_agent import DragonAgent
-from curate_gpt.evaluation.dae_evaluator import DatabaseAugmentedCompletionEvaluator
+from curate_gpt.evaluation.dae_evaluator import \
+    DatabaseAugmentedCompletionEvaluator
 from curate_gpt.evaluation.evaluation_datamodel import Task
 from curate_gpt.evaluation.splitter import stratify_collection_to_store
 

src/curategpt/extract/basic_extractor.py

@@ -8,9 +8,8 @@
 from typing import List
 
 import yaml
-from pydantic import ConfigDict
-
 from curate_gpt.formatters.format_utils import remove_formatting
+from pydantic import ConfigDict
 
 from ..utils.tokens import estimate_num_tokens, max_tokens_by_model
 from .extractor import AnnotatedObject, Extractor

src/curategpt/extract/extractor.py

@@ -7,12 +7,11 @@
 from typing import Any, Dict, List, Optional, Tuple
 
 import llm
+from curate_gpt.store.schema_proxy import SchemaProxy
 from linkml_runtime import SchemaView
 from pydantic import BaseModel as BaseModel
 from pydantic import ConfigDict
 
-from curate_gpt.store.schema_proxy import SchemaProxy
-
 logger = logging.getLogger(__name__)
 
 

src/curategpt/extract/openai_extractor.py

@@ -6,9 +6,8 @@
 from dataclasses import dataclass
 from typing import List
 
-from openai import OpenAI, OpenAIError
-
 from curate_gpt.extract.extractor import AnnotatedObject, Extractor
+from openai import OpenAI, OpenAIError
 
 FUNC_NAME = "extract_data"
 

src/curategpt/store/chromadb_adapter.py

@@ -5,7 +5,8 @@
 import os
 import time
 from dataclasses import dataclass, field
-from typing import Callable, ClassVar, Iterable, Iterator, List, Mapping, Optional, Union
+from typing import (Callable, ClassVar, Iterable, Iterator, List, Mapping,
+                    Optional, Union)
 
 import chromadb
 import yaml
@@ -14,15 +15,14 @@
 from chromadb.api import EmbeddingFunction
 from chromadb.types import Collection
 from chromadb.utils import embedding_functions
-from linkml_runtime.dumpers import json_dumper
-from linkml_runtime.utils.yamlutils import YAMLRoot
-from oaklib.utilities.iterator_utils import chunk
-from pydantic import BaseModel
-
 from curate_gpt.store.db_adapter import DBAdapter
 from curate_gpt.store.metadata import CollectionMetadata
 from curate_gpt.store.vocab import OBJECT, PROJECTION, QUERY, SEARCH_RESULT
 from curate_gpt.utils.vector_algorithms import mmr_diversified_search
+from linkml_runtime.dumpers import json_dumper
+from linkml_runtime.utils.yamlutils import YAMLRoot
+from oaklib.utilities.iterator_utils import chunk
+from pydantic import BaseModel
 
 logger = logging.getLogger(__name__)
 

src/curategpt/store/db_adapter.py

@@ -5,26 +5,18 @@
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from pathlib import Path
-from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, TextIO, Union
+from typing import (ClassVar, Dict, Iterable, Iterator, List, Optional, TextIO,
+                    Union)
 
 import pandas as pd
 import yaml
 from click.utils import LazyFile
-from jsonlines import jsonlines
-
 from curate_gpt.store.metadata import CollectionMetadata
 from curate_gpt.store.schema_proxy import SchemaProxy
-from curate_gpt.store.vocab import (
-    DEFAULT_COLLECTION,
-    DOCUMENTS,
-    EMBEDDINGS,
-    FILE_LIKE,
-    METADATAS,
-    OBJECT,
-    PROJECTION,
-    QUERY,
-    SEARCH_RESULT,
-)
+from curate_gpt.store.vocab import (DEFAULT_COLLECTION, DOCUMENTS, EMBEDDINGS,
+                                    FILE_LIKE, METADATAS, OBJECT, PROJECTION,
+                                    QUERY, SEARCH_RESULT)
+from jsonlines import jsonlines
 
 logger = logging.getLogger(__name__)
 

src/curategpt/store/duckdb_adapter.py

@@ -8,40 +8,30 @@
 import os
 import re
 from dataclasses import dataclass, field
-from typing import Any, Callable, ClassVar, Dict, Iterable, Iterator, List, Mapping, Optional, Union
+from typing import (Any, Callable, ClassVar, Dict, Iterable, Iterator, List,
+                    Mapping, Optional, Union)
 
 import duckdb
 import llm
 import numpy as np
 import openai
 import psutil
 import yaml
+from curate_gpt.store.db_adapter import DBAdapter
+from curate_gpt.store.duckdb_result import DuckDBSearchResult
+from curate_gpt.store.metadata import CollectionMetadata
+from curate_gpt.store.vocab import (DEFAULT_MODEL, DEFAULT_OPENAI_MODEL,
+                                    DISTANCES, DOCUMENTS, EMBEDDINGS, IDS,
+                                    METADATAS, MODEL_MAP, OBJECT, PROJECTION,
+                                    QUERY, SEARCH_RESULT)
+from curate_gpt.utils.vector_algorithms import mmr_diversified_search
 from linkml_runtime.dumpers import json_dumper
 from linkml_runtime.utils.yamlutils import YAMLRoot
 from oaklib.utilities.iterator_utils import chunk
 from openai import OpenAI
 from pydantic import BaseModel
 from sentence_transformers import SentenceTransformer
 
-from curate_gpt.store.db_adapter import DBAdapter
-from curate_gpt.store.duckdb_result import DuckDBSearchResult
-from curate_gpt.store.metadata import CollectionMetadata
-from curate_gpt.store.vocab import (
-    DEFAULT_MODEL,
-    DEFAULT_OPENAI_MODEL,
-    DISTANCES,
-    DOCUMENTS,
-    EMBEDDINGS,
-    IDS,
-    METADATAS,
-    MODEL_MAP,
-    OBJECT,
-    PROJECTION,
-    QUERY,
-    SEARCH_RESULT,
-)
-from curate_gpt.utils.vector_algorithms import mmr_diversified_search
-
 logger = logging.getLogger(__name__)