Refactor configuration management; update S3 integration, add new migration scripts, and implement pre-flight checks

example.config.yaml

@@ -1,50 +1,51 @@
-# System Configuration
-mongo_uri: "mongodb://localhost:27017"
-database_name: "helia"
+# Helia Application Configuration
+# Copy this file to config.yaml and adjust values as needed.
 
-# S3 Configuration (MinIO or AWS)
-s3_endpoint: "https://s3.amazonaws.com"
-s3_access_key: "your_access_key"
-s3_secret_key: "your_secret_key"
-s3_bucket: "your-bucket-name"
-s3_prefix: ""
-s3_region: "us-east-1"
+patient_limit: 5
 
-# Run Configuration
-limit: 5
+mongo:
+  uri: "mongodb://localhost:27017"
+  db_name: "helia"
+
+s3:
+  endpoint: "http://localhost:9000"
+  access_key_id: ""
+  secret_access_key: ""
+  bucket: "helia"
+  prefix: "daic-woz"
+  region: "eu-west-1"
 
 providers:
   openai:
-    # Set api_key here or export OPENAI_API_KEY
     api_base: "https://api.openai.com/v1"
-    api_format: "openai"
+    api_key: "sk-xxx"
+    api_spec: "openai"
 
   anthropic:
-    # Set api_key here or export ANTHROPIC_API_KEY
     api_base: "https://api.anthropic.com/v1"
-    api_format: "anthropic"
+    api_key: "sk-xxx"
+    api_spec: "anthropic"
 
   openrouter:
-    # Set api_key here or export OPENROUTER_API_KEY
     api_base: "https://openrouter.ai/api/v1"
-    api_format: "openai"
+    api_key: "sk-xxx"
+    api_spec: "openai"
 
   local_ollama:
-    # API key optional for local_* providers
     api_base: "http://localhost:11434/v1"
-    api_format: "ollama"
+    api_spec: "ollama"
 
 runs:
-  - run_name: "baseline_gpt4"
+  baseline_gpt4:
     model:
-      provider: openai
+      provider: "openai"
       model_name: "gpt-4o"
-      temperature: 0.0
+      temperature: 1.0
     prompt_id: "default"
 
-  - run_name: "test_llama3"
+  test_llama3:
     model:
-      provider: local_ollama
+      provider: "local_ollama"
       model_name: "llama3"
       temperature: 0.7
     prompt_id: "default"

migrations/init_transcripts.py

@@ -0,0 +1,85 @@
+import asyncio
+import logging
+import re
+from typing import Literal
+
+from helia.configuration import HeliaConfig
+from helia.db import init_db
+from helia.ingestion.s3 import S3DatasetLoader
+from helia.models.transcript import Transcript, Utterance
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def normalize_speaker(speaker: str) -> Literal["Interviewer", "Participant"]:
+    speaker_lower = speaker.lower().strip()
+    if speaker_lower == "ellie":
+        return "Interviewer"
+    if speaker_lower == "participant":
+        return "Participant"
+    raise ValueError(f"Unknown speaker: {speaker}")
+
+
+async def process_transcript(
+    s3_loader: S3DatasetLoader, key: str, id_pattern: re.Pattern[str]
+) -> bool:
+    """Process a single transcript and return True if successful."""
+    if not (match := id_pattern.search(key)):
+        logger.warning("Skipping unexpected file: %s", key)
+        return False
+
+    transcript_id = match.group(1)
+    logger.info("Processing transcript %s...", transcript_id)
+
+    try:
+        raw_data = await s3_loader.load_transcript(key)
+        utterances = [
+            Utterance(
+                start_time=float(row["start_time"]),
+                end_time=float(row["stop_time"]),
+                speaker=normalize_speaker(row["speaker"]),
+                value=row["value"].strip(),
+            )
+            for row in raw_data
+        ]
+
+        if not utterances:
+            logger.warning("No utterances found for transcript %s", transcript_id)
+            return False
+
+        await Transcript(transcript_id=transcript_id, utterances=utterances).insert()
+
+    except Exception:
+        logger.exception("Failed to process %s", key)
+        return False
+    else:
+        return True
+
+
+async def migrate() -> None:
+    logger.info("Starting initialization migration...")
+
+    config = HeliaConfig()  # type: ignore[call-arg]
+    await init_db(config)
+
+    s3_loader = S3DatasetLoader(config.s3)
+    keys = await s3_loader.list_transcripts()
+    logger.info("Found %d transcript files in S3.", len(keys))
+
+    await Transcript.delete_all()
+    logger.info("Cleared existing transcripts.")
+
+    id_pattern = re.compile(r"/(\d+)_TRANSCRIPT\.csv$")
+
+    results = await asyncio.gather(
+        *(process_transcript(s3_loader, key, id_pattern) for key in keys),
+        return_exceptions=True,
+    )
+
+    count = sum(1 for success in results if success is True)
+    logger.info("Successfully processed %d transcripts.", count)
+
+
+if __name__ == "__main__":
+    asyncio.run(migrate())

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
     "pydantic>=2.12.5",
     "beanie>=2.0.1",
     "motor>=3.7.1",
-    "boto3>=1.42.14",
+    "obstore>=0.8.2",
 ]
 
 [tool.hatch.build.targets.wheel]

scripts/preflight.py

@@ -0,0 +1,137 @@
+from __future__ import annotations
+
+import asyncio
+from typing import TYPE_CHECKING
+
+from openai import AsyncOpenAI
+from rich.console import Console
+from rich.table import Table
+
+from helia.configuration import HeliaConfig
+from helia.db import init_db
+from helia.ingestion.s3 import S3DatasetLoader
+
+if TYPE_CHECKING:
+    from helia.configuration import LLMProviderConfig, S3Config
+
+console = Console()
+
+
+async def check_mongo(config: HeliaConfig) -> tuple[str, bool]:
+    """Verify MongoDB connectivity."""
+    try:
+        await init_db(config)
+    except Exception as e:
+        console.print(f"[red]MongoDB error: {e}[/red]")
+        return "MongoDB", False
+    else:
+        return "MongoDB", True
+
+
+async def check_s3(config: S3Config) -> tuple[str, bool]:
+    """Verify S3 connectivity by listing objects."""
+    try:
+        loader = S3DatasetLoader(config)
+        await loader.list_transcripts()
+    except Exception as e:
+        console.print(f"[red]S3 error: {e}[/red]")
+        return "S3", False
+    else:
+        return "S3", True
+
+
+async def check_llm_provider(
+    name: str, config: LLMProviderConfig, model_name: str
+) -> tuple[str, bool]:
+    """Verify connectivity to an LLM provider."""
+    try:
+        client = AsyncOpenAI(
+            api_key=config.api_key,
+            base_url=config.api_base,
+            max_retries=0,
+            timeout=5.0,
+        )
+
+        await client.chat.completions.create(
+            model=model_name,
+            messages=[{"role": "user", "content": "ping"}],
+            max_tokens=1,
+        )
+    except Exception as e:
+        console.print(f"[red]{name} error: {e}[/red]")
+        return name, False
+    else:
+        return name, True
+
+
+async def check_all_connections(config: HeliaConfig) -> bool:
+    """
+    Run all pre-flight checks. Returns True if all checks pass.
+    """
+    console.print("\n[bold cyan]🔍 Starting Pre-flight Checks[/bold cyan]\n")
+
+    checks = []
+    check_names = []
+
+    checks.append(check_mongo(config))
+    check_names.append("MongoDB")
+
+    checks.append(check_s3(config.s3))
+    check_names.append("S3")
+
+    for name, provider_config in config.providers.items():
+        model_name = next(
+            (run.model.model_name for run in config.runs.values() if run.model.provider == name),
+            None,
+        )
+
+        if model_name:
+            checks.append(check_llm_provider(name, provider_config, model_name))
+            check_names.append(f"LLM Provider: {name}")
+        else:
+            console.print(
+                f"[yellow]⊘ Skipping LLM Provider '{name}': "
+                f"defined in config but not used in any run[/yellow]"
+            )
+
+    results = await asyncio.gather(*checks, return_exceptions=True)
+
+    # Create results table
+    table = Table(title="Pre-flight Check Results", show_header=True, header_style="bold")
+    table.add_column("Service", style="cyan")
+    table.add_column("Status", justify="center")
+
+    all_passed = True
+    for i, result in enumerate(results):
+        service_name = check_names[i] if i < len(check_names) else "Unknown"
+
+        if isinstance(result, Exception):
+            table.add_row(service_name, "[bold red]✗ Failed[/bold red]")
+            all_passed = False
+        elif isinstance(result, tuple):
+            name, passed = result
+            if passed:
+                table.add_row(name, "[bold green]✓ Passed[/bold green]")
+            else:
+                table.add_row(name, "[bold red]✗ Failed[/bold red]")
+                all_passed = False
+        elif result is False:
+            table.add_row(service_name, "[bold red]✗ Failed[/bold red]")
+            all_passed = False
+
+    console.print(table)
+
+    if all_passed:
+        console.print("\n[bold green]✓ All Pre-flight Checks Passed[/bold green]\n")
+    else:
+        console.print("\n[bold red]✗ Pre-flight Checks Failed[/bold red]\n")
+
+    return all_passed
+
+
+if __name__ == "__main__":
+    config = HeliaConfig()  # type: ignore[missing-argument, unknown-argument]
+
+    all_ok = asyncio.run(check_all_connections(config))
+    if not all_ok:
+        raise SystemExit(1)

scripts/verify_turns.py

@@ -0,0 +1,39 @@
+import asyncio
+import logging
+
+from helia.configuration import HeliaConfig
+from helia.db import init_db
+from helia.models.transcript import Transcript
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+async def verify() -> None:
+    config = HeliaConfig()  # type: ignore[call-arg]
+    await init_db(config)
+
+    transcript = await Transcript.find_one(Transcript.transcript_id == "300")
+    if not transcript:
+        logger.error("Transcript 300 not found.")
+        return
+
+    logger.info("Transcript 300 found with %d utterances.", len(transcript.utterances))
+
+    turns = transcript.turns
+    logger.info("Aggregated into %d turns.", len(turns))
+
+    for i, turn in enumerate(turns[:5]):
+        logger.info(
+            "Turn %d [%s] (%s - %s): %s... (Merged %d utterances)",
+            i + 1,
+            turn.speaker,
+            turn.start_time,
+            turn.end_time,
+            turn.value[:50],
+            turn.utterance_count,
+        )
+
+
+if __name__ == "__main__":
+    asyncio.run(verify())

src/helia/assessment/core.py

@@ -62,11 +62,6 @@ class PHQ8Evaluator:
             temperature=self.config.temperature,
         )
 
-    def _load_prompt(self, prompt_id: str) -> str:
-        if prompt_id == "default":
-            return DEFAULT_PROMPT
-        raise ValueError(f"Unknown prompt_id: {prompt_id}")
-
     async def evaluate(self, file_path: Path) -> AssessmentResult:
         """
         Asynchronously evaluate a transcript using the configured LLM.
@@ -76,8 +71,7 @@ class PHQ8Evaluator:
         transcript_text = "\n".join([f"{u.speaker}: {u.text}" for u in utterances])
 
         # 2. Prepare Prompt
-        base_prompt = self._load_prompt(self.config.prompt_id)
-        final_prompt = base_prompt.format(transcript_text=transcript_text)
+        final_prompt = DEFAULT_PROMPT.format(transcript_text=transcript_text)
 
         # 3. Call LLM (Async with Structured Output)
         structured_llm = self.llm.with_structured_output(AssessmentResponse)

src/helia/assessment/schema.py

@@ -1,16 +1,10 @@
+from typing import TYPE_CHECKING
+
 from beanie import Document
 from pydantic import BaseModel, Field
 
-
-class RunConfig(BaseModel):
-    model_name: str
-    api_base: str | None = None
-    api_format: str = "openai"
-    # API Key is needed for runtime but excluded from DB persistence for security
-    api_key: str | None = Field(default=None, exclude=True)
-    prompt_id: str
-    temperature: float
-    timestamp: str
+if TYPE_CHECKING:
+    from helia.configuration import RunConfig
 
 
 class Evidence(BaseModel):

src/helia/configuration.py

@@ -1,9 +1,8 @@
 from __future__ import annotations
 
-import os
-from typing import TYPE_CHECKING, Literal, NamedTuple
+from typing import Literal, Self
 
-from pydantic import BaseModel, Field, model_validator
+from pydantic import BaseModel, model_validator
 from pydantic_settings import (
     BaseSettings,
     PydanticBaseSettingsSource,
@@ -11,157 +10,90 @@ from pydantic_settings import (
     YamlConfigSettingsSource,
 )
 
-if TYPE_CHECKING:
-    from pathlib import Path
+
+class MongoConfig(BaseModel):
+    """MongoDB configuration."""
+
+    uri: str
+    db_name: str
 
 
-class S3Config(NamedTuple):
+class S3Config(BaseModel):
     """S3 bucket configuration."""
 
-    bucket_name: str
-    endpoint_url: str
-    aws_access_key_id: str
-    aws_secret_access_key: str
+    endpoint: str
+    bucket: str
+    access_key_id: str
+    secret_access_key: str
     prefix: str = ""
-    region_name: str | None = None
+    region: str = "eu-west-1"
 
 
-class ProviderConfig(BaseModel):
-    """
-    Configuration for an LLM provider.
-    """
+class LLMProviderConfig(BaseModel):
+    """Configuration for an LLM provider."""
 
-    api_key: str | None = None
     api_base: str
-    api_format: Literal["openai", "anthropic", "ollama"] = "openai"
+    api_key: str | None = None
+    api_spec: Literal["openai", "anthropic", "ollama"] = "openai"
 
 
-class ModelSpec(BaseModel):
-    """
-    Specific model configuration for a run.
-    """
+class ModelConfig(BaseModel):
+    """Specific model configuration for a run."""
 
     provider: str
     model_name: str
     temperature: float = 0.0
 
 
-class RunSpec(BaseModel):
-    """
-    Configuration for a single experiment run.
-    """
+class RunConfig(BaseModel):
+    """Configuration for a single experiment run."""
 
-    run_name: str
-    model: ModelSpec
+    model: ModelConfig
     prompt_id: str = "default"
 
 
 class HeliaConfig(BaseSettings):
-    """
-    Unified configuration for Helia.
-    Loads from YAML first, then falls back to Environment variables for system settings.
-    """
-
-    # System Settings (Env Fallback available via HELIA_ prefix)
-    mongo_uri: str = Field(..., description="MongoDB connection string")
-    database_name: str = Field("helia", description="MongoDB database name")
-
-    s3_endpoint: str = Field(..., description="S3 endpoint URL")
-    s3_access_key: str = Field(..., description="S3 access key")
-    s3_secret_key: str = Field(..., description="S3 secret key")
-    s3_bucket: str = Field(..., description="S3 bucket containing the dataset")
-    s3_prefix: str = Field("", description="S3 key prefix for dataset files")
-    s3_region: str | None = Field(None, description="S3 region name (optional)")
-
-    # Run Settings
-    limit: int | None = Field(None, description="Limit the number of transcripts processed")
-    providers: dict[str, ProviderConfig] = Field(default_factory=dict)
-    runs: list[RunSpec] = Field(default_factory=list)
+    """Main application configuration loaded from config.yaml."""
 
     model_config = SettingsConfigDict(
-        env_prefix="HELIA_",
-        env_file=None,  # Disable .env file loading
+        yaml_file="config.yaml",
+        yaml_file_encoding="utf-8",
         extra="ignore",
     )
 
-    def get_s3_config(self) -> S3Config:
-        """Create an S3Config from the system configuration."""
-        return S3Config(
-            bucket_name=self.s3_bucket,
-            endpoint_url=self.s3_endpoint,
-            aws_access_key_id=self.s3_access_key,
-            aws_secret_access_key=self.s3_secret_key,
-            prefix=self.s3_prefix,
-            region_name=self.s3_region,
-        )
+    patient_limit: int = 5
+    concurrency_limit: int = 1
+    mongo: MongoConfig
+    s3: S3Config
+    providers: dict[str, LLMProviderConfig] = {}
+    runs: dict[str, RunConfig] = {}
 
     @model_validator(mode="after")
-    def resolve_provider_api_keys(self) -> HeliaConfig:
-        """Resolve provider API keys from env vars as fallback.
-
-        - If `providers.<name>.api_key` is set in YAML, it is used.
-        - Otherwise, the loader tries `{NAME}_API_KEY` (uppercased provider name).
-        - Providers whose name starts with `local_` may omit an API key.
-        """
-        for name, provider in self.providers.items():
-            if provider.api_key:
-                continue
-
-            env_var_name = f"{name.upper()}_API_KEY"
-            if env_key := os.environ.get(env_var_name):
-                provider.api_key = env_key
-
-        return self
-
-    @model_validator(mode="after")
-    def validate_provider_api_keys(self) -> HeliaConfig:
-        """Enforce API key presence for non-local providers used by runs."""
-        used_providers = {run.model.provider for run in self.runs}
-
-        for provider_name in used_providers:
-            provider = self.providers.get(provider_name)
-            if provider is None:
-                msg = f"Provider '{provider_name}' is used in runs but not configured under 'providers'."
-                raise ValueError(msg)
-
-            if provider_name.startswith("local_"):
-                continue
-
-            if not provider.api_key:
-                env_var_name = f"{provider_name.upper()}_API_KEY"
+    def validate_run_providers(self) -> Self:
+        """Ensure all runs reference configured providers."""
+        for run_name, run_config in self.runs.items():
+            provider = run_config.model.provider
+            if provider not in self.providers:
+                available = ", ".join(self.providers.keys()) or "(none)"
                 msg = (
-                    f"Missing API key for provider '{provider_name}'. "
-                    f"Set providers.{provider_name}.api_key in YAML or export {env_var_name}."
+                    f"Run '{run_name}' references unknown provider '{provider}'. "
+                    f"Available providers: {available}"
                 )
                 raise ValueError(msg)
-
         return self
 
-
-
-
-def load_config(path: str | Path) -> HeliaConfig:
-    """
-    Load configuration from a YAML file, with environment variable fallback.
-    """
-
-    # Create a dynamic subclass to bind the specific yaml_file path
-    class RuntimeHeliaConfig(HeliaConfig):
-        model_config = SettingsConfigDict(yaml_file=path)
-
     @classmethod
     def settings_customise_sources(
         cls,
         settings_cls: type[BaseSettings],
         init_settings: PydanticBaseSettingsSource,  # noqa: ARG003
         env_settings: PydanticBaseSettingsSource,
-            dotenv_settings: PydanticBaseSettingsSource,  # noqa: ARG003
+        dotenv_settings: PydanticBaseSettingsSource,
         file_secret_settings: PydanticBaseSettingsSource,  # noqa: ARG003
     ) -> tuple[PydanticBaseSettingsSource, ...]:
+        """Customize settings sources: init > env > YAML > secrets."""
         return (
             YamlConfigSettingsSource(settings_cls),
+            dotenv_settings,
             env_settings,
-                # No dotenv, no init_settings needed usually
         )
-
-    return RuntimeHeliaConfig()  # type: ignore[call-arg]

src/helia/db.py

@@ -3,17 +3,20 @@ from __future__ import annotations
 from typing import TYPE_CHECKING
 
 from beanie import init_beanie
-from motor.motor_asyncio import AsyncIOMotorClient
+from pymongo.asynchronous.mongo_client import AsyncMongoClient
 
 from helia.assessment.schema import AssessmentResult
+from helia.models.transcript import Transcript
 
 if TYPE_CHECKING:
     from helia.configuration import HeliaConfig
 
 
-async def init_db(config: HeliaConfig) -> None:
-    client = AsyncIOMotorClient(config.mongo_uri)
+async def init_db(config: HeliaConfig) -> AsyncMongoClient:
+    client = AsyncMongoClient(host=[config.mongo.uri])
+    database = client[config.mongo.db_name]
     await init_beanie(
-        database=client[config.database_name],  # type: ignore[arg-type]
-        document_models=[AssessmentResult],
+        database=database,
+        document_models=[AssessmentResult, Transcript],
     )
+    return client

src/helia/ingestion/s3.py

@@ -1,14 +1,14 @@
 from __future__ import annotations
 
-import asyncio
+import csv
+import io
 import logging
 from typing import TYPE_CHECKING
 
-import boto3
+import obstore as obs
+from obstore.store import S3Store
 
 if TYPE_CHECKING:
-    from pathlib import Path
-
     from helia.configuration import S3Config
 
 logger = logging.getLogger(__name__)
@@ -19,48 +19,25 @@ class S3DatasetLoader:
         self,
         s3_config: S3Config,
     ) -> None:
-        self.bucket_name = s3_config.bucket_name
+        self.bucket_name = s3_config.bucket
         self.prefix = s3_config.prefix
-        self.s3 = boto3.client(
-            "s3",
-            endpoint_url=s3_config.endpoint_url,
-            aws_access_key_id=s3_config.aws_access_key_id,
-            aws_secret_access_key=s3_config.aws_secret_access_key,
-            region_name=s3_config.region_name,
+
+        self.s3 = S3Store(
+            s3_config.bucket,
+            access_key_id=s3_config.access_key_id,
+            secret_access_key=s3_config.secret_access_key,
+            endpoint=s3_config.endpoint,
+            region=s3_config.region,
         )
 
-    def list_transcripts(self) -> list[str]:
-        """
-        List all transcript CSV files in the bucket matching the DAIC-WOZ pattern.
-        Pattern: {participant_id}_P/{participant_id}_TRANSCRIPT.csv
-        """
-        logger.info("Listing files in s3://%s/%s", self.bucket_name, self.prefix)
-        paginator = self.s3.get_paginator("list_objects_v2")
-        transcripts = []
+    async def list_transcripts(self) -> list[str]:
+        stream = obs.list(store=self.s3, prefix=self.prefix)
+        entries = await stream.collect_async()
+        return [entry["path"] for entry in entries if entry["path"].endswith("_TRANSCRIPT.csv")]
 
-        for page in paginator.paginate(Bucket=self.bucket_name, Prefix=self.prefix):
-            if "Contents" not in page:
-                continue
-
-            for obj in page["Contents"]:
-                key = obj["Key"]
-                if key.endswith("_TRANSCRIPT.csv"):
-                    transcripts.append(key)
-
-        logger.info("Found %d transcripts", len(transcripts))
-        return transcripts
-
-    def download_file(self, key: str, local_path: Path) -> Path:
-        """
-        Download a file from S3 to a local path (Blocking).
-        """
-        local_path.parent.mkdir(parents=True, exist_ok=True)
-        logger.info("Downloading s3://%s/%s to %s", self.bucket_name, key, local_path)
-        self.s3.download_file(self.bucket_name, key, str(local_path))
-        return local_path
-
-    async def download_file_async(self, key: str, local_path: Path) -> Path:
-        """
-        Download a file from S3 to a local path (Async wrapper around blocking call).
-        """
-        return await asyncio.to_thread(self.download_file, key, local_path)
+    async def load_transcript(self, key: str) -> list[dict[str, str]]:
+        logger.debug("Loading s3://%s/%s into memory", self.bucket_name, key)
+        result = await obs.get_async(store=self.s3, path=key)
+        content = bytes(await result.bytes_async()).decode()
+        reader = csv.DictReader(io.StringIO(content), delimiter="\t")
+        return list(reader)

src/helia/models/transcript.py

@@ -0,0 +1,26 @@
+from typing import ClassVar, Literal
+
+from beanie import Document
+from pydantic import BaseModel
+from pymongo import ASCENDING
+
+
+class Utterance(BaseModel):
+    start_time: float
+    end_time: float
+    speaker: Literal["Interviewer", "Participant"]
+    value: str
+
+
+class Transcript(Document):
+    transcript_id: str
+    utterances: list[Utterance]
+
+    class Settings:
+        name = "transcripts"
+        indexes: ClassVar = [
+            [("transcript_id", ASCENDING)],
+        ]
+        index_defs: ClassVar = [
+            {"key": "transcript_id", "unique": True},
+        ]

src/helia/preflight.py

@@ -1,116 +0,0 @@
-from __future__ import annotations
-
-import asyncio
-import logging
-from typing import TYPE_CHECKING
-
-from openai import AsyncOpenAI
-
-from helia.db import init_db
-from helia.ingestion.s3 import S3DatasetLoader
-
-if TYPE_CHECKING:
-    from helia.configuration import HeliaConfig, ProviderConfig, S3Config
-
-logger = logging.getLogger(__name__)
-
-
-async def check_mongo(config: HeliaConfig) -> bool:
-    """Verify MongoDB connectivity."""
-    try:
-        logger.info("Checking MongoDB connection...")
-        await init_db(config)
-    except Exception:
-        logger.exception("MongoDB connection failed")
-        return False
-    else:
-        logger.info("MongoDB connection successful.")
-        return True
-
-
-async def check_s3(config: S3Config) -> bool:
-    """Verify S3 connectivity by listing objects."""
-    try:
-        logger.info("Checking S3 connection...")
-        loader = S3DatasetLoader(config)
-        loader.list_transcripts()
-    except Exception:
-        logger.exception("S3 connection failed")
-        return False
-    else:
-        logger.info("S3 connection successful.")
-        return True
-
-
-async def check_llm_provider(name: str, config: ProviderConfig, model_name: str) -> bool:
-    """Verify connectivity to an LLM provider."""
-    try:
-        logger.info("Checking LLM provider: %s...", name)
-
-        client = AsyncOpenAI(
-            api_key=config.api_key,
-            base_url=config.api_base,
-            max_retries=0,  # Fail fast
-            timeout=5.0,  # Fail fast
-        )
-
-        await client.chat.completions.create(
-            model=model_name,
-            messages=[{"role": "user", "content": "ping"}],
-            max_tokens=1,
-        )
-    except Exception:
-        logger.exception("LLM provider %s connection failed", name)
-        return False
-    else:
-        logger.info("LLM provider %s connection successful.", name)
-        return True
-
-
-async def check_all_connections(config: HeliaConfig) -> bool:
-    """
-    Run all pre-flight checks. Returns True if all checks pass.
-    """
-    logger.info("--- Starting Pre-flight Checks ---")
-
-    checks = []
-
-    # 1. Check MongoDB
-    checks.append(check_mongo(config))
-
-    # 2. Check S3
-    checks.append(check_s3(config.get_s3_config()))
-
-    # 3. Check All LLM Providers
-    for name, provider_config in config.providers.items():
-        # Find a model used by this provider in the runs to use for the check
-        model_name = next(
-            (run.model.model_name for run in config.runs if run.model.provider == name),
-            None,
-        )
-
-        if model_name:
-            checks.append(check_llm_provider(name, provider_config, model_name))
-        else:
-            logger.warning(
-                "Skipping check for provider '%s': defined in config but not used in any run.",
-                name,
-            )
-
-    results = await asyncio.gather(*checks, return_exceptions=True)
-
-    # Analyze results
-    all_passed = True
-    for result in results:
-        if isinstance(result, Exception):
-            logger.error("Check failed with exception: %s", result)
-            all_passed = False
-        elif result is False:
-            all_passed = False
-
-    if all_passed:
-        logger.info("--- All Pre-flight Checks Passed ---")
-    else:
-        logger.error("--- Pre-flight Checks Failed ---")
-
-    return all_passed

uv.lock

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-[[package]]
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-version = "1.42.14"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
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-version = "1.42.14"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
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-    { name = "python-dateutil" },
-    { name = "urllib3" },
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-]
-
 [[package]]
 name = "certifi"
 version = "2025.11.12"
@@ -219,10 +191,10 @@ version = "0.1.0"
 source = { editable = "." }
 dependencies = [
     { name = "beanie" },
-    { name = "boto3" },
     { name = "langchain", extra = ["openai"] },
     { name = "langgraph" },
     { name = "motor" },
+    { name = "obstore" },
     { name = "pydantic" },
     { name = "pydantic-settings" },
     { name = "pyyaml" },
@@ -230,6 +202,10 @@ dependencies = [
 ]
 
 [package.dev-dependencies]
+cli = [
+    { name = "textual" },
+    { name = "tqdm" },
+]
 dev = [
     { name = "ruff" },
     { name = "ty" },
@@ -238,10 +214,10 @@ dev = [
 [package.metadata]
 requires-dist = [
     { name = "beanie", specifier = ">=2.0.1" },
-    { name = "boto3", specifier = ">=1.42.14" },
     { name = "langchain", extras = ["openai"], specifier = ">=1.2.0" },
     { name = "langgraph", specifier = ">=1.0.5" },
     { name = "motor", specifier = ">=3.7.1" },
+    { name = "obstore", specifier = ">=0.8.2" },
     { name = "pydantic", specifier = ">=2.12.5" },
     { name = "pydantic-settings", specifier = ">=2.12.0" },
     { name = "pyyaml", specifier = ">=6.0.1" },
@@ -249,6 +225,10 @@ requires-dist = [
 ]
 
 [package.metadata.requires-dev]
+cli = [
+    { name = "textual", specifier = ">=6.11.0" },
+    { name = "tqdm", specifier = ">=4.67.1" },
+]
 dev = [
     { name = "ruff", specifier = ">=0.14.10" },
     { name = "ty", specifier = ">=0.0.5" },
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-version = "1.0.1"
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 name = "jsonpatch"
 version = "1.33"
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 ]
 
+[[package]]
+name = "linkify-it-py"
+version = "2.0.3"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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+[[package]]
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+source = { registry = "https://pypi.org/simple" }
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+]
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