core

CORE

Overview

Core utilities for METAINFORMANT bioinformatics toolkit.

Contents

• data/
• engine/
• execution/
• io/
• output/
• ui/
• utils/
• __init__.py

Structure

graph TD
    subgraph "Core Module"
        IO[io/] --> |io.py| RW[Read/Write JSON, YAML, CSV]
        IO --> |download.py| DL[Download with Retry + Resume]
        IO --> |paths.py| PA[Path Security + Resolution]
        IO --> |cache.py| CA[File-level Caching]

        UT[utils/] --> |logging.py| LG[Structured Logging]
        UT --> |config.py| CF[Config + Env Overrides]
        UT --> |errors.py| ER[Error Hierarchy]

        DA[data/] --> |validation.py| VA[Type + Range Validation]
        DA --> |db.py| DB[Database Integration]

        EN[engine/] --> |workflow_manager.py| WM[Pipeline Manager + TUI]
        EX[execution/] --> |workflow.py| WF[Config-driven Workflows]
        UI[ui/] --> |tui.py| TI[Terminal Interface]
    end

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Coordination Role

Core provides the orchestration primitives used by all domain agents:

• engine/workflow_manager.py: BasePipelineManager — generic multi-phase pipeline
• execution/workflow.py: Config-driven execution engine
• execution/parallel.py: Resource-aware thread pool utilities

See Agent Coordination Hub for multi-agent workflow patterns.

Usage

Import module:

from metainformant.core import ...