Package index • HydraR

Core Orchestration

The heart of the HydraR framework.

AgentDAG: Agent Graph R6 Class
AgentNode: Agent Node Base Class
AgentState: Agent State R6 Class

Agent Nodes

Specialized nodes for LLM interaction, logical routing, and scaling.

AgentLLMNode: Agent LLM Node R6 Class
AgentLogicNode: Agent Logic Node R6 Class
AgentRouterNode: Agent Router Node R6 Class
AgentMapNode: Agent Map Node R6 Class
AgentObserverNode: Agent Observer Node R6 Class
AgentBashNode: Bash Execution Node
AgentPythonNode: Python Execution Node
add_llm_node(): Create an LLM Agent Node
add_logic_node(): Create an R Logic Node
dag_add_llm_node(): Add an LLM Agent Node directly to a DAG
dag_add_logic_node(): Add an R Logic Node directly to a DAG
standard_node_factory(): Standard Node Factory for Mermaid
auto_node_factory(): Automatic Node Factory for Mermaid-as-Source

Parallelism & Merge Harmonization

Infrastructure for isolated execution and conflict resolution.

WorktreeManager: Git Worktree Manager R6 Class
ConflictResolver: Git Conflict Resolver R6 Class
create_merge_harmonizer(): Create a Merge Harmonizer Node
RestrictedState: Restricted State R6 Class

LLM Drivers

Provider-agnostic interfaces for CLI-based and API-based LLMs.

AgentDriver: Agent Driver R6 Class
GeminiCLIDriver: Gemini CLI Driver R6 Class
GeminiAPIDriver: Gemini API Driver R6 Class
GeminiImageDriver: Gemini Image API Driver R6 Class
OpenAIAPIDriver: OpenAI API Driver
AnthropicAPIDriver: Anthropic API Driver
OllamaDriver: Ollama Driver R6 Class
AnthropicCLIDriver: Anthropic CLI Driver
CopilotCLIDriver: Copilot CLI Driver R6 Class
OpenAICodexCLIDriver: OpenAI Codex CLI Driver R6 Class

Dynamic Registry & Workflow Lifecycle

Tools for hot-swapping drivers, registering domain-specific logic, and spawning DAGs.

DriverRegistry: Driver Registry R6 Class
get_driver_registry(): Global Driver Registry Accessor
list_logic(): List Registered Components
get_logic(): Get Logic Function
register_logic(): Register Logic Function
get_agent_roles(): List Registered Roles
get_role(): Get an LLM Role (System Prompt)
register_role(): Register an LLM Role (System Prompt)
set_default_driver(): Set the Default Agent Driver
get_default_driver(): Get the Default Agent Driver
get_role_prompt(): Get a Role-specific System Prompt
resolve_default_driver(): <!– APAF Bioinformatics | factory.R | Approved | 2026-03-30 –> Resolve a Default Driver from Shorthand ID
spawn_dag(): Spawn an AgentDAG from a Workflow Object
load_workflow(): Load Multi-Agent Workflow from File

Messaging & Persistence

State persistence, inter-node messaging, and telemetry infrastructure.

MessageLog: Message Log Base R6 Class
MemoryMessageLog: Memory Message Log R6 Class
DuckDBMessageLog: DuckDB Message Log R6 Class
JSONLMessageLog: JSONL Message Log R6 Class
Checkpointer: Checkpointer Interface
MemorySaver: MemorySaver Checkpointer
DuckDBSaver: DuckDBSaver Checkpointer
RDSSaver: RDS File Checkpointer
init_bot_history(): Initialize Bot History DuckDB

Utilities & Parsing

Helper functions for mermaid visualization, validation, and maintenance.

AgentTool: Agent Tool R6 Class
dag_create(): Create an Agent Graph
parse_mermaid(): Parse Mermaid Flowchart Syntax
mermaid_to_dag(): Create AgentDAG from Mermaid
extract_r_code_advanced(): Extract R Code from LLM Response
is_named_list(): Check if an object is a named list
format_toolset(): Format Toolset for Prompt
reducer_merge_list(): Built-in Reducer: Merge List
reducer_append(): Built-in Reducer: Append
validate_workflow_file(): Validate Workflow File Syntax and Consistency
validate_workflow_full(): Validate HydraR Workflow Integration
render_workflow_file(): Render Workflow Diagram from File
cleanup_jules_branches(): Cleanup Stale GitHub Branches