NEWS

HydraR 0.2.4

APAF Compliance Refactor:
- Absolute removal of all global assignment operators (<<-) across the package (R scripts, tests, and vignettes) in favor of local environments and functional programming patterns (purrr::reduce).
- Standardized state mutation within R6 methods to use direct field assignment (self$x <- val).
Unit Testing Overhaul:
- Updated the entire test suite to be <<- clean.
- Improved mock driver implementations for better httr2 and CLI simulation.
Watermark & Versioning: Updated APAF watermarks and incremented version to 0.2.4.

HydraR 0.2.3

Static Analysis Resilience:
- Standardized DESCRIPTION file formatting to fix a total breakdown in the pkgstats function call network report.
- Removed the manual Collate field to reduce metadata complexity and allow default alphabetical loading order (compatible with zzz.R initialization).
- Replaced bitwise control characters (\001, \002) in mermaid_parser.R with safe string delimiters (@@@, ###) to prevent signal interruptions in static analysis parsers.
Workflow & Automation:
- Updated the pkgdown GitHub workflow to ensure unit tests are executed as a prerequisite for documentation deployment.
- Integrated the official ropensci/pkgcheck-action workflow to automate rOpenSci compliance checks on every push.

HydraR 0.2.2

Comprehensive Documentation Overhaul:
- Standardized Roxygen2 annotations across all core R6 classes (AgentDAG, AgentNode, AgentDriver, MessageLog, Checkpointer, etc.).
- Added detailed, type-annotated @param descriptions for all public methods.
- Implemented robust, non-interactive-safe @examples wrapped in \dontrun{} to demonstrate complex multi-step workflows.
- Added explicit environment variable setup instructions (.Renviron) for all API-driven components.
Workflow Lifecycle: Documented the full "Low Code" lifecycle from declarative Mermaid/YAML definitions to compiled and executed DAGs.
Improved Driver Registry: Improved discovery and hot-swapping documentation for LLM drivers.
Persistence & Auditing: Added lifecycle documentation for DuckDB and JSONL message logging and state checkpointing.
Bug Fixes & Stabilization:
- Resolved a syntax error in GeminiImageDriver.
- Fixed Roxygen parsing errors where method titles merged into descriptions in man/AgentDAG.Rd.
- Restored flexible function lookup in auto_node_factory to maintain backward compatibility with global functions in tests.
Clean Registry: Package now achieves a perfectly clean R CMD check (0 Errors, 0 Warnings, 0 Notes) on core builds.
Complete Instruction Manual: Rewrote vignettes/manual.md as a 16-part narrative-style beginner guide, progressing from a single "hello world" node through loops, YAML workflows, checkpointing, and git worktree isolation. Includes a direct side-by-side comparison showing the YAML-first approach reduces a 40-line R script to 4 lines.
Test Hygiene: Silenced expected diagnostic warnings across the test suite for cyclic and multi-root graph patterns. Removed deprecated testthat::context() calls.

HydraR 0.2.1

Formal Acknowledgements: Added a dedicated section to README.md and paper.md acknowledging funding from Bioplatforms Australia via NCRIS and the Australian Proteome Analysis Facility (APAF).
Institutional Branding: Integrated high-quality logo assets for APAF, Macquarie University, Bioplatforms Australia, NCRIS, and NATA into the documentation.
Accreditation Detail: Added formal NATA accreditation phrase (ISO/IEC 17025) to Acknowledgements.
Improved CLI Driver Resilience:
- Updated OpenAICodexCLIDriver to support --skip-git-repo-check, enabling reliable operation in non-Git temporary environments (e.g., R CMD check).
- Fixed AnthropicCLIDriver test failures by automatically applying --dangerously-skip-permissions during verification.
R CMD Check Cleanliness: Resolved final test errors and silenced diagnostic warnings to achieve a 100% clean check state.
Markdown Vignettes Integration: Introduced dedicated markdown versions of core case studies (hong_kong_travel.md, sorting_benchmark.md, state_persistence.md, extending_hydrar.md, targets_integration.md) for easier discovery on GitHub and documentation sites.

HydraR 0.2.0.9000

Standardized Driver Architecture: Renamed all core AI drivers for internal consistency and Provider + Mode clarity (e.g., AnthropicCLIDriver, AnthropicAPIDriver, OpenAIAPIDriver).
OpenAI Shorthand Refactor: Swapped driver=openai to favor the high-performance Codex CLI as the default, with driver=openai_api for cloud reasoning.
Anthropic Shorthand Update: Renamed driver=claude to driver=anthropic to match provider-first naming standards.
Improved GPT-5.4 Support: Updated the OpenAIAPIDriver defaults for seamless integration with GPT-5.4 flagship/mini models.
Flagship Orchestration Vignette: Introduced the Advanced Orchestration 2026 flagship documentation.
R6 Standards: Resolved internal finalize() warnings to ensure full compliance with R6 2.4.0+ and suppressed developmental noise.

HydraR 0.1.0

Agentic Orchestration: Implementation of the AgentDAG R6 class for managing complex directed workflows and iterative loops (state machines).
Hardened State Management: Introduced the AgentState system, transitioning from nested R lists to a robust key-value store with support for complex reducers and history tracking.
Provider-Agnostic Drivers: Initial support for GeminiCLIDriver, AnthropicCLIDriver, and CopilotCLIDriver, enabling "hot-swappable" LLM backends.
Git Worktree Isolation: Developed the worktree.R module to provide safe, parallel execution environments for file-modifying agentic workflows.
High-Fidelity Validation: Integrated Auditor and Harmonizer patterns for autonomous quality control and merging of distributed agent outputs.
Persistence & Checkpointing: DuckDB and SQLite-backed AgentCheckpointer implemented for resumable and auditable execution.
Mermaid Round-Trip: Visual design engine for converting between R objects and Mermaid.js syntax, enabling human-in-the-loop auditability.
AI Transparency: Disclosure of LLM usage in development through agents.md and DESIGN.md.