Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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.