Package: HydraR
Type: Package
Title: Stateful Agentic Orchestration for Scientific Reproducibility
Version: 0.2.4
Authors@R: c(person(given = c("Chi", "Nam", "Ignatius"), family =
        "Pang", role = c("aut", "cre"), email =
        "ignatius.pang@mq.edu.au", comment = c(ORCID =
        "0000-0001-9703-5741")), person(given = "Aidan", family =
        "Tay", role = "aut", comment = c(ORCID =
        "0000-0003-1315-4896")), person(given = c("APAF", "Agentic"),
        family = "Workflow", role = "ctb"))
Description: A high-performance framework for orchestrating complex
        agentic workflows in R, specifically designed for scientific
        reproducibility and auditability. HydraR provides a robust,
        state-managed engine for Directed Acyclic Graphs (DAGs) and
        iterative state machines, prioritizing CLI-native LLM
        interactions (e.g., Gemini, Claude, Copilot) and hardened state
        persistence (DuckDB/SQLite). It features isolated execution via
        Git Worktrees for parallel file-modifying tasks, autonomous
        quality control through integrated auditors, and human-readable
        visualization using Mermaid.js. Ideal for creating auditable,
        resumable research assistants and complex bioinformatics
        pipelines.
URL: https://github.com/APAF-bioinformatics/HydraR,
        https://APAF-bioinformatics.github.io/HydraR/
BugReports: https://github.com/APAF-bioinformatics/HydraR/issues
License: LGPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: R (>= 4.1.0)
Imports: uuid, DBI, digest, furrr, igraph, jsonlite, purrr, R6, yaml,
        httr2, base64enc
Suggests: testthat (>= 3.0.0), duckdb, knitr, rmarkdown, future,
        devtools, withr, reticulate, DiagrammeR, ggplot2,
        DiagrammeRsvg, lintr, rsvg, mockery, RSQLite, htmltools
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'checkpointer.R' 'dag.R' 'driver.R' 'driver_registry.R'
        'drivers_api.R' 'drivers_cli.R' 'factory.R' 'git_cleanup.R'
        'init_duckdb.R' 'logic_node.R' 'map_node.R'
        'merge_harmonizer.R' 'mermaid_parser.R' 'message_log.R'
        'node.R' 'node_languages.R' 'node_llm.R' 'observer_node.R'
        'registry.R' 'router_node.R' 'state.R' 'state_restricted.R'
        'tools.R' 'utils.R' 'validation.R' 'worktree.R' 'zzz.R'
Config/pak/sysreqs: libglpk-dev libxml2-dev libssl-dev
Repository: https://ropensci-staging.r-universe.dev
Date/Publication: 2026-04-23 14:30:55 UTC
RemoteUrl: https://github.com/APAF-bioinformatics/HydraR
RemoteRef: HEAD
RemoteSha: ceb3c632cd464cf6ea6c5c6b078d713b47af5ca0
NeedsCompilation: no
Packaged: 2026-10-17 08:36:01 UTC; root
Author: Chi Nam Ignatius Pang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9703-5741>),
  Aidan Tay [aut] (ORCID: <https://orcid.org/0000-0003-1315-4896>),
  APAF Agentic Workflow [ctb]
Maintainer: Chi Nam Ignatius Pang <ignatius.pang@mq.edu.au>