pub-pipeline

Audit an R package against CRAN Repository Policy

Evaluate an R package against the JOSS reviewer checklist

Draft a JOSS paper (paper.md and paper.bib)

Publish a Python package to PyPI

Orchestrate the full R package publication pipeline

Reviews community and open-source practice against JOSS requirements: CONTRIBUTING.md, CODE_OF_CONDUCT.md, LICENSE, issue tracker accessibility, development history, and installation instructions. Lightweight audit focused on repository hygiene. Launched by the joss-reviewer orchestrator. <example> Context: Orchestrator needs community guidelines check. user: "Check if this repo has CONTRIBUTING and CODE_OF_CONDUCT" assistant: "I'll launch the community-auditor to check open-source practice requirements." </example> <example> Context: Package needs JOSS community requirements verified. user: "Does this repo meet JOSS community standards?" assistant: "I'll launch the community-auditor to evaluate community guidelines and repo hygiene." </example>

Searches for competing packages and related tools in the same domain as the package under review. Maps the "State of the Field" by finding CRAN/PyPI packages, GitHub projects, and published papers that address the same problem. Reports what each competitor does and what gap the reviewed package fills. Launched by the joss-writer or joss-reviewer orchestrator. <example> Context: Writer needs competing packages for State of the Field section. user: "Find competing R packages for survival analysis with hazard functions" assistant: "I'll launch the field-scout to map competing packages and identify gaps." </example> <example> Context: Reviewer needs to verify State of the Field completeness. user: "Are there packages missing from this paper's State of the Field?" assistant: "I'll launch the field-scout to find packages that should be mentioned." </example>

JOSS submission review orchestrator. Acts as a JOSS editor: reads the package and paper.md, spawns specialist auditors in parallel (software-auditor, community-auditor, field-scout), cross-verifies findings, and synthesizes a unified report against the JOSS reviewer checklist. Produces an actionable gap report with severity ratings and fix suggestions. <example> Context: User wants to check JOSS readiness before submitting. user: "Audit my package for JOSS submission" assistant: "I'll launch the joss-reviewer agent for a comprehensive JOSS readiness audit." </example> <example> Context: User has paper.md and wants it reviewed against JOSS standards. user: "Review my JOSS paper" assistant: "I'll launch the joss-reviewer agent to evaluate against the full JOSS checklist." </example>

JOSS paper drafting orchestrator. Reads the package source, README, vignettes, and existing manuscripts, spawns a field-scout to map competing packages, then drafts a complete paper.md and paper.bib following current JOSS format requirements (2025+). Produces publication-ready output with all required sections: Summary, Statement of Need, State of the Field, Software Design, Research Impact, AI Usage Disclosure, Acknowledgements, and References. <example> Context: User wants to draft a JOSS paper for their R package. user: "Draft a JOSS paper for flexhaz" assistant: "I'll launch the joss-writer agent to analyze the package and draft paper.md." </example> <example> Context: User has an existing manuscript to reshape into JOSS format. user: "Convert my paper to JOSS format" assistant: "I'll launch the joss-writer agent to reshape your manuscript into JOSS paper.md." </example>

Reviews software quality against JOSS functionality criteria: API design, documentation completeness, test coverage, CI/CD setup, installation, and error handling. Produces a structured findings report with severity ratings. Launched by the joss-reviewer orchestrator. <example> Context: Orchestrator needs software quality assessment. user: "Audit the software quality of this R package" assistant: "I'll launch the software-auditor to evaluate tests, docs, CI, and API design." </example> <example> Context: Package needs functionality verification before JOSS submission. user: "Does this package meet JOSS software requirements?" assistant: "I'll launch the software-auditor to check against JOSS functionality criteria." </example>

This skill should be used when the user asks to "audit for CRAN", "check CRAN readiness", "prepare for CRAN submission", "CRAN check", "is my package CRAN ready", "submit to CRAN", or mentions CRAN submission compliance. It audits an R package against CRAN Repository Policy and submission requirements, producing a structured gap report with actionable fixes.

This skill should be used when the user asks to "audit for JOSS", "check JOSS readiness", "JOSS reviewer checklist", "prepare for JOSS submission", "is my package JOSS ready", "JOSS requirements", or mentions JOSS submission compliance. It evaluates an R package and its paper.md against the complete JOSS reviewer checklist, producing a structured gap report.

This skill should be used when the user asks to "draft a JOSS paper", "write paper.md", "create JOSS paper", "write JOSS submission", "draft paper.md for JOSS", "convert paper to JOSS format", or mentions writing a JOSS software paper. It discovers existing manuscripts and package content, then drafts a complete paper.md and paper.bib following JOSS format requirements.

This skill should be used when the user asks to "publish my package", "publication pipeline", "get this published", "how do I publish this", or mentions publication without specifying an ecosystem. It detects the project type (R package or Python package) and routes to the appropriate ecosystem-specific publication skill.

This skill should be used when the user asks to "publish to PyPI", "upload to PyPI", "PyPI release", "publish my Python package", "package for PyPI", "submit to PyPI", "PyPI submission", or mentions PyPI publishing. It guides the complete workflow: auditing package metadata, running tests, building distributions, testing on TestPyPI, and publishing to PyPI.

This skill should be used when the user asks to "publish my R package", "R publication pipeline", "get this R package published", "CRAN and JOSS pipeline", "publish to CRAN and JOSS", or mentions an end-to-end R package publication workflow. It orchestrates the full CRAN → JOSS → (optionally JSS) publication pipeline for R packages, coordinating audits, paper drafting, and review cycles.