{ "_id": "6a1efe79b401979e73419dd5", "Package": "putior", "Title": "Generate Workflow Diagrams from Code Annotations", "Version": "0.2.0", "Authors@R": "person(\"Philipp\", \"Thoss\", , \"ph.thoss@gmx.de\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4672-2792\"))", "Description": "Provides tools for extracting and processing structured\nannotations from source files in 30+ programming languages to\nfacilitate workflow visualization. The package scans source\nfiles for special 'PUT' annotations that define nodes,\nconnections, and metadata within a data processing workflow.\nSupports R, Python, SQL, JavaScript, TypeScript, Go, Rust,\nJava, and more with automatic comment syntax detection. These\nannotations can then be used to generate visual representations\nof data flows and processing steps across polyglot software\nenvironments. Builds on concepts from literate programming\nKnuth (1984) and utilizes directed\nacyclic graph (DAG) theory for workflow representation Foraita,\nSpallek, and Zeeb (2014) .\nDiagram generation powered by 'Mermaid' Sveidqvist (2014)\n.", "Language": "en-US", "License": "MIT + file LICENSE", "URL": "https://pjt222.github.io/putior/, https://github.com/pjt222/putior", "BugReports": "https://github.com/pjt222/putior/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Repository": "https://pjt222.r-universe.dev", "Date/Publication": "2026-03-19 11:44:49 UTC", "RemoteUrl": "https://github.com/pjt222/putior", "RemoteRef": "HEAD", "RemoteSha": "9cec4b6030630205f75c5e7b6024fb8345b91b8b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 09:44:03 UTC", "User": "root" }, "Author": "Philipp Thoss [aut, cre] (ORCID:\n)", "Maintainer": "Philipp Thoss ", "MD5sum": "8821356c71d14e78a6f72a3fc13dd3bf", "_user": "pjt222", "_type": "src", "_file": "putior_0.2.0.tar.gz", "_fileid": "a108168ae8ac6e67748b680670f62fab2c7ba7820e2ad00f1c99d37556e7970b", "_filesize": 1013114, "_sha256": "a108168ae8ac6e67748b680670f62fab2c7ba7820e2ad00f1c99d37556e7970b", "_created": "2026-05-18T09:44:03.000Z", "_published": "2026-06-02T16:02:01.603Z", "_distro": "noble", "_jobs": [ { "job": 79114831989, "time": 161, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7054534520" }, { "job": 79114831995, "time": 159, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7054534090" }, { "job": 79114831799, "time": 170, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7054525495" }, { "job": 79114830990, "time": 161, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7054519538" }, { "job": 79114830984, "time": 205, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7054476425" }, { "job": 79114830485, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7363074267" }, { "job": 79114832227, "time": 160, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7054534174" }, { "job": 79114831885, "time": 119, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7054519928" }, { "job": 79114831957, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7054519902" } ], "_buildurl": "https://github.com/r-universe/pjt222/actions/runs/26025661598", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/pjt222/putior", "_commit": { "id": "9cec4b6030630205f75c5e7b6024fb8345b91b8b", "author": "Philipp Thoss ", "committer": "Philipp Thoss ", "message": "feat: add dark mode toggle, align colors with agent-almanac/viz, add skill links\n\n- Enable bslib light-switch for light/dark/auto mode toggle in navbar\n- Dark mode Mermaid diagrams use agent-almanac/viz cyberpunk palette\n (deep bg #1a1a2e, cyan accent #00f0ff, light text #e0e0e8)\n- Mermaid JS re-renders diagrams on theme switch via MutationObserver\n- Dark mode CSS for inline code, tables, focus indicators, blockquotes\n- Add clickable GitHub links to all 6 agent-almanac skills in\n ai-integration.Rmd and inst/GUIDE.md\n- Fix blank line in api-reference.Rmd YAML frontmatter\n\nCo-Authored-By: Claude Opus 4.6 (1M context) \n", "time": 1773920689 }, "_maintainer": { "name": "Philipp Thoss", "email": "ph.thoss@gmx.de", "login": "pjt222", "linkedin": "in/philipp-thoss-148a2a1ab", "orcid": "0000-0002-4672-2792", "description": "AI Engineer · ML · DS · Chemist · Maille Artisan", "uuid": 47758568 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "tools", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": 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"_contributors": [ { "user": "pjt222", "count": 200, "uuid": 47758568 } ], "_userbio": { "uuid": 47758568, "type": "user", "name": "Philipp J. Thoss", "description": "AI Engineer · ML · DS · Chemist · Maille Artisan" }, "_downloads": { "count": 180, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/putior" }, "_devurl": "https://github.com/pjt222/putior", "_pkgdown": "https://pjt222.github.io/putior/", "_searchresults": 105, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/putior.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pjt222/putior", "_realowner": "pjt222", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2025-06-19" } ], "_exports": [ "ext_to_language", "get_comment_prefix", "get_detection_patterns", "get_diagram_themes", "get_supported_extensions", "is_valid_put_annotation", "list_supported_languages", "put", "put_auto", "put_diagram", "put_generate", "put_merge", "put_theme", "putior_acp_manifest", "putior_acp_server", "putior_guide", "putior_help", "putior_mcp_server", "putior_mcp_tools", "run_sandbox", "set_putior_log_level", "split_file_list" ], "_help": [ { "page": "ext_to_language", "title": "Get Language Name from File Extension", "concept": [ "language-support" ], "topics": [ "ext_to_language" ] }, { "page": "get_comment_prefix", "title": "Get Comment Prefix for File Extension", "concept": [ "language-support" ], "topics": [ "get_comment_prefix" ] }, { "page": "get_detection_patterns", "title": "Get Detection Patterns for a Language", "concept": [ "language-support" ], "topics": [ "get_detection_patterns" ] }, { "page": "get_diagram_themes", "title": "Get available themes for put_diagram", "concept": [ "utilities" ], "topics": [ "get_diagram_themes" ] }, { "page": "get_supported_extensions", "title": "Get All Supported File Extensions", "concept": [ "language-support" ], "topics": [ "get_supported_extensions" ] }, { "page": "is_valid_put_annotation", "title": "Validate PUT annotation syntax", "concept": [ "utilities" ], "topics": [ "is_valid_put_annotation" ] }, { "page": "list_supported_languages", "title": "List All Supported Languages", "concept": [ "language-support" ], "topics": [ "list_supported_languages" ] }, { "page": "print.putior_theme", "title": "Print a putior_theme Object", "concept": [ "core-workflow" ], "topics": [ "print.putior_theme" ] }, { "page": "print.putior_workflow", "title": "Print a putior workflow", "concept": [ "core-workflow" ], "topics": [ "print.putior_workflow" ] }, { "page": "put", "title": "Scan Source Files for PUT Annotations", "concept": [ "core-workflow" ], "topics": [ "put" ] }, { "page": "put_auto", "title": "Auto-Annotation Functions for putior", "concept": [ "auto-annotation" ], "topics": [ "put_auto" ] }, { "page": "put_diagram", "title": "Create Mermaid Diagram from PUT Workflow", "concept": [ "core-workflow" ], "topics": [ "put_diagram" ] }, { "page": "put_generate", "title": "Generate PUT Annotation Comments", "concept": [ "auto-annotation" ], "topics": [ "put_generate" ] }, { "page": "put_merge", "title": "Merge Manual and Auto-Detected Annotations", "concept": [ "auto-annotation" ], "topics": [ "put_merge" ] }, { "page": "put_theme", "title": "Create a Custom Theme Palette for Workflow Diagrams", "concept": [ "core-workflow" ], "topics": [ "put_theme" ] }, { "page": "putior_acp_manifest", "title": "Get putior ACP Agent Manifest", "concept": [ "integration" ], "topics": [ "putior_acp_manifest" ] }, { "page": "putior_acp_server", "title": "Start putior ACP Server", "concept": [ "integration" ], "topics": [ "putior_acp_server" ] }, { "page": "putior_guide", "title": "Access putior Guide for AI Assistants", "concept": [ "integration" ], "topics": [ "putior_guide" ] }, { "page": "putior_help", "title": "Quick Reference Help for putior", "concept": [ "integration" ], "topics": [ "putior_help" ] }, { "page": "putior_mcp_server", "title": "Start putior MCP Server", "concept": [ "integration" ], "topics": [ "putior_mcp_server" ] }, { "page": "putior_mcp_tools", "title": "Get putior MCP Tool Definitions", "concept": [ "integration" ], "topics": [ "putior_mcp_tools" ] }, { "page": "run_sandbox", "title": "Launch putior Interactive Sandbox", "concept": [ "interactive" ], "topics": [ "run_sandbox" ] }, { "page": "set_putior_log_level", "title": "Set putior Log Level", "concept": [ "interactive" ], "topics": [ "set_putior_log_level" ] }, { "page": "split_file_list", "title": "Split comma-separated file list", "concept": [ "utilities" ], "topics": [ "split_file_list" ] }, { "page": "summary.putior_workflow", "title": "Summarize a putior workflow", "concept": [ "core-workflow" ], "topics": [ "summary.putior_workflow" ] } ], "_pkglogo": "https://github.com/pjt222/putior/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/pjt222/putior/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "ai-integration.Rmd", "filename": "ai-integration.html", "title": "AI Integration Guide", "engine": "knitr::rmarkdown", "headings": [ "About This Vignette", "For Humans", "For AI Assistants", "Programmatic Access", "MCP/ACP Integration", "Agent-Almanac Integration", "Guide Documentation", "See Also" ], "created": "2026-03-19 09:56:30", "modified": "2026-03-19 11:44:49", "commits": 2 }, { "source": "annotation-guide.Rmd", "filename": "annotation-guide.html", "title": "Annotation Guide", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Annotation Basics", "Extracting Annotations", "Complete Syntax Reference", "Basic Format", "Flexible Syntax Options", "Multiline Annotations", "Multi-Language Support", "Block Comments", "Core Properties", "Standard Node Types", "Custom Properties", "Advanced Usage", "Processing Individual Files", "Recursive Directory Scanning", "Custom File Patterns", "Including Line Numbers", "Validation Control", "Automatic ID Generation", "Automatic Output Defaulting", "Tracking Source Relationships", "Variable References with .internal Extension", "Key Concepts", "Correct Usage Pattern", "What NOT to Do", "Complete Example", "Real-World Example", "1. 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Group Related Operations", "Troubleshooting", "See Also" ], "created": "2026-02-01 18:12:02", "modified": "2026-03-19 09:56:30", "commits": 11 }, { "source": "api-reference.Rmd", "filename": "api-reference.html", "title": "API Reference", "engine": "knitr::rmarkdown", "headings": [ "Function Overview", "Core Functions", "put() - Extract Annotations from Files", "put_diagram() - Generate Mermaid Diagrams", "Auto-Annotation Functions", "put_auto() - Auto-detect Workflow from Code", "put_generate() - Generate Annotation Comments", "put_merge() - Combine Manual and Auto Annotations", "Configuration Functions", "get_detection_patterns() - View Detection Patterns", "list_supported_languages() - List Supported Languages", "get_comment_prefix() - Get Comment Prefix for Extension", "get_supported_extensions() - List All Supported Extensions", "get_diagram_themes() - List Available Themes", "put_theme() - Create Custom Theme", "set_putior_log_level() - Configure Logging", "Utility Functions", "is_valid_put_annotation() - Validate Annotation Syntax", "split_file_list() - Parse File Lists", "run_sandbox() - Launch Interactive Sandbox", "Workflow Examples", "Basic Workflow", "Auto-Detection Pipeline", "Interactive Documentation", "Debugging", "See Also" ], "created": "2026-02-01 16:00:03", "modified": "2026-03-19 11:44:49", "commits": 12 }, { "source": "features-tour.Rmd", "filename": "features-tour.html", "title": "Features Tour", "engine": "knitr::rmarkdown", "headings": [ "Contents", "Feature Overview", "Auto-Annotation System", "Why Auto-Annotation?", "put_auto() - Detect Workflow Automatically", "put_generate() - Generate Annotation Comments", "put_merge() - Combine Manual + Auto", "Auto-Annotation Workflow", "Interactive Diagrams", "show_source_info - Display File Information", "enable_clicks - Clickable Nodes", "Detection Patterns", "get_detection_patterns() - View Patterns", "Supported Languages", "Pattern Categories", "Interactive Sandbox", "Launch the Sandbox", "Sandbox Features", "Sandbox Use Cases", "Debugging with Logging", "Enable Logging", "Log Levels", "Per-Call Override", "Debugging Scenarios", "Themes and Customization", "Available Themes", "Standard Themes", "Colorblind-Safe Themes (Viridis Family)", "Custom Palettes with put_theme()", "Theme Examples", "Styling Options", "Direction Options", "Performance", "Time Complexity", "Memory Usage", "Performance Benchmarks", "Tips for Large Codebases", "When Performance Matters", "Putting It All Together", "Complete Interactive Documentation Workflow", "Quick Visualization of Unknown Code", "Try the Examples", "See Also" ], "created": "2026-02-01 16:00:03", "modified": "2026-03-19 09:56:30", "commits": 12 }, { "source": "quick-reference.Rmd", "filename": "quick-reference.html", "title": "Quick Reference", "engine": "knitr::rmarkdown", "headings": [ "Quickest Start", "Annotation Syntax", "Comment Prefixes", "Core Functions", "Key Parameters", "Common Patterns", "Configuration & Utilities", "Themes and Direction", "Node Types", "See Also" ], "created": "2026-02-01 18:16:26", "modified": "2026-03-19 09:56:30", "commits": 9 }, { "source": "quick-start.Rmd", "filename": "quick-start.html", "title": "Quick Start", "engine": "knitr::rmarkdown", "headings": [ "Your First Diagram in 2 Minutes", "Step 1: Install", "Step 2: Add Annotations to Your Code", "Step 3: Generate Diagram", "Try It Now", "Annotation Syntax at a Glance", "Multi-Language Support", "Common Patterns", "Scan a Directory", "Include Subdirectories", "Auto-Detect Workflow (No Annotations!)", "Choose a Theme", "Save to File", "Interactive Sandbox", "Quick Reference", "See Also" ], "created": "2026-02-01 18:12:02", "modified": "2026-03-19 09:56:30", "commits": 10 }, { "source": "showcase.Rmd", "filename": "showcase.html", "title": "Showcase: Real-World Examples", "engine": "knitr::rmarkdown", "headings": [ "Small Workflows (3-5 nodes)", "Example: Simple ETL Pipeline", "Example: Report Generation", "Medium Workflows (10-15 nodes)", "Example: Machine Learning Pipeline", "Example: Multi-Source Data Integration", "Large Workflows (20+ nodes)", "Example: Complete Analytics Platform", "Multi-Language Workflows", "Language-Specific Comment Syntax", "JavaScript/TypeScript Example", "Go Example", "MATLAB Example", "Example: R + Python + SQL Pipeline", "Domain-Specific Examples", "Bioinformatics Pipeline", "Financial Analysis Pipeline", "Web Scraping Pipeline", "Multi-Language ML Pipeline", "Improving Existing Annotations", "Before: A Messy Starting Point", "Step-by-Step Improvement", "After: Clean Annotations", "Key Improvements Made", "Workflow for Legacy Code", "Tips for Large Workflows", "Try It Yourself", "See Also" ], "created": "2026-02-01 16:00:03", "modified": "2026-03-19 09:56:30", "commits": 8 }, { "source": "troubleshooting.Rmd", "filename": "troubleshooting.html", "title": "Troubleshooting Guide", "engine": "knitr::rmarkdown", "headings": [ "Contents", "Most Common Issues", "1. 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