# put id:"complex_step", \
#     label:"Multi-step Process", \
#     input:"file1.csv, file2.csv", \
#     output:"combined.rds"

/**
 * put id:"handler", label:"Request Handler", input:"request.json", output:"response.json"
 */
function handleRequest(req, res) { ... }

-- query.sql
-- put id:"fetch", label:"Fetch Customers", output:"customers"
SELECT * FROM customers;

// transform.js
// put id:"process", label:"Transform JSON", input:"data.json", output:"output.json"
const result = data.map(transform);

% analysis.m
% put id:"stats", label:"Statistical Analysis", input:"data.mat", output:"results.mat"
results = compute_statistics(data);

# Scan directory for annotations
workflow <- put("./R/")

# Scan specific file
workflow <- put("./scripts/pipeline.R")

# Custom file pattern
workflow <- put("./src/", pattern = "\\.py$")

# Enable debug logging
workflow <- put("./R/", log_level = "DEBUG")

# Exclude test files
workflow <- put("./R/", exclude = "test")

# Basic diagram
put_diagram(workflow)

# Customize appearance
put_diagram(workflow,
  direction = "LR",           # Left-to-right (default: "TD", top-down)
  theme = "github",           # Theme: github, light, dark, auto, minimal
  show_artifacts = TRUE       # Show data files as nodes (script --> file --> script)
)
put_diagram(workflow, show_artifacts = TRUE, artifact_edges = "both")  # Also the direct edges

# Colorblind-safe themes (viridis family)
put_diagram(workflow, theme = "viridis")  # Purple-blue-green-yellow
put_diagram(workflow, theme = "magma")    # Warm: purple-red-yellow
put_diagram(workflow, theme = "plasma")   # Vibrant: purple-pink-yellow
put_diagram(workflow, theme = "cividis")  # Blue-yellow (max accessibility)

# Interactive features
put_diagram(workflow,
  enable_clicks = TRUE,       # Clickable nodes; need a renderer with securityLevel "loose" (not GitHub/GitLab/Quarto defaults)
  click_protocol = "vscode",  # vscode or file
  show_source_info = TRUE     # Show source file in nodes
)

# Output options
put_diagram(workflow, output = "clipboard")        # Copy to clipboard
put_diagram(workflow, output = "file", file = "workflow.md")  # Save to file
mermaid_code <- put_diagram(workflow, output = "raw")  # Return as string

# Mermaid configuration in the diagram's frontmatter
put_diagram(workflow, mermaid_config = "classic")  # Default: Mermaid 11's look, also on GitHub's Mermaid 12
put_diagram(workflow, mermaid_config = "none")     # No configuration
put_diagram(workflow, mermaid_config = list(look = "neo"))  # Your own; a theme key is left out

# Screen reader text: accTitle (from title) and accDescr (a summary) are on by default
put_diagram(workflow, title = "Sales Pipeline")
put_diagram(workflow, accessibility = FALSE)       # Leave them out

# Auto-detect from R files
workflow <- put_auto("./R/")

# Control what to detect
workflow <- put_auto("./src/",
  detect_inputs = TRUE,
  detect_outputs = TRUE,
  detect_dependencies = TRUE
)

# Combine with manual annotations
workflow <- put_merge("./src/", merge_strategy = "supplement")

# Exclude vendor/test directories
workflow <- put_auto("./src/", exclude = c("vendor", "test"))

# Print suggested annotations
put_generate("./R/")

# Copy to clipboard
put_generate("./R/", output = "clipboard")

# Multiline style
put_generate("./R/", style = "multiline")

# 1. Auto-generate annotation suggestions
put_generate("./R/", output = "clipboard")

# 2. Paste into source files and customize
# 3. Extract and visualize
workflow <- put("./R/")
put_diagram(workflow)

# Instant workflow diagram from code analysis
workflow <- put_auto("./src/")
put_diagram(workflow, show_artifacts = TRUE)

# Manual annotations for key files, auto-detect the rest
workflow <- put_merge("./src/", merge_strategy = "supplement")
put_diagram(workflow)

# Save Mermaid diagram to markdown file
put_diagram(workflow, output = "file", file = "docs/workflow.md")

# Get raw Mermaid code for embedding
mermaid_code <- put_diagram(workflow, output = "raw")