## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----setup--------------------------------------------------------------------
# library(putior)

## ----eval=FALSE---------------------------------------------------------------
# # Run the complete example
# source(system.file("examples", "reprex.R", package = "putior"))

## -----------------------------------------------------------------------------
# # Scan all R and Python files in a directory
# workflow <- put("./src/")
# 
# # View the extracted workflow
# print(workflow)

## ----echo=FALSE, eval=TRUE----------------------------------------------------
# Create example output for documentation
example_output <- data.frame(
  file_name = c("data_processing.R", "data_processing.R", "analysis.py"),
  file_type = c("r", "r", "py"),
  input = c(NA, "raw_data.csv", "clean_data.csv"),
  label = c("Load Customer Data", "Clean and Validate", "Sales Analysis"),
  id = c("load_data", "clean_data", "analyze_sales"),
  node_type = c("input", "process", "process"),
  output = c("raw_data.csv", "clean_data.csv", "sales_report.json"),
  stringsAsFactors = FALSE
)
print(example_output)

## -----------------------------------------------------------------------------
# # Process a single file
# workflow <- put("./scripts/analysis.R")

## -----------------------------------------------------------------------------
# # Search subdirectories recursively
# workflow <- put("./project/", recursive = TRUE)

## -----------------------------------------------------------------------------
# # Only R files
# workflow <- put("./src/", pattern = "\\.R$")
# 
# # R and SQL files only
# workflow <- put("./src/", pattern = "\\.(R|sql)$")
# 
# # All supported file types (default)
# workflow <- put("./src/", pattern = "\\.(R|r|py|sql|sh|jl)$")

## -----------------------------------------------------------------------------
# # Include line numbers for debugging
# workflow <- put("./src/", include_line_numbers = TRUE)

## -----------------------------------------------------------------------------
# # Enable validation (default) - provides helpful warnings
# workflow <- put("./src/", validate = TRUE)
# 
# # Disable validation warnings
# workflow <- put("./src/", validate = FALSE)

## -----------------------------------------------------------------------------
# # Annotations without explicit IDs get auto-generated UUIDs
# #put label:"Load Data", node_type:"input", output:"data.csv"
# #put label:"Process Data", node_type:"process", input:"data.csv", output:"clean.csv"
# 
# # Extract workflow - IDs will be auto-generated
# workflow <- put("./")
# print(workflow$id)  # Will show UUIDs like "a1b2c3d4-e5f6-7890-abcd-ef1234567890"

## -----------------------------------------------------------------------------
# # In process_data.R:
# #put label:"Process Step", node_type:"process", input:"raw.csv"
# # No output specified - will default to "process_data.R"
# 
# # In analyze_data.R:
# #put label:"Analyze", node_type:"process", input:"process_data.R", output:"results.csv"
# # This creates a connection from process_data.R to analyze_data.R

## -----------------------------------------------------------------------------
# # In main.R (sources other scripts):
# #put label:"Main Analysis", input:"load_data.R,process_data.R", output:"report.pdf"
# source("load_data.R")    # Reading load_data.R into main.R
# source("process_data.R") # Reading process_data.R into main.R
# 
# # In load_data.R (sourced by main.R):
# #put label:"Data Loader", node_type:"input"
# # output defaults to "load_data.R"
# 
# # In process_data.R (sourced by main.R, depends on load_data.R):
# #put label:"Data Processor", input:"load_data.R"
# # output defaults to "process_data.R"

## -----------------------------------------------------------------------------
# # Extract workflow from all files
# complete_workflow <- put("./sales_project/", recursive = TRUE)
# print(complete_workflow)

## -----------------------------------------------------------------------------
# # Test annotation syntax
# is_valid_put_annotation('#put name:"test", label:"Test Node"') # Should return TRUE
# is_valid_put_annotation("#put invalid syntax") # Should return FALSE
# 
# # Check what files are found
# list.files("./src/", pattern = "\\.(R|py)$")