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Changelog

Source: NEWS.md

picard 0.0.2

  • Split production and test mode for pipeline runs
  • Add better vignettes for using picard
  • bug fixes

picard 0.0.1

New Features

Core Study Management

  • UlyssesStudy: R6 class for comprehensive study repository configuration and initialization
  • StudyMeta: Metadata container for study information including title, therapeutic area, type, contributors, tags, and links
  • ExecutionSettings: Configuration class for managing execution environment and database connections
  • ExecOptions: Settings and database connection block management

Study Repository Initialization

  • Automatic R project creation and configuration
  • Git repository initialization with remote support
  • Standard directory structure creation for study artifacts
  • README, NEWS, and configuration file templating
  • Quarto documentation setup integration
  • Agent skills configuration for repository automation

Cohort Management

  • CohortDef: R6 class for defining cohorts with ATLAS specifications
  • CohortManifest: Management system for cohort collection with validation
  • Cohort JSON and SQL file organization
  • ATLAS cohort import and integration

Concept Set Management

  • ConceptSetDef: R6 class for defining concept sets
  • ConceptSetManifest: Management system for concept set collections
  • Concept set JSON file organization
  • ATLAS concept set import and integration

Study Execution

  • Study pipeline orchestration and execution
  • Task-based execution framework with status tracking
  • Pipeline export functionality
  • Result validation and cohort comparison tools

Data Processing

  • Cohort building with temporal and demographic subsetting
  • Union and complement cohort operations
  • Dissemination data preparation
  • Standard data type handling and formatting
  • Column name standardization

Configuration & Integration

  • DbConfigBlock: Database connection configuration for multiple databases
  • DBMS-specific settings (CDM schema, working schema, temp schema)
  • Configuration file generation and management
  • ATLAS connection setup
  • Contributor and team management

Utilities

  • Repository validation framework
  • Task history and execution tracking
  • Environment hash detection for dependency tracking
  • File and directory management utilities
  • Archive and export functionality