Changes in version 0.2.0 (2025-11-11)                  

Major Update: Bioinformatics Focus

This release adds comprehensive support for bioinformatics and
computational biology workflows, with enhancements specifically designed
for NGS analysis, HPC environments, and large-scale data processing.

New Features - Critical for Bioinformatics

  - External Tool Version Tracking
    
      - track_external_tools(): Track versions of command-line tools
        (samtools, STAR, BWA, etc.)
      - get_tool_versions(): Retrieve tracked tool versions
      - Automatically detects and tracks 18+ common bioinformatics tools

  - Conda/Mamba Environment Support
    
      - track_conda_env(): Export and track conda environments
      - restore_conda_env(): Restore conda environments from YAML
      - get_conda_env_info(): Retrieve conda environment information
      - Full support for both conda and mamba

  - Reference Genome Tracking
    
      - track_reference_genome(): Track reference genomes, annotations,
        and indices
      - get_reference_info(): Retrieve reference genome information
      - list_reference_sources(): Display common reference genome
        sources
      - Tracks FASTA files, GTF/GFF annotations, and aligner indices
        (STAR, BWA, etc.)

New Features - High Priority

  - Large File Handling
    
      - Enhanced track_data() with smart checksumming for large files
        (>1GB)
      - xxHash64 support for 10-100x faster checksumming of BAM/FASTQ
        files
      - Metadata-based fingerprinting for very large files
      - Automatic algorithm selection based on file size

  - System Library Detection
    
      - capture_system_libraries(): Detect system library versions
      - Tracks libcurl, libxml2, BLAS/LAPACK implementations
      - Essential for documenting system dependencies

  - Hardware Information Capture
    
      - capture_hardware(): Capture CPU, RAM, and GPU specifications
      - NVIDIA GPU detection via nvidia-smi
      - Cross-platform support (Linux, macOS, Windows)
      - Essential for HPC job documentation

New Features - Containerization & HPC

  - Singularity/Apptainer Support
      - generate_singularity(): Generate Singularity definition files
      - Full support for HPC environments where Docker is unavailable
      - Automatic build script generation
      - Conda environment integration

New Features - Pipeline Integration

  - Workflow Manager Integration
      - export_for_nextflow(): Export data for Nextflow pipelines
      - export_for_snakemake(): Export data for Snakemake workflows
      - export_for_wdl(): Export data for WDL workflows
      - export_for_cwl(): Export data for CWL workflows
      - Seamless integration with major workflow managers

New Features - Snapshot Management

  - Snapshot Comparison
      - compare_snapshots(): Compare two workflow snapshots
      - list_snapshots(): List all available snapshots with metadata
      - Detailed diff reports showing package, parameter, and data
        changes
      - Markdown report generation

Enhancements

  - Updated DESCRIPTION with bioinformatics focus
  - Enhanced documentation with bioinformatics examples
  - Improved error handling and user feedback
  - Better cross-platform compatibility
  - Added utils to imports for better compatibility

Bug Fixes

  - Fixed issue with checksum verification for legacy tracked files
  - Improved handling of missing files in verification
  - Better error messages for conda/mamba detection

                        Changes in version 0.1.0                        

Initial Release

Features

  - Session Tracking: Comprehensive R session information capture
    
      - capture_session(): Capture R version, platform, and system info
      - capture_environment(): Capture global environment state

  - Package Management: Complete package version tracking
    
      - snapshot_packages(): Create detailed package manifests
      - create_renv_lockfile(): Generate renv lockfiles
      - Automatic dependency graph creation

  - Data Provenance: Track data files with integrity verification
    
      - track_data(): Record data source, checksums, and metadata
      - verify_data(): Verify data integrity via SHA-256 checksums
      - get_data_lineage(): Retrieve complete data provenance

  - Parameter Tracking: Document analysis parameters
    
      - track_params(): Store analysis parameters with metadata
      - get_param_history(): Retrieve parameter history

  - Random Seed Management: Reproducible random number generation
    
      - set_seed(): Set and track random seeds
      - restore_seed(): Restore previously tracked seeds
      - Complete RNG state tracking

  - Script Generation: Create reproducible analysis scripts
    
      - generate_repro_script(): Generate executable R scripts
      - create_repro_report(): Generate markdown reports
      - Automatic integration of all tracked components

  - Docker Support: Containerization for perfect reproducibility
    
      - generate_docker(): Generate Dockerfile and docker-compose.yml
      - RStudio Server support
      - Automatic system dependency configuration

  - Workflow Management: Complete workflow orchestration
    
      - init_capsule(): Initialize Capsule in projects
      - snapshot_workflow(): Create complete workflow snapshots
      - Automatic artifact generation

Documentation

  - Comprehensive README with quick start guide
  - Complete function documentation with examples
  - Example workflow demonstrating all features
  - Docker usage instructions

Infrastructure

  - MIT License
  - Complete test suite
  - Package structure following R best practices