environment.yml

name: raptor
channels:
  - conda-forge
  - defaults

dependencies:
  # ==========================================================================
  # Python - v2.2.1 supports Python 3.8-3.12
  # ==========================================================================
  - python>=3.8,<3.13
  
  # ==========================================================================
  # Core Scientific Computing
  # ==========================================================================
  - numpy>=1.19.0
  - pandas>=1.1.0
  - scipy>=1.5.0
  - scikit-learn>=0.24.0
  - joblib>=1.0.0
  
  # ==========================================================================
  # Visualization
  # ==========================================================================
  - matplotlib>=3.3.0
  - seaborn>=0.11.0
  - plotly>=5.0.0
  
  # ==========================================================================
  # Statistics
  # ==========================================================================
  - statsmodels>=0.12.0
  
  # ==========================================================================
  # Configuration Management
  # ==========================================================================
  - pyyaml>=5.3.0
  - toml>=0.10.0              # NEW in v2.2.0 - TOML config support
  
  # ==========================================================================
  # CLI and Utilities
  # ==========================================================================
  - click>=7.0
  - colorama>=0.4.0
  - tqdm>=4.50.0
  
  # ==========================================================================
  # Optional: Dashboard (comment out if not needed)
  # ==========================================================================
  - streamlit>=1.20.0
  - altair>=4.0.0
  
  # ==========================================================================
  # Optional: Development Tools (comment out for production)
  # ==========================================================================
  # - pytest>=6.0.0
  # - pytest-cov>=2.10.0
  # - pytest-mock>=3.6.0
  # - black>=21.0
  # - flake8>=3.8.0
  # - isort>=5.0.0
  # - mypy>=0.900
  
  # ==========================================================================
  # Optional: Documentation (comment out if not building docs)
  # ==========================================================================
  # - sphinx>=3.5.0
  # - sphinx_rtd_theme>=0.5.0
  # - myst-parser>=0.15.0
  
  # ==========================================================================
  # Pip packages and RAPTOR installation
  # ==========================================================================
  - pip
  - pip:
    # Install RAPTOR from PyPI
    - raptor-rnaseq>=2.2.1
    
    # Optional: Advanced features (uncomment if needed)
    # - bayesian-optimization>=1.2.0   # Bayesian optimization for Module 8
    # - jinja2>=3.0.0                  # PDF report generation
    # - markdown>=3.3.0                # PDF report generation
    # - psutil>=5.8.0                  # Resource monitoring
    # - colorlog>=6.6.0                # Colored logging


# =============================================================================
# USAGE INSTRUCTIONS
# =============================================================================

# Create environment:
#   conda env create -f environment.yml

# Activate environment:
#   conda activate raptor

# Update environment:
#   conda env update -f environment.yml --prune

# Remove environment:
#   conda env remove -n raptor

# Export current environment:
#   conda env export > environment-current.yml


# =============================================================================
# NOTES
# =============================================================================

# This is the CORE environment for RAPTOR Python package only.
# 
# Does NOT include:
#   - Bioinformatics tools (STAR, Salmon, Kallisto, etc.)
#   - R packages (DESeq2, edgeR, limma)
#   - Development tools (by default)
#   - Documentation tools (by default)
#
# For full bioinformatics environment, see: environment-full.yml
#
# External tools required for pipelines (install separately):
#   - STAR, HISAT2, Salmon, Kallisto (for alignment/quantification)
#   - Samtools, featureCounts, RSEM (for post-processing)
#   - R with DESeq2, edgeR, limma (for differential expression)
#
# Install R packages:
#   Rscript raptor/external_modules/module6_de_analysis/r_scripts/install_packages.R