environment.yml

name: nih-grant-typst
channels:
  - conda-forge
  - bioconda
  - r
  - defaults
dependencies:
  # Python core
  - python=3.10
  - pip>=23.0

  # Python packages for reference formatting and data analysis
  - pandas>=2.0.0
  - numpy>=1.24.0
  - matplotlib>=3.7.0
  - seaborn>=0.12.0
  - regex>=2022.10.0
  - requests>=2.28.0
  - pathlib>=1.0.1

  # R and core packages
  - r-base>=4.2.0
  - r-essentials

  # R packages for data visualization and analysis
  - r-tidyverse>=2.0.0
  - r-ggplot2>=3.4.0
  - r-dplyr>=1.1.0
  - r-patchwork>=1.1.0
  - r-viridis>=0.6.0
  - r-scales>=1.2.0
  - r-knitr>=1.40
  - r-rmarkdown>=2.20

  # Document processing
  - pandoc>=3.1.0

  # Statistics and machine learning
  - r-lme4>=1.1.0
  - r-nlme>=3.1.0
  - r-broom>=1.0.0
  - r-car>=3.1.0
  - scikit-learn>=1.2.0

  # Bioinformatics
  - bioconductor-limma
  - bioconductor-deseq2
  - bioconductor-edger
  - r-pheatmap>=1.0.0

  # Additional dependencies
  - quarto>=1.3.0
  - jupyter>=1.0.0
  - pip:
      # Additional Python packages from PyPI
      - typst   # Typst compiler
      - bibtexparser>=1.4.0
      - pylatexenc
      - scholarly>=1.7.0  # For fetching citation data
      - pyparsing>=3.0.0
      - pygments>=2.15.0  # Syntax highlighting
      - pypst # Classes for typst
      - questionary

      # Development tools
      - black>=23.0.0     # Code formatting
      - pytest>=7.3.0     # Testing
      - ruff>=0.0.260     # Linting

# Variables to set
variables:
  # Set environment variables
  PYTHONPATH: ${CONDA_PREFIX}/lib/python3.10/site-packages
  R_LIBS_USER: ${CONDA_PREFIX}/lib/R/library