environment.lock.yml

# WASP2 Runtime Environment
# Source of truth for reproducible installs (conda-lock target)
# Build deps (rust, libclang, clang, maturin) excluded — only needed to compile
name: WASP2
channels:
  - bioconda
  - conda-forge

# plink2 and all bioconda bio tools only support linux-64 and osx-64
# (not osx-arm64, linux-aarch64, or win-64)
platforms:
  - linux-64
  - osx-64

dependencies:
  # Core Python
  - python=3.11.*

  # Data processing
  - numpy>=1.21,<2.0
  - pandas>=1.5,<3.0
  - polars>=0.19
  - scipy>=1.10

  # Bioinformatics (bioconda)
  - pysam>=0.21
  - pybedtools>=0.9
  - bedtools>=2.30
  - bcftools>=1.10
  - samtools>=1.10
  - htslib>=1.10
  - bwa>=0.7
  - anndata>=0.8,<0.12
  - scanpy>=1.9
  - plink2

  # CLI
  - typer>=0.12
  - rich>=13.0
  - typing_extensions

  # Dev
  - pytest>=7.0
  - pytest-cov>=4.0
  - mypy>=1.0
  - ruff>=0.9

  # Pip-only runtime deps
  - pip
  - pip:
    - Pgenlib>=0.90