# SampleDisco core (CPU) dependencies.
# GPU acceleration is optional and environment/driver-specific: see
# requirements-gpu.txt and .claude/CLAUDE.md.
numpy>=1.23
pandas>=1.5
scipy>=1.9
scikit-learn>=1.2
scikit-misc>=0.3
statsmodels>=0.13
patsy>=0.5
scanpy>=1.11
anndata>=0.10
muon>=0.1
harmony-pytorch>=0.1
harmonypy>=0.0.9
scglue>=0.3
torch>=2.0
python-igraph>=0.10
leidenalg>=0.9
networkx>=3.0
POT>=0.9
pygam>=0.9
numba>=0.57
matplotlib>=3.6
seaborn>=0.12
pyyaml>=6.0
psutil>=5.9
ruamel.yaml>=0.17
pybedtools>=0.9

# multi-omics gene annotation (scGLUE path, imported at module top)
pyensembl>=2.3
# cluster-DGE (RAISIN) — both on the live downstream path
combat>=0.3
adjustText>=1.0
# NOTE: scGLUE must be installed from PyPI (`pip install scglue`), NOT bioconda —
# the bioconda recipe caps numpy<1.22 and breaks the rest of the stack.
