logmuse>=0.2.8
ubiquerg>=0.6.3
peppy>=0.40.7
requests>=2.31.0
botocore>=1.34.54
boto3>=1.34.54
genomicranges>=0.4.1
gtars>=0.1.1
pybiocfilecache>=0.6.0
zarr>=2.17.2
pyyaml>=6.0.1
s3fs>=2024.3.1
pyarrow>=17.0.0
iranges>=0.2.11
numpy>=1.24.0
rich>=13.9.4

[ml]
anndata>0.9.0
fastembed>=0.2.5
gensim>=4.3.3
huggingface_hub>=0.25.1
qdrant_client>=1.11.2
hnswlib>=0.8.0
paramiko>=3.0.0
pyBigWig>=0.3.23
scanpy>=1.10.3
torch>=2.3.0
lightning>=2.4.0
langchain-huggingface==0.0.2
hmmlearn>=0.3.2
scipy>=1.13.1

[test]
pytest
pytest-remotedata
pytest-mock
black
ruff
isort
