# medaka requirements. 
# Add comments to keep track of why we are using particular versions
# don't do these on the same line as CI likes to fiddle them occasionally
cffi
edlib
h5py
intervaltree
numpy>=2.0
ont-mappy
ont_fast5_api
ont-parasail
packaging
# 0.16.0 is broken, various others too
# 0.23.1-? is broken for test-coverage for py3.13: https://github.com/pysam-developers/pysam/issues/1350
pysam>=0.16.0.1,<=0.23.0
# 0.2.0 has `min_coverage` parameter
pyspoa>=0.2.1
requests
tensordict
toml
torch~=2.9
tqdm
wurlitzer
