# general requirements
ont-bonito==1.0.0
torch==2.9.1
sageattention==1.0.6
torchaudio==2.9.1
torchvision==0.24.1
ont-koi==0.6.5
Cython==3.2.9
setuptools==77.0.3
numpy==1.23.5
pyranges==0.1.4
pybigwig==0.3.25
pyfaidx==0.9.0.4
torchmetrics==1.9.0
mappy
fitter==1.7.1
gtfparse==2.0.1
pyslow5==1.3.1
blue-crab==0.4.0
toml==0.10.2
tqdm>4,<5
scipy==1.14.1
pysam==0.21.0
parasail==1.3.4
pandas==1.5.3
requests~=2.32.2
ont-fast5-api==4.1.3
fast-ctc-decode==0.3.5
python-dateutil==2.8.2
pytorch-ranger==0.1.1
dtaidistance==2.3.11
torch_pruning==1.3.7
ruptures==1.1.9
tslearn==0.6.3
patchworklib==0.6.3
plotnine==0.12.4
matplotlib==3.10.8
seaborn==0.13.2
biopython==1.86
igv==0.9.6
deap==1.4.1
tabulate==0.9.0
onnx-simplifier==0.4.36
#onnx==0.16.1
onnx2torch==1.5.14
onnxconverter-common==1.14.0
onnxmltools==1.12.0
onnxruntime-gpu==1.22.0
onnxscript==0.5.1
memory-efficient-attention-pytorch==0.1.6
edlib==1.3.9
ont-remora==3.3.0
rotary-embedding-torch==0.8.3
debugpy==1.8.8
statsmodels
transformers
uncalled4
lhotse
nltk==3.9.1
muon_optimizer==0.1.0
accelerate
flashlight==0.1.1
flashlight-text==0.0.7
pyabf
hyperopt
tensorboard
#flashligth-text
#pip install sageattention==1.0.6 --no-build-isolation
#pip install https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/v0.9.0/flash_attn-2.8.3+cu128torch2.9-cp310-cp310-linux_x86_64.whl
#wget https://hf-mirror.com/csukuangfj/k2/resolve/main/ubuntu-cuda/1.24.4.dev20241029/k2-1.24.4.dev20241030+cuda12.4.torch2.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#pip install ./k2-1.24.4.dev20241030+cuda12.1.torch2.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#TMPDIR=./tmp pip install torch-tensorrt==2.9.0 --no-deps --extra-index-url https://download.pytorch.org/whl/cu128
#TMPDIR=./tmp pip install tensorrt-cu12-libs==10.13.3.9 --extra-index-url https://pypi.nvidia.com/
#TMPDIR=./tmp pip install torch-tensorrt==2.9.0 tensorrt-cu12 --extra-index-url https://download.pytorch.org/whl/cu128