# Essential to run pipeline
click<=8.2.0
cookiecutter<=2.1.1
loguru<=0.7.2
more-itertools
numpy<=1.26.4
pandas<=2.1.2
PuLP<2.8.0
pyranges<=0.1.2
snakemake_wrapper_utils
snakemake<=7.32.4

# Essential for CLI
capcruncher-tools>=0.2.0
cooler<=0.10.3
h5py
ibis-framework[duckdb]>6.1.0,<=8.0.0
multiqc
matplotlib>=3.8.4,<3.9.0
pandera<=0.22.1
panel<=1.3.0
papermill
plotly>5.0.0,<=5.18.0
polars<=1.27.1
protobuf<=6.30.2
pyarrow>11.0.0,<19.0.1
pybedtools<=0.9.1
pydantic>2.4.0,<2.11.0
pydeseq2<=0.5.0
pysam>0.15.0,<=0.21.0
quarto
ray>=2.8.0
seaborn<=0.12.2
toml
tqdm<=4.65.0
trackhub<=0.2.4
tracknado
ujson<=5.8.0
xopen
xxhash<=3.4.1