setuptools
pip
tqdm
thefuzz[speedup]
wasabi
spacy==3.7.5
torch==2.1.2
transformers==4.36.2
sentencepiece==0.1.99
protobuf==4.23.4
requests==2.31.0
pandas==2.3.1
text-processing-utils==0.0.0
quinex-utils==0.0.0

[api]
fastapi==0.110.1
uvicorn[standard]
pydantic==2.5.3

[dev]
pytest
snakemake==7.32.4
tensorboard==2.15.1
sentence-transformers==2.2.2
datasets==2.16.1
accelerate==0.25.0
evaluate==0.4.1
seqeval==1.2.2
scikit-learn==1.3.2
optuna==3.5.0
numpy==1.26.3

[optional]
pymongo
pymupdf
papermage

[paper_analysis]
fastapi==0.110.1
uvicorn[standard]
werkzeug==3.0.1
pydantic==2.5.3
streamlit==1.41.1
streamlit_agraph
networkx
pandas
numpy==1.26.3
lxml
beautifulsoup4
python-multipart==0.0.20

[plotting]
scipy==1.11.4
plotly==5.24.1
numpy==1.26.3
geopy==2.4.1
kaleido
