numpy>=1.20.0
pandas>=1.3.0
torch>=2.0.0
torchvision>=0.15.0
torchaudio>=2.0.0
transformers>=4.30.0
accelerate>=0.20.0
bitsandbytes>=0.40.0
scikit-image>=0.19.0
scipy>=1.7.0
matplotlib>=3.3.0
imageio>=2.9.0
tqdm>=4.60.0
Pillow>=9.0.0
opencv-python>=4.5.0
huggingface_hub>=0.16.0

[all]
honeybee-ml[clinical,database,models,molecular,pathology,radiology,visualization]

[clinical]
unstructured[image,pdf]>=0.10.0
pymupdf>=1.23.0
langchain-text-splitters>=0.3.0
pdf2image>=1.16.0
PyPDF2>=3.0.0
scispacy>=0.5.0
spacy>=3.5.0
fhir.resources>=7.0.0
hl7apy>=1.3.0
requests>=2.28.0
dateparser>=1.1.0
litellm>=1.0.0
pytesseract>=0.3.8

[clinical-full]
honeybee-ml[clinical]
medspacy>=1.0.0
medcat>=1.9.0

[database]
pymongo>=4.0.0

[dev]
pytest>=7.0.0
pytest-cov>=4.0.0
black>=23.0.0
ruff>=0.1.0
mypy>=1.0.0

[models]
timm>=0.9.0
onnxruntime>=1.15.0
peft>=0.5.0

[molecular]
pyarrow>=10.0.0
fastparquet>=2023.0.0

[pathology]
openslide-python>=1.2.0
colour-science>=0.4.0
albumentations>=1.3.0
cucim>=23.0.0
umap-learn>=0.5.0
scikit-learn>=1.0.0

[radiology]
SimpleITK>=2.2.0
monai>=1.0.0
torchio>=0.19.0
pydicom>=2.3.0
nibabel>=5.0.0
lungmask>=0.2.0
TotalSegmentator>=2.0.0
dipy>=1.7.0
intensity-normalization>=2.0.0
neuroCombat>=0.2.0
nnunetv2>=2.0

[visualization]
ipykernel>=6.0.0
ipywidgets>=8.0.0
