emb-explorer/pyproject.toml at main · Imageomics/emb-explorer · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "emb-explorer"
version = "1.0.0"
description = "Image clustering tool using embeddings with Streamlit interface"
readme = "README.md"
license = {file = "LICENSE"}
authors = [
    { name = "Net Zhang", email = "zhang.11091@osu.edu" },
    { name = "Elizabeth G. Campolongo", email = "e.campolongo479@gmail.com" },
    { name = "Matthew J. Thompson", email = "thompson.m.j@outlook.com" },
    { name = "Sreejith Menon", email = "sreejithmenon@google.com" },
    { name = "Jianyang Gu", email = "gu.1220@osu.edu" },
    { name = "Arnab Nandi", email = "nandi.9@osu.edu" }
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Multimedia :: Graphics",
]
requires-python = ">=3.10,<3.14"
dependencies = [
    # Core UI and web framework
    "streamlit>=1.50.0",
    # Data processing and numerical computing
    "numpy<2.3",  # capped: numba 0.61.x requires numpy <2.3
    "pandas>=2.0.0",
    "pillow>=9.0.0",
    "pyarrow>=10.0.0",
    # Visualization
    "altair>=5.0.0",
    # Machine learning
    "scikit-learn>=1.0.0",
    # Intel oneDAL acceleration for sklearn (PCA / TSNE / KMeans) auto-patched at runtime.
    # Disable with EMB_EXPLORER_DISABLE_SKLEARNEX=1 if you need vanilla sklearn behavior for debugging.
    "scikit-learn-intelex>=2025.0; platform_machine == 'AMD64' or platform_machine == 'x86_64'",
    "umap-learn>=0.5.0",
    "numba>=0.57.0",
    # Vision-language models
    "open-clip-torch>=2.20.0",
    # Image embedding pipeline (used directly in shared/utils/image_pipeline.py)
    "torch>=1.11.0",
]

[project.optional-dependencies]
dev = [
    "jupyter>=1.0.0",
    "notebook>=6.0.0",
    "ipykernel>=6.0.0",
    "pytest>=7.0.0",
    "black>=22.0.0",
    "flake8>=4.0.0",
    "mypy>=0.950",
]
# GPU acceleration — pick the extra matching your system CUDA version:
#   pip install -e ".[gpu-cu12]"   # CUDA 12.x (e.g. OSC Pitzer)
#   pip install -e ".[gpu-cu13]"   # CUDA 13.x
# "gpu" is an alias for gpu-cu12 (most common HPC setup).
gpu = [
    "emb-explorer[gpu-cu12]",
]
# cuML pins use PEP 440 normalization of RAPIDS CalVer: 26.8 == cuML 26.08.
gpu-cu12 = [
    "torch>=2.0.0",
    "cuml-cu12>=26.8",
    "pynvml>=11.0.0",
]
gpu-cu13 = [
    "torch>=2.0.0",
    "cuml-cu13>=26.8",
    "pynvml>=11.0.0",
]
# Minimal GPU support for image embeddings generation (just PyTorch, no RAPIDS)
gpu-minimal = [
    "torch>=2.0.0",
]
all = [
    "emb-explorer[dev,gpu]",
]

[project.urls]
Homepage = "https://github.com/Imageomics/emb-explorer"
Repository = "https://github.com/Imageomics/emb-explorer"
Issues = "https://github.com/Imageomics/emb-explorer/issues"

[project.scripts]
emb-embed-explore = "apps.embed_explore.app:main"
emb-precalculated = "apps.precalculated.app:main"
list-models = "shared.utils.models:print_available_models"

[tool.hatch.version]
path = "shared/__init__.py"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.wheel]
packages = ["shared", "apps"]

[tool.hatch.build.targets.sdist]
include = [
    "/shared",
    "/apps",
    "/README.md",
    "/LICENSE",
]

[tool.black]
line-length = 88
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'
extend-exclude = '''
/(
  __pycache__
| \.git
| \.mypy_cache
| \.pytest_cache
| \.venv
| _build
| build
| dist
)/
'''

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = "-v --tb=short"
markers = ["gpu: requires GPU hardware (deselect with '-m not gpu')"]