pyproject.toml

[build-system]
requires = ["flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "scSemiProfiler"
authors = [{name = "Jingtao Wang", email = "jingtao.wang@mail.mcgill.ca"}]
dynamic = ["version", "description"]
    dependencies = [
    'numpy== 1.26.2',
    'scanpy== 1.9.6',
    'scipy== 1.11.4',
    'anndata== 0.10.3',
    'faiss-cpu== 1.7.4',
    'torch== 1.12.1',
    'scikit-learn== 1.3.2',
    'pandas== 2.1.3',
    'jax== 0.4.19',
    'igraph==0.9.9',
    'gseapy==1.0.4',    
    'lightning==2.0.0',
    'lightning-cloud==0.5.55',
    'lightning-utilities==0.10.0',
    'pytorch-lightning==2.1.1',
    'scvi-tools== 1.0.4']

[project.optional-dependencies]
doc = [
    #"sphinx==7.1.2",
    "sphinx<4",
    "sphinx-rtd-theme==1.3.0rc1",
    "sphinx-copybutton",
    "nbsphinx",
    "sphinx-rtd-theme",
    "ipython",
    "jinja2<3.1",
    "prompt-toolkit<3.0.0",
    "sphinxcontrib-applehelp==1.0.1" ,
    #"sphinx_autodoc_typehints"
    "sphinx-autodoc-typehints<1.12",
    "sphinxcontrib_devhelp==1.0.2",
    "sphinxcontrib_htmlhelp==2.0.1",
    "sphinxcontrib-jquery==4.1",
    "sphinxcontrib-qthelp==1.0.3", 
    "sphinxcontrib-serializinghtml==1.1.5"
]