pyproject.toml

[tool.poetry]
name = "scyan"
version = "1.6.2"
description = "Single-cell Cytometry Annotation Network"
documentation = "https://mics-lab.github.io/scyan/"
homepage = "https://mics-lab.github.io/scyan/"
repository = "https://github.com/MICS-Lab/scyan"
authors = ["Blampey Quentin <quentin.blampey@gmail.com>"]
license = "BSD-3-Clause"
readme = "README.md"
classifiers = [
  "License :: OSI Approved :: BSD License",
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: POSIX :: Linux",
  "Operating System :: Microsoft :: Windows",
  "Programming Language :: Python :: 3",
  "Topic :: Scientific/Engineering",
]
packages = [{ include = "scyan" }]

[tool.poetry.dependencies]
python = ">=3.8,<3.13"
anndata = ">=0.8.0"
torch = ">=1.13"
pytorch-lightning = ">=1.6.4"
seaborn = ">=0.12.2"
umap-learn = ">=0.5.3"
llvmlite = ">=0.38.1"
FlowUtils = ">=1.0.0"
fcsparser = ">=0.2.4"
fcswrite = ">=0.6.2"

wandb = { version = ">=0.13.7", optional = true }
hydra-core = { version = ">=1.2.0", optional = true }
hydra-colorlog = { version = ">=1.2.0", optional = true }
hydra-optuna-sweeper = { version = ">=1.2.0", optional = true }

pytest = { version = ">=7.1.2", optional = true }
ipykernel = { version = ">=6.15.0", optional = true }
ipywidgets = { version = ">=7.7.1", optional = true }
isort = { version = ">=5.10.1", optional = true }
black = { version = ">=22.6.0", optional = true }
mkdocs-material = { version = ">=8.5.0", optional = true }
mkdocstrings = { version = ">=0.19.0", optional = true }
mkdocstrings-python = { version = ">=0.7.1", optional = true }
mkdocs-jupyter = { version = ">=0.21.0", optional = true }

leidenalg = { version = ">=0.8.10", optional = true }

[tool.poetry.extras]
dev = [
  "pytest",
  "ipykernel",
  "ipywidgets",
  "isort",
  "black",
  "mkdocs-material",
  "mkdocstrings",
  "mkdocstrings-python",
  "mkdocs-jupyter",
]
hydra = ["wandb", "hydra-core", "hydra-colorlog", "hydra-optuna-sweeper"]
discovery = ["leidenalg"]

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"


[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = "test_*.py"
filterwarnings = [
  "ignore::DeprecationWarning",
  "ignore::UserWarning",
  "ignore:::.*anndata*",
]

[tool.black]
line-length = 90
include = '\.pyi?$'
exclude = '''
/(
      \.eggs         # exclude a few common directories in the
    | \.git          # root of the project
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
'''

[tool.isort]
profile = "black"
skip_glob = ["*/__init__.py"]