pyproject.toml

[build-system]
requires = [
    "setuptools",
    "wheel",
    "setuptools_scm[toml]>=6.2",
]
build-backend = "setuptools.build_meta"

[project]
dependencies = [
    "numpy>=1.20",
    "ark-analysis>=0.6.0",
    "spektral>=1",
    "scikit-image>=0.16",
    "scikit-learn>=1.2.2",
    "tifffile>=2023",
    "tqdm>=4",
    "imgaug>=0.4.0",
    "opencv-python>=4.6",
    "toml",
    "seaborn>=0.12",
    "alpineer>=0.1.5",
    "natsort>=7.1",
    "tensorflow~=2.8.0",
    "tensorflow_addons~=0.16.1",
    "pydot>=1.4.2,<2",
    "protobuf",
    "wandb"
]
name = "cell_classification"
authors = [{ name = "Angelo Lab", email = "theangelolab@gmail.com" }]
description = "Cell classification tool for classifying cells into marker positive and negative for arbitrary markers."
readme = "README.md"
requires-python = ">=3.9"
license = { text = "Modified Apache License 2.0" }
classifiers = [
    "Development Status :: 4 - Beta",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "License :: OSI Approved :: Apache Software License",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Processing",
]
dynamic = ["version"]
urls = { repository = "https://github.com/angelolab/Nimbus" }

[project.optional-dependencies]
test = [
    "attrs",
    "coveralls[toml]",
    "pytest",
    "pytest-cases",
    "pytest-cov",
    "pytest-mock",
    "pytest-pycodestyle",
    "pytest-randomly",
]

[tool.setuptools_scm]
version_scheme = "release-branch-semver"
local_scheme = "no-local-version"

# Coverage
[tool.coverage.paths]
source = ["src", "*/site-packages"]

[tool.coverage.run]
branch = true
source = ["cell_classification"]

[tool.coverage.report]
exclude_lines = [
    "except ImportError",
    "raise AssertionError",
    "raise NotImplementedError",
]

# Pytest Options
[tool.pytest.ini_options]
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]
addopts = [
    "-v",
    "-s",
    "--durations=20",
    "--randomly-seed=42",
    "--randomly-dont-reorganize",
    "--cov=cell_classification",
    "--cov-report=lcov",
    "--pycodestyle",
]
console_output_style = "count"
testpaths = ["tests"]