pyproject.toml

[tool.poetry]
name = "cellseg_models_pytorch"
version = "0.1.25"
description = "Python library for 2D cell/nuclei instance segmentation models written with PyTorch."
authors = ["Okunator <oskari.lehtonen@helsinki.fi>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/okunator/cellseg_models.pytorch"
repository = "https://github.com/okunator/cellseg_models.pytorch"
keywords = [
    "cell segmentation",
    "nuclei segmentation",
    "pytorch",
    "pytorch-lightning",
]

[tool.poetry.dependencies]
python = "^3.10"
numpy = "^1.24"
pathos = "^0.3.0"
timm = "^1.0.7"
numba = "^0.60.0"
torch = "2.1.1"
scipy = "^1.14"
scikit-image = "^0.24"
opencv-python = "^4.8"
tqdm = "^4.64.0"
scikit-learn = "^1.3.0"
lightning = "^2.3.0"
albumentations = "1.4.0"
tables = "^3.9.2"
requests = "^2.28.0"
geopandas = "^1.0.1"
pyarrow = "^16.1.0"

[tool.poetry.dev-dependencies]
pytest = "^7.2.0"
pytest-cov = "^3.0.0"
pytest-xdist = "^2.5.0"
flake8 = "^4.0.1"
flake8-docstrings = "^1.6.0"
flake8-bugbear = "^22.1.11"
pyproject-flake8 = "^4.0.1"
pre-commit = "^2.17.0"
matplotlib = "^3.5.1"
mypy = "^0.931"
isort = "^5.10.1"
black = "^22.3.0"

[tool.poetry.group.dev.dependencies]
scriv = { extras = ["toml"], version = "^0.16.0" }

[tool.scriv]
format = "md"
version = "literal: cellseg_models_pytorch/__init__.py: __version__"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra -v"
markers = ["cuda (deselect with '-m \"nocuda\"')"]

[tool.coverage.run]
source = ["cellseg_models_pytorch"]

[tool.coverage.report]
omit = ["*/tests/*", "*/__init__.py", "*/datamodules/*", "*/wandb_callbacks.py"]
exclude_lines = [
    "raise TypeError",
    "raise ImportError",
    "raise NotImplementedError",
    "raise ZeroDivisionError",
    "raise ValueError",
    "raise IOError",
    "except ImportError",
    "except TypeError",
    "except Exception",
    "def extra_repr",
]

[tool.ruff]
select = [
    "A",     # flake8-builtins
    "B",     # flake8-bugbear
    "D",     # pydocstyle, need to enable for docstrings check.
    "E",     # pycodestyle - Error
    "F",     # pyflakes
    "G",     # flake8-logging-format
    "I",     # Isort
    "N",     # pep8-naming
    "S",     # flake8-bandit
    "W",     # pycodestyle - Warning
    "Q",     # flake8-quotes
    "C4",    # flake8-comprehensions
    "FA",    # flake8-future-annotations
    "EM",    # flake8-errmsg
    "PD",    # pandas-vet
    "PL",    # Pylint
    "PT",    # flake8-pytest-style
    "TD",    # flake8-todos
    "UP",    # pyupgrade
    "C90",   # mccabe
    "T10",   # flake8-debugger
    "T20",   # flake8-print
    "ANN",   # flake8-annotations
    "ARG",   # flake8-unused-arguments
    "BLE",   # flake8-blind-except
    "COM",   # flake8-commas
    "DTZ",   # flake8-datetimez
    "ERA",   # eradicate
    "FBT",   # flake8-boolean-trap
    "FIX",   # flake8-fixme
    "FLY",   # flynt
    "ICN",   # flake8-import-conventions
    "INP",   # flake8-no-pep420
    "INT",   # flake8-gettext
    "ISC",   # flake8-implicit-str-concat
    "NPY",   # NumPy-specific rules
    "PGH",   # pygrep-hooks
    "PIE",   # flake8-pie
    "PTH",   # flake8-use-pathlib
    "PYI",   # flake8-pyi
    "RET",   # flake8-return
    "RSE",   # flake8-raise
    "RUF",   # Ruff-specific rules
    "SLF",   # flake8-self
    "SIM",   # flake8-simplify
    "TID",   # flake8-tidy-imports
    "TCH",   # flake8-type-checking
    "TRY",   # tryceratops
    "YTT",   # flake8-2020
    "PERF",  # Perflint
    "SLOT",  # flake8-slots
    "ASYNC", # flake8-async
]

include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
extend-include = ["*.ipynb"]
# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "conftest.py",
    "old",
    "test",
    "tests",
    "__pypackages__",
    "__pycache__",
    "_build",
    "docs",
    "source",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]

# Same as Black.
line-length = 88
indent-width = 4

# Assume Python 3.10
target-version = "py310"

[tool.ruff.pydocstyle]
 # Use numpy-style docstrings.
convention = "google"

[tool.ruff.lint]
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
select = ["E4", "E7", "E9", "F"]
ignore = ["E203", "D103", "D104", "E501"]

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = ["B"]

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

# format docs
docstring-code-format = true

# docstr code line length
# docstring-code-line-length = "dynamic"

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402"]
"**/{tests,docs,tools}/*" = ["E402"]

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