pyproject.toml

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.poetry]
name = "ome2024-ngff-challenge"
version = "0.0.0"
authors = [
  "Josh Moore <josh@openmicroscopy.org>",
  "Francois Sherwood <fsherwood@ebi.ac.uk>",
  "Will Moore <w.moore@dundee.ac.uk>",
  "Joost de Folter <folterj@gmail.com>",
  "Tom Boissonnet <tom.boissonnet@hhu.de>",
]
homepage = "https://github.com/ome/ome2024-ngff-challenge"
repository = "https://github.com/ome/ome2024-ngff-challenge"
license = "BSD-3-Clause"
description = "Tools for converting OME-Zarr data within the ome2024-ngff-challenge (see https://forum.image.sc/t/ome2024-ngff-challenge/97363)"
readme = "README.md"

classifiers = [
  "Development Status :: 1 - Planning",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "Operating System :: OS Independent",
  "Topic :: Scientific/Engineering",
  "Typing :: Typed",
]

[tool.poetry.dependencies]
python = "^3.10"
rocrate = "^0.10"
s3fs = ">=2024.6.1"
tensorstore = ">=0.1.63"
tqdm = "^4.66"
zarr = "3.0.0a0"

furo = { version = ">=2023.08.17", optional = true }
myst_parser = { version = ">=0.13", optional = true }
pytest = { version = ">=6", optional = true }
pytest-cov = { version = ">=3", optional = true }
sphinx = { version = ">=7.0", optional = true }
sphinx_copybutton = { version = ">=0.3.0", optional = true }
sphinx-autodoc-typehints = { version = "*", optional = true }

[tool.poetry.dev-dependencies]
ipython = "^8.22.2"
pytest = "^7.4.3"
pytest-mock = "^3.14.0"


[tool.poetry.extras]
test = ["pytest", "pytest-cov"]
dev = ["pytest", "pytest-cov"]
docs = [
  "furo",
  "myst_parser",
  "sphinx",
  "sphinx_autodoc_typehints",
  "sphinx_copybutton",
]

[tool.poetry-dynamic-versioning]
enable = true
substitution.files = ["src/ome2024_ngff_challenge/__init__.py"]

[tool.poetry.scripts]
ome2024-ngff-challenge = "ome2024_ngff_challenge:dispatch"

[tool.setuptools_scm]
write_to = "src/ome2024_ngff_challenge/_version.py"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [
  "error",
]
log_cli_level = "INFO"
testpaths = [
  "tests",
]

[tool.codespell]
ignore-words-list = 'crate,ome'

[tool.coverage]
run.source = ["ome2024_ngff_challenge"]
report.exclude_also = [
  '\.\.\.',
  'if typing.TYPE_CHECKING:',
]

[tool.mypy]
files = ["src", "tests"]
python_version = "3.10"
warn_unused_configs = true
strict = true
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
warn_unreachable = true
disallow_untyped_defs = false
disallow_incomplete_defs = false

[[tool.mypy.overrides]]
module = "ome2024_ngff_challenge.*"
disallow_untyped_defs = true
disallow_incomplete_defs = true


[tool.ruff]
src = ["src"]
target-version = "py38"

[tool.ruff.lint]
extend-select = [
  "B",        # flake8-bugbear
  "I",        # isort
  "ARG",      # flake8-unused-arguments
  "C4",       # flake8-comprehensions
  "EM",       # flake8-errmsg
  "ICN",      # flake8-import-conventions
  "G",        # flake8-logging-format
  "PGH",      # pygrep-hooks
  "PIE",      # flake8-pie
  "PL",       # pylint
  "PT",       # flake8-pytest-style
  "PTH",      # flake8-use-pathlib
  "RET",      # flake8-return
  "RUF",      # Ruff-specific
  "SIM",      # flake8-simplify
  "T20",      # flake8-print
  "UP",       # pyupgrade
  "YTT",      # flake8-2020
  "EXE",      # flake8-executable
  "NPY",      # NumPy specific rules
  "PD",       # pandas-vet
]
ignore = [
  "PLR09",    # Too many <...>
  "PLR2004",  # Magic value used in comparison
  "ISC001",   # Conflicts with formatter
  "G004",     # Logging statement with f-string
  "EM102",    # Exception must not use an f-string
]
isort.required-imports = ["from __future__ import annotations"]
# Uncomment if using a _compat.typing backport
# typing-modules = ["ome2024_ngff_challenge._compat.typing"]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20"]
"noxfile.py" = ["T20"]


[tool.pylint]
py-version = "3.10"
generated-members = "tensorstore.*"
ignore-paths = [".*/_version.py"]
reports.output-format = "colorized"
similarities.ignore-imports = "yes"
messages_control.disable = [
  "design",
  "fixme",
  "line-too-long",
  "missing-module-docstring",
  "missing-function-docstring",
  "wrong-import-position",
  # Added to get release out
  "broad-exception-caught",
  "broad-exception-raised",
  "consider-using-f-string",
  "consider-using-generator",
  "logging-fstring-interpolation",
  "missing-class-docstring",
  "no-member",
  "no-value-for-parameter",
  "super-init-not-called",
  "unsupported-assignment-operation",
]