pyproject.toml

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "eitprocessing"
version = "1.4.5"
description = "Processing of lung image data from electrical impedance tomography."
readme = "README.md"
requires-python = ">=3.10"
keywords = [
    "Mechanical lung ventilation",
    "Electrical impedance tomography",
    "Image/data processing",
    "Advanced respiratory care",
]
authors = [
    { name = "Dani Bodor", email = "d.bodor@esciencecenter.nl" },
    { name = "Peter Somhorst", email = "p.somhorst@erasmusmc.nl" },
    { name = "Annemijn Jonkman", email= "a.jonkman@erasmusmc.nl"}, 
    { name = "Walter Baccinelli", email = "w.baccinelli@esciencecenter.nl" },
    { name = "Jantine Wisse-Smit", email = "j.j.smit@erasmusmc.nl"},
    { name = "Juliette Francovich", email = "j.francovich@erasmusmc.nl"}
]
license = { text = "Apache-2.0 license" }
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Apache Software License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
dependencies = [
    "matplotlib >= 3.7.1",
    "numpy >= 1.24.2",
    "scipy >= 1.10.1",
    "strenum >= 0.4.10",
    "anytree >= 2.12.1 ",
    "typing_extensions",
    "pyyaml",
]

[project.optional-dependencies]
# development dependency groups
dev = [
    "pytest >= 7.4.0",
    "bump-my-version",
    "coverage",
    "pytest-cov",
    "coveralls",
    "ruff == 0.6.9",
]
testing = [
    "pytest >= 7.4.0",
    "pytest-cov",
    "coveralls",
]
docs = [
    "mkdocs",
    "mkdocs-material",
    "mkdocstrings",
    "mkdocstrings-python",
    "mkdocs-exclude",
    "mike",
    "pymdown-extensions",
    "black",
]
notebooks = [
    "jupyter >= 1.0.0",
    "jupytext >= 1.14.5",
    "tqdm >= 4.65.0",
    "ipympl"
]
publishing = ["build"]

[project.urls]
Documentation = "https://github.com/EIT-ALIVE/eitprocessing/blob/main/README.md"
Repository = "https://github.com/EIT-ALIVE/eitprocessing/"
Changelog = "https://github.com/EIT-ALIVE/eitprocessing/blob/main/CHANGELOG.md"

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.coverage.run]
branch = true
source = ["eitprocessing"]
command_line = "-m pytest"

[tool.coverage.report]
exclude_lines = ["if TYPE_CHECKING:"]

[tool.setuptools.packages.find]
include = ["eitprocessing*", "eitprocessing.*"]
exclude = ["tests*", "*tests.*", "*tests"]

[tool.setuptools.package-data]
eitprocessing = ["config/*.yaml", "py.typed"]

[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py37,py38,py39,py310,py311
skip_missing_interpreters = true
[testenv]
commands = pytest
extras = dev
"""

[tool.ruff]
output-format = "concise"
line-length = 120

[tool.ruff.lint]
select = ["ALL"]
pydocstyle.convention = "google" # docstring settings
ignore = [
    # Unwanted (potentially)
    "FBT",    # Using boolean arguments
    "ANN002", # Missing type annotation for `*args`
    "ANN003", # Missing type annotation for `**kwargs`
    "ANN101", # Missing type annotation for `self` in method
    "ANN102", # Missing type annotation for `cls` in classmethod
    "ANN204", # Missing return type annotation for special (dunder) method
    "S105",   # Possible hardcoded password
    "S311",   # insecure random generators
    "PT011",  # pytest-raises-too-broad
    "PD011",  # Use of .values. Assumes .values refers to pandas dataframes, not object attributes
    "TD",     # TODOs
    "FIX002", # Resolve TODOs
    "B028",   # No explicit `stacklevel` keyword argument found in warning
    # "SIM108", # Use ternary operator (not sure if we want to ignore this)
    # Unneeded docstrings
    "D100",   # Missing module docstring
    "D104",   # Missing public package docstring
    "D105",   # Missing docstring in magic method
    "D107",   # Missing docstring in `__init__`
    "COM812", # missing trailing comma
    "ISC001", # single line implicit string concatenation
]

# Set autofixing.
fixable = ["ALL"]
unfixable = [
    "F401",   # unused imports (should not disappear while editing)
    "RUF100", # unused noqa (should not disappear while editing)
    "B905",   # autofill strictness of zip (think about preferred behavior)
]
extend-safe-fixes = [
    "D415",   # First line should end with a period, question mark, or exclamation point
    "D300",   # Use triple double quotes `"""`
    "D200",   # One-line docstring should fit on one line
    "TCH",    # Format type checking only imports
    "ISC001", # Implicitly concatenated strings on a single line
    "EM",     # Exception message variables
    "RUF013", # Implicit Optional
    "B006",   # Mutable default argument
    "TID252", # Absolute imports over relative imports
]

# Override default settings for specific rules
pylint.max-args = 9
flake8-tidy-imports.ban-relative-imports = "all" # Disallow all relative imports.
isort.known-first-party = ["eitprocessing"]

[tool.ruff.lint.per-file-ignores]
"*.ipynb" = [
    "ERA001",
    "T201",
    "T203",
] # Commented out code, print() / pprint() statement
"notebooks/**/*.py" = [
    "ERA001",
    "T201",
    "T203",
] # Commented out code, print() / pprint() statement
"tests/*" = [
    "S101",    # Use of `assert` detected
    "ANN201",  # Missing return type
    "D103",    # Missing function docstring
    "PLR2004", # Comparison against unnamed value
    "SLF001",  # Private member accessed
]
"docs/*" = ["ALL"]

[tool.bumpversion]
current_version = "1.4.5"

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'

[[tool.bumpversion.files]]
filename = "CITATION.cff"
search = 'version: "{current_version}"'
replace = 'version: "{new_version}"'

[[tool.bumpversion.files]]
filename = "eitprocessing/__init__.py"
search = '__version__ = "{current_version}"'
replace = '__version__ = "{new_version}"'