pyproject.toml

[tool.pytest.ini_options]
pythonpath = [
    ".",
]
testpaths = [
    ".",
    "./test",
]
# ignore any of these paths
norecursedirs = [

]

[tool.poetry]
name = "shuntclf"
package-mode = false
version = "1.0.0"
description = "Machine learning algorithms used for the prediction of chronic shunt-dependent hydrocephalus after spontaneous subarachnoid hemorrhage"
authors = [
    "Markus Steindl <ma.steindl@gmail.com>",
]

[tool.poetry.dependencies]
python = "~3.11"
pandas = "^2.1.1"
matplotlib = "^3.8.0"
tensorboard = "^2.14.1"
seaborn = "^0.13.0"
numpy = "^1.25.2"
imbalanced-learn = "^0.12.0"
xgboost = "^2.0.3"
scikit-learn = "^1.4.1.post1"
gradio = "^5.35.0"
openpyxl = "^3.1.5"

[tool.poetry.group.dev.dependencies]
pytest = "^8.4.1"
pytest-cov = "^6.2.1"
pytest-xdist = "^3.7.0"
poethepoet = "^0.36.0"
ruff = "^0.12.1"
black = "^25.1.0"
ipykernel = "^6.29.5"
#liccheck = "^0.9.1"
#pip-licenses = "^4.3.2"
isort = "^6.0.1"

[tool.liccheck]
# see also: https://pypi.org/project/liccheck/
# Authorized and unauthorized licenses in LOWER CASE
authorized_licenses = [
    "bsd",
    "new bsd",
    "bsd 3-clause",
    "bsd license",
    "freebsd",
    "3-clause bsd",
    "isc license",
    "isc license (iscl)",
    "apache",
    "apache 2.0",
    "apache software",
    "apache license 2.0",
    "apache license, version 2.0",
    "apache software license",
    "gnu lgpl",
    "historical permission notice and disclaimer (hpnd)",
    "lgpl with exceptions or zpl",
    "mozilla public license 2.0 (mpl 2.0)",
    "mit",
    "mit license",
    "new bsd license",
    "python software foundation license",
    "python software foundation",
    "simplified bsd",
    "the unlicense (unlicense)",
]
unauthorized_licenses = [
    "gpl v3",
    "gnu general public license v2 or later (gplv2+)",
]
level = "standard"  # alternatives: "cautious", "paranoid"
requirement_txt_file = "./requirements.txt"
reporting_txt_file = "./liccheck_reporting.txt" # by default is None

[tool.liccheck.authorized_packages]
# Python software license (see http://zesty.ca/python/uuid.README.txt)
uuid = "1.30"

[tool.poe.tasks]
format = "black ."
sort_imports = "isort ."
lint = "ruff check . --ignore F841"
precommit = ["format", "sort_imports", "lint"]
test = "pytest -ra --doctest-modules --junitxml=python-junit.xml --cov --cov-report=html --cov-report term"

# license handling
_convert_to_req_txt = { shell = "poetry export --without-hashes --format=requirements.txt > requirements.txt" }
# check authorization of the licenses of dependencies as defined in [tool.liccheck] section
_check_licenses = "liccheck -s liccheck.ini -r requirements.txt"
_export_licenses = """pip-licenses --from=mixed --with-system --order=license --format=json --with-license-file
    --with-notice-file --output-file=LICENSES.json"""
_license_json_postprocess.script = """
    utils.license_utils:postprocess_licenses_json(
        file_in_path="LICENSES.json",
        file_out_path="LICENSES.json",
    )
"""

check_licenses = [
    "_convert_to_req_txt",
    "_check_licenses",
]

export_licenses = [
    "_export_licenses",
    "_license_json_postprocess"
]

[tool.ruff]
line-length = 120
exclude = [
]

[tool.isort]
profile = "black"
line_length = 120
skip_glob  = [
]

[tool.black]
line-length = 120
force-exclude = """
(
    some_path
  | some_other_path
)
"""

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "raise NotImplementedError",
    "pass",
]

[build-system]
requires = ["poetry-core>=1.5.0"]
build-backend = "poetry.core.masonry.api"