pyproject.toml

[tool.poetry]
name = "biosim_client"
version = "0.0.1"
description = "This is a library to access biosimulations.org APIs."
authors = ["Jim Schaff <schaff@uchc.edu>"]
repository = "https://github.com/biosimulations/biosim-client"
documentation = "https://jcschaff.github.io/biosim-client/"
readme = "README.md"
packages = [
  {include = "biosim_client"}
]

[tool.poetry.dependencies]
python = ">=3.10,<4.0"
pydantic = "^2.9.2"
numpy = "^2.1.3"
pandas = "^2.2.3"
urllib3 = "^2.2.3"
typing-extensions = "^4.12.2"
python-dateutil = "^2.9.0.post0"
matplotlib = "^3.9.2"

[tool.poetry.group.dev.dependencies]
pytest = "^8.0.0"
pytest-cov = "^6.0.0"
deptry = "^0.21.0"
mypy = "^1.5.1"
pre-commit = "^3.4.0"
tox = "^4.11.1"
types-python-dateutil = "^2.9.0.20241003"
pandas-stubs = "^2.2.3.241009"

[tool.poetry.group.docs.dependencies]
mkdocs = "^1.4.2"
mkdocs-material = "^9.2.7"
mkdocstrings = {extras = ["python"], version = "^0.27.0"}

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

[tool.mypy]
files = ["biosim_client"]
explicit_package_bases = "True"
disallow_untyped_defs = "True"
disallow_any_unimported = "True"
no_implicit_optional = "True"
check_untyped_defs = "True"
warn_return_any = "True"
warn_unused_ignores = "True"
show_error_codes = "True"

[[tool.mypy.overrides]]
module = [ "biosim_client.simdata_api.*" ]
disable_error_code = ["no-untyped-def", "no-any-return", "var-annotated"]

[[tool.mypy.overrides]]
module = [ "biosim_client.simdata_api.test/*" ]
disable_error_code = ["return"]

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

[tool.ruff]
target-version = "py39"
line-length = 120
fix = true
lint.select = [
    # flake8-2020
    "YTT",
    # flake8-bandit
    "S",
    # flake8-bugbear
    "B",
    # flake8-builtins
    "A",
    # flake8-comprehensions
    "C4",
    # flake8-debugger
    "T10",
    # flake8-simplify
    "SIM",
    # isort
    "I",
    # mccabe
    "C90",
    # pycodestyle
    "E", "W",
    # pyflakes
    "F",
    # pygrep-hooks
    "PGH",
    # pyupgrade
    "UP",
    # ruff
    "RUF",
    # tryceratops
    "TRY",
]
lint.ignore = [
    # LineTooLong
    "E501",
    # DoNotAssignLambda
    "E731"
]

[tool.ruff.lint.per-file-ignores]
"biosim_client/simdata_api/*" = [
    "B904",
    "C405",
    "C409",
    "C901",
    "E721",
    "RUF012",
    "S101",
    "S110",
    "SIM101",
    "SIM105",
    "SIM108",
    "TRY003",
    "TRY004",
    "TRY201",
    "TRY300",
    "TRY302",
    "UP006",
    "UP007",
    "UP008",
    "UP030",
    "UP031",
    "UP035",
]
"biosim_client/*" = [
    "PGH003",
    "TRY003",
]
"tests/*" = [
    "S101",
]

[tool.ruff.format]
preview = true

[tool.coverage.report]
skip_empty = true

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