pyproject.toml

[project]
name = "compose-api"
version = "0.4.0"
description = "An API server for reproducible biological workflows and cosimulations."
authors = [{ name = "Jim Schaff", email = "schaff@uchc.edu" }]
requires-python = ">=3.13.2,<4.0"
readme = "README.md"
keywords = ['python']
dependencies = [
    "uvicorn>=0.35.0,<0.36",
    "dotenv>=0.9.9,<0.10",
    "fastapi>=0.116.1,<0.117",
    "pydantic>=2.11.5,<3",
    "asyncssh>=2.21.0,<3",
    "pydantic-settings>=2.9.1,<3",
    "pyyaml>=6.0.2,<7",
    "typing-extensions>=4.14.0,<5",
    "pymongo>=4.13.0,<5",
    "sqlalchemy[asyncio]>=2.0.41,<3",
    "asyncpg>=0.30.0,<0.31",
    "nats-py>=2.10.0,<3",
    "alembic>=1.16.2,<2",
    "async-lru>=2.0.5,<3",
    "httpx>=0.28.1,<0.29",
    "polars-lts-cpu[pyarrow]>=1.31.0,<2",
    "python-multipart>=0.0.20,<0.0.21",
    "numpy>=2.3.1,<3",
    "ruff>=0.12.2,<0.13",
    "nbformat>=5.10.4,<6",
    "vl-convert-python>=1.8.0,<2",
    "tqdm>=4.67.1,<5",
    "seaborn>=0.13.2,<0.14",
    "python-dateutil>=2.9.0.post0,<3",
    "spython",
    "jinja2>=3.1.6",
    "python-libsedml>=2.0.33",
    "biosimulators-utils>=0.2.3",
    "python-libsbml>=5.20.5",
    "pbest==0.4.0",
]

[project.urls]
Homepage = "https://biosimulations.github.io/compose-api/"
Repository = "https://github.com/biosimulations/compose-api"
Documentation = "https://biosimulations.github.io/compose-api/"

[dependency-groups]
dev = [
    "pytest>=8.3.5,<9",
    "pytest-cov>=4.0.0,<5",
    "deptry>=0.23.0,<0.24",
    "mypy>=1.5.1,<2",
    "pre-commit>=3.4.0,<4",
    "tox>=4.11.1,<5",
    "types-requests>=2.32.0.20250602,<3",
    "types-pyyaml>=6.0.12.20250516,<7",
    "pytest-asyncio>=1.0.0,<2",
    "testcontainers[nats, postgres]>=4.10.0,<5",
    "types-tqdm>=4.67.0.20250516,<5",
    "openapi-python-client>=0.25.2,<0.26",
    "types-python-dateutil>=2.9.0.20250708,<3"
]
docs = [
    "mkdocs>=1.4.2,<2",
    "mkdocs-material>=9.2.7,<10",
    "mkdocstrings[python]>=0.26.1,<0.27",
    "sphinx>=8.2.3,<9",
    "sphinx-autodoc-typehints>=3.2.0,<4",
    "sphinx-rtd-theme>=3.0.2,<4",
]

[tool.uv]
default-groups = [
    "dev",
    "docs",
]

[tool.uv.sources]
bsander = { git = "https://github.com/biosimulators/bsander.git" }


[tool.hatch.build.targets.sdist]
include = [
    "compose_api",
    "tests",
]

[tool.hatch.build.targets.wheel]
include = [
    "compose_api",
    "tests",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.mypy]
files = ["compose_api", "tests"]
strict = true
exclude = ['^compose_api/api/client/.*']

[[tool.mypy.overrides]]
module = ["process_bigraph.*"]
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--cov-report=html"

[tool.deptry]
exclude = [".venv/*"]
ignore = ["DEP002", "DEP003", "DEP004"]

[tool.ruff]
target-version = 'py39'
line-length = 120
fix = true

[tool.ruff.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",
]
ignore = [
#    # A001 Variable `sum` is shadowing a Python builtin
#    "A001",
#    # B008 Do not perform function call `Body` in argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable
#    "B008",
#    # B026 Star-arg unpacking after a keyword argument is strongly discouraged
#    "B026",
    # B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
    "B904",
#    # C414 Unnecessary `list` call within `tuple()`
#    "C414",
#    # C416 Unnecessary `list` comprehension (rewrite using `list()`)
#    "C416",
#    # C417 Unnecessary `map` usage (rewrite using a `list` comprehension)
#    "C417",
#    # C419 Unnecessary list comprehension
#    "C419",
#    # E501 Line too long (131 > 120)
#    "E501",
#    # E722 Do not use bare `except`
#    "E722",
#    # E731 Do not assign a `lambda` expression, use a `def`
#    "E731",
#    # F841 Local variable `keys` is assigned to but never used
#    "F841",
#    # PGH003 Use specific rule codes when ignoring type issues
#    "PGH003",
#    # RUF009 Do not perform function call `Field` in dataclass defaults
#    "RUF009",
    # RUF012 Mutable class attributes should be annotated with `typing.ClassVar`
    "RUF012",
#    # RUF013 PEP 484 prohibits implicit `Optional
#    "RUF013",
#    # S101 Use of `assert` detected
#    "S101",
#    # *** S113 Probable use of `requests` call without timeout
#    "S113",
#    # S301 `pickle` and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue
#    "S301",
#    # S307 Use of possibly insecure function
#    "S307",
#    # S603 `subprocess` call: check for execution of untrusted input
#    "S603",
#    # S608 Possible SQL injection vector through string-based query construction
#    "S608",
#    # SIM101 Multiple `isinstance` calls for expression, merge into a single call
#    "SIM101",
#    # SIM105 Use `contextlib.suppress(KeyError)` instead of `try`-`except`-`pass`
#    "SIM105",
#    # SIM108 Use ternary operator `source = self.model_source.value if isinstance(self.model_source, ModelFilepath) else self.model_source` instead of `if`-`else`-block
#    "SIM108",
#    # SIM118 Use `key not in dict` instead of `key not in dict.keys()`
#    "SIM118",
    # TRY002 Create your own exception
    "TRY002",
    # TRY003 Avoid specifying long messages outside the exception class
    "TRY003",
#    # TRY004 Prefer `TypeError` exception for invalid type
#    "TRY004",
    # TRY201 Use `raise` without specifying exception name
    "TRY201",
    # TRY300 Consider moving this statement to an `else` block
    "TRY300",
#    # TRY400 Use `logging.exception` instead of `logging.error`
#    "TRY400",
    # UP006 Use `dict` instead of `Dict` for type annotation
    "UP006",
#    # UP035 `typing.Dict` is deprecated, use `dict` instead
#    "UP035",
]
exclude = [".venv/*", "compose_api/api/client/*", "documentation/*"]

[tool.ruff.format]
preview = true

[tool.coverage.report]
skip_empty = true

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

[tool.ruff.per-file-ignores]
"tests/*" = ["S101"]