mortiscope-api/pyproject.toml at main · mortiscope/mortiscope-api · GitHub

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[tool.poetry]
name = "mortiscope-api"
version = "1.0.0"
description = "A backend API for a deep learning system that provides endpoints to analyze images of Chrysomya megacephala for Post-Mortem Interval (PMI) estimation."
authors = [
    "Neil Ivan Orencia <mortiscope@gmail.com>",
    "Precious Andal <mortiscope@gmail.com>",
]
readme = "README.md"
packages = [{include = "app"}]
keywords = ["fastapi", "computer-vision", "forensic-entomology", "forensic-science", "pmi", "deep-learning"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Image Recognition",
    "License :: Other/Proprietary License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Framework :: FastAPI",
    "Operating System :: OS Independent",
]

[tool.poetry.urls]
Homepage = "https://github.com/mortiscope/mortiscope-api"
Repository = "https://github.com/mortiscope/mortiscope-api"
"Bug Tracker" = "https://github.com/mortiscope/mortiscope-api/issues"

[tool.poetry.dependencies]
python = ">=3.11,<3.15"
aiosqlite = "0.22.1"
boto3 = "1.39.4"
botocore = "1.39.4"
cuid2 = "2.0.1"
fastapi = "0.116.1"
jinja2 = "3.1.6"
kaleido = "1.1.0"
loguru = "0.7.3"
modal = "1.3.0.post1"
numpy = ">=2,<2.3.0"
onnxruntime = "1.22.1"
opencv-python = "4.12.0.88"
opencv-python-headless = "4.12.0.88"
pandas = "2.3.1"
pikepdf = "9.11.0"
pillow = "11.3.0"
plotly = "6.3.1"
psycopg = "3.2.9"
psycopg-binary = "3.2.9"
pydantic = "2.11.7"
pydantic-settings = "2.10.1"
python-dotenv = "1.1.1"
python-magic = "0.4.27"
python-magic-bin = "0.4.14"
pyzipper = "0.3.6"
reportlab = "4.4.4"
sahi = "*"
sqlalchemy = "2.0.41"
torch = "2.9.1"
torchvision = "0.24.1"
ultralytics = "8.3.239"
uvicorn = "0.38.0"
weasyprint = "66.0"

[tool.poetry.group.dev.dependencies]
bandit = "1.9.3"
faker = "38.2.0"
greenlet = "3.2.3"
httpx = "0.28.1"
moto = "5.1.19"
mypy = "1.18.2"
pre-commit = "4.2.0"
pytest = "9.0.1"
pytest-asyncio = "1.3.0"
pytest-cov = "7.0.0"
pytest-mock = "3.15.1"
ruff = "0.12.3"
pytest-dotenv = "^0.5.2"

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "W", "I", "B", "C4", "UP", "A"]
ignore = [
    "E501",
    "B905",
]
isort.known-first-party = ["mortiscope-api"]
pydocstyle.convention = "google"

[tool.ruff.format]
quote-style = "double"

[tool.mypy]
python_version = "3.11"

# Exclude directories
exclude = [
    "notebooks/",
]

# Catch real bugs
warn_return_any = true
warn_unused_configs = true
warn_redundant_casts = true
warn_unused_ignores = true
no_implicit_optional = true
strict_equality = true

# Allow gradual typing
disallow_untyped_defs = false
disallow_incomplete_defs = false
disallow_untyped_calls = false
check_untyped_defs = true

# Third-party libraries
ignore_missing_imports = true

# Project structure
explicit_package_bases = true
namespace_packages = true

# SQLAlchemy models
[[tool.mypy.overrides]]
module = "app.database.models.*"
disable_error_code = ["misc"]

# Libraries without type stubs
[[tool.mypy.overrides]]
module = ["cv2.*", "magic.*", "reportlab.*", "weasyprint.*"]
ignore_missing_imports = true

# Pytest Configuration
[tool.pytest.ini_options]
pythonpath = ["."]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]

# Async test support (required for FastAPI endpoint testing)
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"

# Load test environment variables
env_files = [
    ".env.test",
]

# Test markers for categorizing and selectively running tests
markers = [
    "unit: Unit tests for individual components",
    "integration: Integration tests with real database and services",
    "no_cover: Skip coverage instrumentation for these tests",
]

# Default pytest command-line options
addopts = [
    "-v",
    "--strict-markers",
    "--tb=short",
    "--cov=app",
    "--cov-report=term-missing",
    "--cov-report=xml",
    "--cov-fail-under=80",
]

# Suppress expected warnings
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore:The NumPy module was reloaded:UserWarning",
]