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pyproject.toml
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[build-system]
requires = ["setuptools>=62.0", "wheel>=0.37"]
build-backend = "setuptools.build_meta"
[project]
name = "aeon_mecha"
version = "0.1.0"
requires-python = ">=3.11"
description = '''
Code for managing acquired data from Project Aeon experiments. Includes general file IO,
data QC, querying, and analysis modules.
'''
authors = [
{ name = "Jai Bhagat", email = "[email protected]" },
{ name = "Goncalo Lopes", email = "[email protected]" },
{ name = "Thinh Nguyen", email = "[email protected]" },
{ name = "Joseph Burling", email = "[email protected]" },
{ name = "Chang Huan Lo", email = "[email protected]" },
{ name = "Jaerong Ahn", email = "[email protected]" },
]
license = { file = "license.md" }
readme = "readme.md"
dependencies = [
"bottleneck>=1.2.1,<2",
"datajoint-utilities @ git+https://github.com/datajoint-company/datajoint-utilities",
"datajoint>=0.13.6",
"dotmap",
"fastparquet",
"graphviz",
"ipykernel",
"jupyter",
"jupyterlab",
"matplotlib",
"numba>=0.46.0, <1",
"numexpr>=2.6.8, <3",
"numpy>=1.21.0, <2",
"opencv-python",
"pandas>=1.3",
"plotly",
"pyarrow",
"pydotplus",
"pymysql",
"pyyaml",
"scikit-learn",
"scipy",
"seaborn",
"xarray>=0.12.3",
]
[project.optional-dependencies]
dev = [
"bandit",
"black[jupyter]",
"gh",
"ipdb",
"pre-commit",
"pyan3 @ git+https://github.com/Technologicat/pyan.git",
"pydantic",
"pyright",
"pytest",
"pytest-cov",
"sphinx",
"ruff",
"tox",
]
gpu = [
"cupy",
"dask"
]
[project.scripts]
aeon_ingest = "aeon.dj_pipeline.ingest.process:cli"
[project.urls]
Homepage = "https://sainsburywellcomecentre.github.io/aeon_docs/"
Repository = "https://github.com/sainsburyWellcomeCentre/aeon_mecha"
Documentation = "https://sainsburywellcomecentre.github.io/aeon_docs/"
DataJoint = "https://docs.datajoint.org/"
[tool.setuptools]
packages = ["aeon"]
[tool.black]
line-length = 108
color = false
exclude = '''
/(
\.git
| \.mypy_cache
| \.tox
| \.venv
| _build
| build
| dist
| env
| venv
)/
'''
[tool.ruff]
select = ["E", "W", "F", "I", "D", "UP", "S", "B", "A", "C4", "ICN", "PIE", "PT", "SIM", "PL"]
line-length = 108
ignore = [
"E201", "E202", "E203", "E231", "E731", "E702",
"S101",
"PT013",
"PLR0912", "PLR0913", "PLR0915"
]
extend-exclude = [".git", ".github", ".idea", ".vscode"]
[tool.ruff.pydocstyle]
convention = "google"
[tool.pyright]
reportMissingImports = "none"
reportImportCycles = "error"
reportUnusedImport = "error"
reportUnusedClass = "error"
reportUnusedfunction = "error"
reportUnusedVariable = "error"
reportDuplicateImport = "error"
reportWildcardImportFromLibrary = "error"
reportPrivateUsage = "error"
reportCallInDefaultInitializer = "error"
reportUnnecessaryIsInstance = "error"
reportUnnecesaryCast = "error"
reportUnnecesarryComparison = "error"
reportUnnecessaryContains = "error"
reportAssertAlwaysTrue = "error"
reportSelfClsParameterName = "error"
reportUnusedExpression = "error"
reportMatchNotExhaustive = "error"
reportShadowedImports = "error"
# *Note*: we may want to set all 'ReportOptional*' rules to "none", but leaving 'em default for now
venvPath = "."
venv = ".venv"
[tool.pytest.ini_options]
markers = [
"api",
]