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pyproject.toml
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[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=65", "wheel", "setuptools_scm[toml]>=3.4"]
[tool.setuptools_scm]
write_to = "flyvis/version.py"
[tool.setuptools]
include-package-data = true
[tool.setuptools.package-data]
flyvis = [
"connectome/*.json",
"analysis/visualization/matplotlibrc",
"analysis/__main__.ipynb",
"analysis/__main_per_model__.ipynb",
"config/**/*.yaml",
"config/**/*.yml",
]
[project]
classifiers = [
"Intended Audience :: Developers",
"Intended Audience :: Education",
"Intended Audience :: Science/Research",
"Topic :: Adaptive Technologies",
"Topic :: Scientific/Engineering",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Mathematics",
"""License :: OSI Approved :: MIT License""",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Development Status :: 3 - Alpha",
]
dependencies = [
"ipython",
"numba",
"datamate",
"scipy",
"matplotlib",
"networkx",
"scikit-learn",
"umap-learn",
"ffmpeg-python",
"pytest",
"torch",
"torchvision",
"python-dotenv",
"hydra-core",
"toolz",
"tqdm",
"requests",
"google-api-python-client",
"xarray",
"pandas",
"joblib",
"colorama",
]
description = "Connectome and task-constrained vision models of the fruit fly."
dynamic = ["version"]
name = "flyvis"
readme = "readme.md"
requires-python = ">=3.9,<3.13"
[project.optional-dependencies]
dev = [
"pre-commit",
"ruff",
"pytest",
"pytest-cov",
"jupyter",
"papermill",
"tabulate",
"tqdm",
"ipywidgets",
]
docs = [
"mkdocs",
"mkdocs-material",
"markdown-include",
"mkdocs-redirects",
"mkdocstrings[python] >= 0.18",
"nbconvert",
"mike",
"mkdocs-macros-plugin",
"jupyter",
"tabulate",
"tqdm",
"ipywidgets",
]
examples = ["jupyter", "tabulate", "tqdm", "ipywidgets"]
pretrained = [
"numba==0.55.2",
"matplotlib==3.7.1",
"scikit-learn==1.1.1",
"umap-learn==0.5.3",
"xarray==2023.7.0",
"pandas==2.2.2",
"joblib==1.3.2",
]
# Package installation configuration
[tool.setuptools.packages.find]
exclude = [] # exclude packages matching these glob patterns (empty by default)
include = [
"flyvis*",
"flyvis_cli*",
] # package names should match these glob patterns (["*"] by default)
namespaces = false # to disable scanning PEP 420 namespaces (true by default)
where = ["."] # list of folders that contain the packages (["."] by default)
# ruff configs
[tool.ruff]
extend-include = []
line-length = 90
[tool.ruff.lint]
# pycodestyle, Pyflakes, pyupgrade, flake8-bugbear, flake8-simplify, isort
ignore = [
"E731", # allow naming lambda functions.
"B006", # allow mutable default arguments.
"B008", # allow function calls in default args.
"F841", # allow unused variables.
]
select = ["E", "F", "W", "B", "SIM", "I"]
[tool.ruff.lint.extend-per-file-ignores]
"__init__.py" = [
"I001",
"E402",
"F401",
"F403",
] # allow unused imports and undefined names
"test_*.py" = ["F403", "F405"]
# [tool.ruff.lint.isort]
# case-sensitive = true
# lines-between-types = 0 # like isort default.
# relative-imports-order = "furthest-to-closest" # like isort default.
# known-first-party = ["flyvis", "tests", "examples", "scripts"]
[tool.ruff.format]
# exclude = ["*.ipynb"]
preview = true
quote-style = "preserve"
# Pytest configuration
[tool.pytest.ini_options]
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
"gpu: marks tests that require a gpu (deselect with '-m \"not gpu\"')",
"require_large_download: tests that require large data downloads (deselect with '-m \"not require_large_download\"')",
"require_download: tests that require data downloads (deselect with '-m \"not require_download\"')",
]
testpaths = ["tests"]
# Pyright configuration
[tool.pyright]
exclude = [
"**/__pycache__",
"**/__node_modules__",
".git",
"docs",
".fonts",
".ruff_cache",
"config",
"data",
"images",
]
ignore = []
include = ["flyvis", "flyvis_cli", "tests", "examples"]
python_version = "3.x"
reportUnsupportedDunderAll = false
[project.scripts]
flyvis = "flyvis_cli.flyvis_cli:main"
[project.urls]
"Homepage" = "https://github.com/TuragaLab/flyvis"
"Documentation" = "https://turagalab.github.io/flyvis"
"Source Code" = "https://github.com/TuragaLab/flyvis"
"Bug Tracker" = "https://github.com/TuragaLab/flyvis/issues"