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pyproject.toml
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[project]
name = "voxel"
description = "A python package for generalized microscope control"
license = { file = "LICENSE" }
requires-python = ">=3.10, <=3.12"
authors = [
{ name = "Micah Woodard", email = "[email protected]" },
{ name = "Adam Glaser", email = "[email protected]" },
{ name = "Walter Mwaniki", email = "[email protected]" },
]
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
]
readme = "README.md"
keywords = [
"microscopy",
"microscope",
"acquisition",
"imaging",
]
dynamic = ["version"]
dependencies = [
"ruamel-yaml>=0.18.5",
"inflection>=0.5.1",
"pydantic>=2.7.3",
"imohash>=1.0.5",
"numpy>=2.1",
# device driver dependencies
"pyserial>=3.5",
"pyusb>=1.2.1",
"psutil>=5.9.8",
"PyVISA>=1.14.1",
"PyVISA-py>=0.7.2",
"pylablib>=1.4.2",
"nidaqmx>=0.9.0",
# data handling dependencies
"h5py>=3.0.0",
# processing and utils dependencies
"pyclesperanto>=0.8.2",
"scikit-image>=0.20.0",
"gputools>0.2.14",
"tensorstore>=0.1.56",
"matplotlib>=3.8.2",
"scipy>=1.12.0",
"fast_histogram>=0.14",
"sympy>=1.12.1",
"numpy>2.0.0",
"siphash24>=1.7",
]
[project.optional-dependencies]
imaris-writer = ["PyImarisWriter>=0.7.0"]
tifffile-writer = ["tifffile>=2024.1.30"]
acquire-zarr-writer = ["acquire-zarr>=0.0.5"]
pycobolt-laser = ["pycobolt @ git+https://github.com/cobolt-lasers/pycobolt.git"]
coherent-laser = ["coherent-lasers @ https://github.com/AllenNeuralDynamics/coherent-lasers/releases/download/v0.1.0/coherent_lasers-0.1.0-py3-none-any.whl"]
vortran-laser = ["vortran_laser @ git+https://github.com/AllenNeuralDynamics/vortran_laser.git"]
oxxius-laser = ["oxxius_laser @ git+https://github.com/AllenNeuralDynamics/oxxius_laser.git"]
obis-laser = ["obis_laser @ git+https://github.com/AllenNeuralDynamics/obis-laser.git"]
egrabber-camera = ["egrabber @ https://github.com/adamkglaser/egrabber-python/releases/download/v24.09.0.5/egrabber-24.09.0.5-py2.py3-none-any.whl"]
pco-camera = ["pco"]
ximea-camera = ["ximea-python @ https://github.com/adamkglaser/ximea-python/releases/download/v4.29.10/ximea_python-4.29.10-py3-none-any.whl"]
optokummenberg-etl = ["optokummenberg @https://github.com/adamkglaser/optotune-icc4c/releases/download/v2.0.4922/optoKummenberg-1.0.4894-py3-none-any.whl"]
optoicc-etl = ["optoicc @https://github.com/adamkglaser/optotune-icc4c/releases/download/v2.0.4922/optoICC-2.0.4922-py3-none-any.whl"]
tigerasi-controller = ["tigerasi"]
scikit-tensor = ["scikit-tensor-py3 @ https://github.com/adamkglaser/scikit-tensor-py3/releases/download/v0.1.0/scikit_tensor_py3-0.4.1-py3-none-any.whl"]
dev = [
"pytest>=8.2.1",
"black",
"coverage",
"flake8",
"interrogate",
"isort",
"Sphinx",
"furo",
]
all = [
"voxel[imaris-writer]",
"voxel[tifffile-writer]",
"voxel[acquire-zarr-writer]",
"voxel[pycobolt-laser]",
"voxel[coherent-laser]",
"voxel[vortran-laser]",
"voxel[oxxius-laser]",
"voxel[obis-laser]",
"voxel[egrabber-camera]",
"voxel[pco-camera]",
"voxel[ximea-camera]",
"voxel[optokummenberg-etl]",
"voxel[optoicc-etl]",
"voxel[tigerasi-controller]",
"voxel[scikit-tensor]",
"voxel[dev]",
]
[project.urls]
"Homepage" = "https://github.com/AllenNeuralDynamics/voxel"
"Issues" = "https://github.com/AllenNeuralDynamics/voxel/issues"
[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
package-dir = { "" = "src" }
packages = ["voxel"]
[tool.setuptools.dynamic]
version = { attr = "voxel.__version__" }
[tool.black]
line-length = 120
target-version = ["py311"]
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| build
| dist
)/
| .gitignore
)
'''
[tool.coverage.run]
omit = ["*__init__*"]
source = ["voxel", "tests"]
[tool.coverage.report]
exclude_lines = [
"if __name__ == .__main__.:",
"from",
"import",
"pragma: no cover",
]
fail_under = 100
[tool.isort]
line_length = 120
profile = "black"
[tool.interrogate]
exclude = ["setup.py", "docs", "build"]
fail_under = 100