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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools >= 61", "setuptools_scm[toml]>=3.4", "wheel"]
[project]
name = "mantis"
description = "Acquisition engine for collecting data on the mantis microscope"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.10, <4.0"
# the dynamically determined project metadata attributes
dynamic = ["version"]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
]
# list package dependencies here
dependencies = [
"copylot @ git+https://github.com/czbiohub-sf/coPylot",
"iohub==0.1.0",
"matplotlib",
"napari; 'arm64' in platform_machine", # without Qt5 and skimage
"napari[all]; 'arm64' not in platform_machine", # with Qt5 and skimage
"PyQt6; 'arm64' in platform_machine",
"natsort",
"ndtiff>=2.0",
"nidaqmx",
"numpy<2",
"monai",
"pandas~=2.1",
"pycromanager==0.28.1",
"pydantic",
"pylablib==1.4.1",
"scipy",
"slurmkit @ git+https://github.com/royerlab/slurmkit",
"tifffile",
"waveorder @ git+https://github.com/mehta-lab/waveorder",
"largestinteriorrectangle",
"antspyx",
"pystackreg",
]
[project.optional-dependencies]
# note that dev dependencies are only pinned to major versions
dev = [
"black==22.3.0",
"flake8~=5.0",
"isort~=5.12",
"pre-commit~=2.19",
"pylint~=2.14",
"pytest~=7.1",
]
build = ["build", "twine"]
[project.scripts]
mantis = "mantis.cli.main:cli"
[tool.setuptools]
# explicitly specify the package name
# TODO: is there a better way to do this?
packages = ["mantis"]
# allow use of __file__ to load data files included in the package
zip-safe = false
[tool.setuptools.dynamic]
version = { attr = "mantis.__version__" }
[tool.black]
line-length = 95
target-version = ['py39', 'py310']
include = '\.pyi?$'
skip-string-normalization = true
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| build
| dist
| notebooks
| ignore
| examples
)/
)
'''
[tool.isort]
profile = "black"
line_length = 95
lines_between_types = 1
default_section = "THIRDPARTY"
no_lines_before = ["STDLIB"]
ensure_newline_before_comments = true
skip_glob = ["examples/*"]
[tool.pylint]
# disable all conventions, refactors, warnings (C, R, W) and the following:
# E0401: unable-to-import (since it is possible that no one environment has all required packages)
# E1136: unsubscriptable-object (anecdotal false positives for numpy objects)
disable = ["C", "R", "W", "import-error", "unsubscriptable-object"]
msg-template = "{line},{column},{category},{symbol}:{msg}"
reports = "n"
[tool.pytest.ini_options]
addopts = "--ignore examples/"