xenium_analysis_tools/pyproject.toml at main · AllenInstitute/xenium_analysis_tools · GitHub

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[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[project]
name = "xenium_analysis_tools"
description = "Generated from aind-library-template"
license = {text = "MIT"}
requires-python = ">=3.11"
authors = [
    {name = "Allen Institute for Neural Dynamics"}
]
classifiers = [
    "Programming Language :: Python :: 3"
]
readme = "README.md"
dynamic = ["version"]

dependencies = [
    "pyarrow>=21.0.0",
    "scanpy>=1.11.5",
    "spatialdata>=0.6.1",
    "spatialdata-plot",
    "spatialdata-io",
    "numpy",
    "pandas"
]

[project.optional-dependencies]
mapping = [
    "cell-type-mapper @ git+https://github.com/AllenInstitute/cell_type_mapper.git@c8ee12659c4b8a8e260b091ce1aa0a145088ede5"
]
napari = [
    "napari-spatialdata @ git+https://github.com/scverse/napari-spatialdata#egg=napari-spatialdata"
]

[dependency-groups]
dev = [
      "black",
      "coverage",
      "flake8",
      "interrogate",
      "isort",
      "Sphinx",
      "furo",
    ]

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.dynamic]
version = {attr = "xenium_analysis_tools.__version__"}

[tool.black]
line-length = 79
target_version = ['py310']
exclude = '''

(
  /(
      \.eggs         # exclude a few common directories in the
    | \.git          # root of the project
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | build
    | dist
    | .conda
  )/
  | .gitignore
)
'''

[tool.coverage.run]
omit = ["*__init__*"]
source = ["xenium_analysis_tools", "tests"]

[tool.coverage.report]
exclude_lines = [
    "if __name__ == .__main__.:",
    "^from .* import .*",
    "^import .*",
    "pragma: no cover"
]
fail_under = 0  # Changed from 100

[tool.isort]
line_length = 79
profile = "black"
skip = [".conda"]

[tool.interrogate]
exclude = ["setup.py", "docs", "build", ".conda"]
fail-under = 0 # Changed from 100