CytoTable/pyproject.toml at main · cytomining/CytoTable · GitHub

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[build-system]
build-backend = "poetry_dynamic_versioning.backend"
requires = [ "poetry-core>=1", "poetry-dynamic-versioning>=1,<2" ]

[tool.poetry]
name = "CytoTable"
# note: version data is maintained by poetry-dynamic-versioning (do not edit)
version = "0.0.0"
description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools."
authors = [ "Cytomining Community" ]
license = "BSD-3-Clause License"
packages = [ { include = "cytotable" } ]
readme = "readme.md"
repository = "https://github.com/cytomining/CytoTable"
documentation = "https://cytomining.github.io/CytoTable/"
keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ]

[tool.poetry.dependencies]
python = ">=3.10,<3.15"
pyarrow = ">=13.0.0"
cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.24" }
duckdb = ">=0.8.0,!=0.10.0,>=0.10.1"
parsl = ">=2023.9.25"
pyiceberg = { version = ">=0.11,<0.12", optional = true }
ome-arrow = [
  { version = ">=0.0.8,<0.1", optional = true, python = ">=3.11" },
]
numpy = [
  { version = "<=1.24.4", python = "<3.11" },
  { version = ">=1.26.0", python = ">=3.11" },
]
scipy = [
  { version = "<1.12.0", python = "<3.9" },
  { version = "^1.12.0", python = ">=3.9" },
]
anndata = [
  { version = "<0.12.2", python = "<3.11" },
  { version = ">=0.12.2", python = ">=3.11" },
]
# Explicit zarr dependency for
# anndata <0.12.2 and Python <3.11
zarr = [
  { version = "<3.1.1", python = "<3.11" },
  { version = ">=3.1.1", python = ">=3.11" },
]
botocore = "^1.34.133"

[tool.poetry.extras]
iceberg = [ "pyiceberg" ]
images = [ "ome-arrow" ]
iceberg-images = [ "pyiceberg", "ome-arrow" ]

[tool.poetry.group.dev.dependencies]
pytest = ">=7.4,<10.0"
pytest-cov = ">=4.1,<8.0"
cytominer-database = "^0.3.4"
pycytominer = "^1.1.0"
dunamai = "^1.19.0"
pillow = ">=11.3,<13.0"       # added to help visualize images within examples

[tool.poetry.group.docs.dependencies]
jupyterlab = "^4.4.3"
jupyterlab-code-formatter = "^3.0.2"
black = ">=25.1,<27.0"
isort = ">=6.0.1,<9.0.0"
jupytext = "^1.17.1"
Sphinx = ">=6,<9"
myst-parser = ">=2,<5"
sphinxcontrib-mermaid = ">=0.9,<2.1"
myst-nb = "^1.2.0"
typing-extensions = "^4.14.0"

[tool.poetry.requires-plugins]
poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] }

[tool.poetry-dynamic-versioning]
enable = true
style = "pep440"
vcs = "git"

[tool.setuptools_scm]
root = "."

[tool.isort]
profile = "black"

[tool.codespell]
ignore-words = ".codespell-ignore"

[tool.pytest.ini_options]
filterwarnings = [
  "ignore::DeprecationWarning:pkg_resources",
  "ignore::DeprecationWarning:cytominer_database",
]
markers = [
  "large_data_tests: tests which involve the use of large data.",
]

[tool.jupytext]
formats = "ipynb,py:light"

[tool.vulture]
min_confidence = 80
paths = [ "cytotable" ]
sort_by_size = true
verbose = true

[tool.bandit]
exclude_dirs = [ "tests" ]
skips = [ "B608" ]