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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]
[project]
name = "squidpy"
dynamic = ["version"]
description = "Spatial Single Cell Analysis in Python"
readme = "README.rst"
requires-python = ">=3.10"
license = {file = "LICENSE"}
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"License :: OSI Approved :: BSD License",
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS :: MacOS X",
"Typing :: Typed",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Environment :: Console",
"Framework :: Jupyter",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization",
]
keywords = [
"single-cell",
"bio-informatics",
"spatial transcriptomics",
"spatial data analysis",
"image analysis",
"spatial data analysis",
]
authors = [
{name = "Giovanni Palla"},
{name = "Michal Klein"},
{name = "Hannah Spitzer"},
]
maintainers = [
{name = "Giovanni Palla", email = "[email protected]"},
{name = "Michal Klein", email = "[email protected]"},
{name = "Tim Treis", email = "[email protected]"}
]
dependencies = [
"aiohttp>=3.8.1",
"anndata>=0.9",
"cycler>=0.11.0",
"dask-image>=0.5.0",
"dask[array]>=2021.02.0",
"docrep>=0.3.1",
"fsspec>=2021.11.0",
"leidenalg>=0.8.2",
"matplotlib>=3.3",
"matplotlib-scalebar>=0.8.0",
"networkx>=2.6.0",
"numba>=0.56.4",
"numpy>=1.23.0",
"omnipath>=1.0.7",
"pandas>=2.1.0",
"Pillow>=8.0.0",
"scanpy>=1.9.3",
"scikit-image>=0.20",
# due to https://github.com/scikit-image/scikit-image/issues/6850 breaks rescale ufunc
"scikit-learn>=0.24.0",
"statsmodels>=0.12.0",
# https://github.com/scverse/squidpy/issues/526
"tifffile!=2022.4.22",
"tqdm>=4.50.2",
"validators>=0.18.2",
"xarray>=0.16.1,<2024.10.0",
"zarr>=2.6.1",
"spatialdata>=0.2.5",
]
[project.optional-dependencies]
dev = [
"pre-commit>=3.0.0",
"tox>=4.0.0",
]
test = [
"pytest>=7",
"pytest-xdist>=3",
"pytest-mock>=3.5.0",
"pytest-cov>=4",
"coverage[toml]>=7",
]
docs = [
"ipython",
"ipywidgets>=8.0.0",
"sphinx>=5.3",
"sphinx-autodoc-annotation",
"sphinx-autodoc-typehints>=1.10.3",
"sphinx_rtd_theme",
"sphinxcontrib-bibtex>=2.3.0",
"sphinxcontrib-spelling>=7.6.2",
"nbsphinx>=0.8.1",
"myst-nb>=0.17.1",
"sphinx_copybutton>=0.5.0",
]
[project.urls]
Homepage = "https://github.com/scverse/squidpy"
"Bug Tracker" = "https://github.com/scverse/squidpy/issues"
Documentation = "https://squidpy.readthedocs.io/en/stable"
"Source Code" = "https://github.com/scverse/squidpy"
[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true
[tool.setuptools_scm]
[tool.hatch.version]
source = "vcs"
[tool.hatch.metadata]
allow-direct-references = true
[tool.ruff]
line-length = 120
exclude = [
".git",
".tox",
"__pycache__",
"build",
"docs/_build",
"dist",
"setup.py"
]
[tool.ruff.format]
docstring-code-format = true
[tool.ruff.lint]
ignore = [
# line too long -> we accept long comment lines; formatter gets rid of long code lines
"E501",
# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
"E731",
# allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
"E741",
# Missing docstring in public package
"D104",
# ... imported but unused
"F401",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Do not perform function calls in argument defaults.
"B008",
# Missing docstring in magic method
"D105",
# Missing blank line before section
"D411",
# D100 Missing docstring in public module
"D100",
# D107 Missing docstring in __init__,
"D107",
# B008 Do not perform function calls in argument defaults.
"B008",
# B024 Do not use `__class__` for string comparisons.
"B024",
## Flake8 rules not supported by ruff:
# RST201 Block quote ends without a blank line; unexpected unindent.
# "RST201",
# RST301 Unexpected indentation.
# "RST301",
# RST306 Unknown target name.
# "RST306",
# RST203 Definition list ends without a blank line; unexpected unindent.
# "RST203",
# line break before a binary operator -> black does not adhere to PEP8
# "W503",
# line break occured after a binary operator -> black does not adhere to PEP8
# "W504",
# whitespace before : -> black does not adhere to PEP8
# "E203",
# whitespace before : -> black does not adhere to PEP8
# "E203",
# missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
# "E231",
# continuation line over-indented for hanging indent -> black does not adhere to PEP8
# "E126",
# inline comment should start with '#' -> Scanpy allows them for specific explanations
# "E266",
# format string does contain unindexed parameters
# "P101",
# indentation is not a multiple of 4
# "E111",
# "E114",
]
select = [
"I", # isort
"E", # pycodestyle
"F", # pyflakes
"W", # pycodestyle
# below are not autofixed
"UP", # pyupgrade
"C4", # flake8-comprehensions
"B", # flake8-bugbear
"BLE", # flake8-blind-except
]
unfixable = ["B", "C4", "BLE"]
[tool.ruff.lint.isort]
required-imports = ["from __future__ import annotations"]
[tool.ruff.lint.per-file-ignores]
"*/__init__.py" = ["D104", "F401"]
"tests/*"= ["D"]
"docs/*"= ["D","B"]
"src/squidpy/pl/_ligrec.py"= ["D","B"]
"src/squidpy/_constants/_pkg_constants.py"= ["D101","D102","D106"]
"src/squidpy/_constants/_constants.py"= ["D101"]
"src/squidpy/pl/_interactive/_widgets.py"= ["D"]
"src/squidpy/pl/_interactive/interactive.py"= ["F","E"]
".scripts/ci/download_data.py"= ["D","B"]
# "squidpy/*.py"= ["RST303"]
[tool.ruff.lint.flake8-tidy-imports]
# Disallow all relative imports.
ban-relative-imports = "all"