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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "rapids_singlecell"
description = "running single cell analysis on Nvidia GPUs"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [{name = "Severin Dicks"}]
readme = {file = "README.md", content-type="text/markdown"}
dynamic = ["version"]
dependencies = [
"anndata>=0.10.0",
"scanpy>=1.10.0",
"numpy>=1.17.0",
"scipy>=1.4",
"pandas",
"natsort",
"scikit-misc>=0.1.3",
"matplotlib>=3.4",
"tqdm",
"statsmodels>=0.12.0",
"scikit-image",
]
[project.optional-dependencies]
rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"]
rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"]
doc = [
"sphinx>=4.5.0",
"sphinx-copybutton",
"nbsphinx>=0.8.12",
"myst-nb",
"scanpydoc[typehints,theme]>=0.9.4",
"readthedocs-sphinx-ext",
"sphinx_copybutton",
"pytest",
]
test = [
"pytest",
"profimp",
"scanpy>=1.10.0",
"bbknn",
]
[project.urls]
Documentation = "https://rapids-singlecell.readthedocs.io"
Source = "https://github.com/scverse/rapids_singlecell"
[tool.ruff]
src = ["src"]
line-length = 88
lint.select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"TID251", # Banned imports
"RUF100", # Report unused noqa directives
"ICN", # Follow import conventions
"PTH", # Pathlib instead of os.path
"TCH", # manage type checking blocks
"PLR0917", # Ban APIs with too many positional parameters
]
lint.ignore = [
# line too long -> we accept long comment lines; formatting 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
"E741",
# Missing docstring in public package
"F403",
]
[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
"src/rapids_singlecell/preprocessing/_harmonypy_gpu.py" = ["PLR0917"]
"src/rapids_singlecell/decoupler_gpu/_method_mlm.py" = ["PLR0917"]
"src/rapids_singlecell/decoupler_gpu/_method_wsum.py" = ["PLR0917"]
[tool.ruff.lint.isort]
known-first-party = ["rapids_singlecell"]
required-imports = ["from __future__ import annotations"]
[tool.pytest.ini_options]
addopts = [
"--import-mode=importlib",
"--strict-markers",
]
markers = [
"gpu: tests that use a GPU (currently unused, but needs to be specified here as we import anndata.tests.helpers, which uses it)",
]
[tool.hatch.build]
# exclude big files that don’t need to be installed
exclude = [
"tests",
"docs",
"notebooks"
]
[tool.hatch.build.hooks.vcs]
version-file = "src/rapids_singlecell/_version.py"
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.targets.wheel]
packages = ['src/rapids_singlecell']
[tool.codespell]
skip = '*.ipynb,*.csv'
ignore-words-list = "nd"