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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
name = "visionpy-sc"
version = "0.2.0"
description = "Signature Analysis and Visualization for Single-Cell RNA-seq"
readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
authors = [
{name = "Adam Gayoso"},
]
maintainers = [
{name = "Adam Gayoso", email = "[email protected]"},
]
urls.Documentation = "https://visionpy.readthedocs.io/"
urls.Source = "https://github.com/yoseflab/visionpy"
urls.Home-page = "https://github.com/yoseflab/visionpy"
dependencies = [
"anndata",
"scanpy>=1.9",
"click",
"flask",
"flask-compress",
"leidenalg",
"rich",
]
[project.optional-dependencies]
dev = [
# CLI for bumping the version number
"bump2version",
"pre-commit"
]
doc = [
"sphinx",
"sphinx-book-theme>=1.0",
"myst-nb",
"sphinxcontrib-bibtex>=1.0.0",
"scanpydoc[typehints]>=0.7.4",
# For notebooks
"ipython",
"ipykernel",
"sphinx-copybutton",
]
test = [
"pytest",
"pytest-cov",
# For vscode Python extension testing
"flake8",
"black",
]
[project.scripts]
visionpy = "visionpy.api:_start_vision_cli"
[tool.hatch.build.targets.wheel]
packages = ['src/visionpy']
[tool.coverage.run]
source = ["visionpy"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
[tool.ruff]
src = ["src"]
line-length = 119
target-version = "py38"
select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"RUF100", # Report unused noqa directives
]
ignore = [
# line too long -> we accept long comment lines; black 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
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __magic__ methods are are often self-explanatory, allow missing docstrings
"D105",
# first line should end with a period [Bug: doesn't work with single-line docstrings]
"D400",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
# Missing argument description in the docstring TODO: enable
"D417",
]
[tool.ruff.per-file-ignores]
"docs/*" = ["I", "BLE001"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
[tool.black]
line-length = 120
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''
[tool.jupytext]
formats = "ipynb,md"
[tool.cruft]
skip = [
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb"
]