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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 = "pici-vitessce"
version = "0.0.1"
description = "A very interesting piece of code"
readme = "README.md"
license = { file = "LICENSE" }
maintainers = [
{ name = "Sricharan Reddy Varra", email = "[email protected]" },
]
authors = [
{ name = "Sricharan Reddy Varra" },
]
requires-python = ">=3.10"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
]
dependencies = [
"anndata",
"numpy",
"polars>=1.13.1",
"pyarrow>=18",
"pydantic>=2.9.2",
# for debug logging (referenced from the issue template)
"session-info",
"universal-pathlib>=0.2.5",
"vitessce[all]",
]
optional-dependencies.dev = [
"pre-commit",
"twine>=4.0.2",
]
optional-dependencies.doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"ipykernel",
"ipython",
"myst-nb>=1.1",
"pandas",
# Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"setuptools",
"sphinx>=4",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
"sphinx-tabs",
"sphinxcontrib-bibtex>=1",
"sphinxext-opengraph",
]
optional-dependencies.nb = [
"ipywidgets>=8.1.5",
"jupyter>=1.1.1",
"tqdm>=4.67",
]
optional-dependencies.test = [
"coverage",
"pytest",
]
# https://docs.pypi.org/project_metadata/#project-urls
urls.Documentation = "https://pici-vitessce.readthedocs.io/"
urls.Homepage = "https://github.com/angelolab/pici-vitessce"
urls.Source = "https://github.com/angelolab/pici-vitessce"
[tool.hatch.envs.default]
installer = "uv"
features = [ "dev" ]
[tool.hatch.envs.docs]
features = [ "doc" ]
scripts.build = "sphinx-build -M html docs docs/_build {args}"
scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"
[tool.hatch.envs.hatch-test]
features = [ "test" ]
[tool.ruff]
line-length = 120
src = [ "src" ]
extend-include = [ "*.ipynb" ]
format.docstring-code-format = true
lint.select = [
"B", # flake8-bugbear
"BLE", # flake8-blind-except
"C4", # flake8-comprehensions
"D", # pydocstyle
"E", # Error detected by Pycodestyle
"F", # Errors detected by Pyflakes
"I", # isort
"RUF100", # Report unused noqa directives
"TID", # flake8-tidy-imports
"UP", # pyupgrade
"W", # Warning detected by Pycodestyle
]
lint.ignore = [
"B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
"D100", # Missing docstring in public module
"D104", # Missing docstring in public package
"D105", # __magic__ methods are often self-explanatory, allow missing docstrings
"D107", # Missing docstring in __init__
# Disable one in each pair of mutually incompatible rules
"D203", # We don’t want a blank line before a class docstring
"D213", # <> We want docstrings to start immediately after the opening triple quote
"D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
"D401", # First line should be in imperative mood; try rephrasing
"E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
"E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
"E741", # allow I, O, l as variable names -> I is the identity matrix
]
lint.per-file-ignores."*/__init__.py" = [ "F401" ]
lint.per-file-ignores."docs/*" = [ "I" ]
lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "numpy"
[tool.pytest.ini_options]
testpaths = [ "tests" ]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
[tool.coverage.run]
source = [ "pici_vitessce" ]
omit = [
"**/test_*.py",
]
[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",
]
[tool.uv.sources]
vitessce = { git = "https://github.com/vitessce/vitessce-python" }