pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]

[project]
name = "scvi-tools"
version = "1.1.5"
description = "Deep probabilistic analysis of single-cell omics data."
readme = "README.md"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
    {name = "The scvi-tools development team"},
]
maintainers = [
    {name = "The scvi-tools development team", email = "martinkim@berkeley.edu"},
]
urls.Documentation = "https://scvi-tools.org"
urls.Source = "https://github.com/scverse/scvi-tools"
urls.Home-page = "https://scvi-tools.org"
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Science/Research",
  "Natural Language :: English",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: POSIX :: Linux",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "anndata",
    "docrep>=0.3.2",
    "flax",
    "jax",
    "jaxlib",
    "lightning>=2.0",
    "ml-collections>=0.1.1",
    "mudata>=0.1.2",
    "numpy<2.0",
    "numpyro>=0.12.1",
    "pandas",
    "pyro-ppl>=1.6.0",
    "optax",
    "rich>=12.0.0",
    "scikit-learn>=0.21.2",
    "scipy",
    "sparse>=0.14.0",
    "tensorboard>=2.0",
    "torch",
    "torchmetrics>=0.11.0",
    "tqdm",
    "xarray>=2023.2.0",
]


[project.optional-dependencies]
tests = ["pytest", "pytest-pretty", "coverage", "scvi-tools[optional]"]
editing = ["jupyter", "pre-commit"]
dev = ["scvi-tools[editing,tests]"]

docs = [
    "docutils>=0.8,!=0.18.*,!=0.19.*", # see https://github.com/scverse/cookiecutter-scverse/pull/205
    "sphinx>=4.1",
    "ipython",
    "sphinx-book-theme>=1.0.1",
    "sphinx_copybutton",
    "sphinx-design",
    "sphinxext-opengraph",
    "sphinx-hoverxref",
    "sphinxcontrib-bibtex>=1.0.0",
    "myst-parser",
    "myst-nb",
    "sphinx-autodoc-typehints",
]
docsbuild = ["scvi-tools[docs,optional]"]

# scvi.autotune
autotune = ["hyperopt>=0.2", "ray[tune]>=2.5.0"]
# scvi.hub.HubModel.pull_from_s3
aws = ["boto3"]
# scvi.data.cellxgene
census = ["cellxgene-census"]
# scvi.hub dependencies
hub = ["huggingface_hub"]
# scvi.model.utils.mde dependencies
pymde = ["pymde"]
# scvi.data.add_dna_sequence
regseq = ["biopython>=1.81", "genomepy"]
# read loom
loompy = ["loompy>=3.0.6"]
# scvi.criticism and read 10x
scanpy = ["scanpy>=1.6"]

optional = [
    "scvi-tools[autotune,aws,hub,loompy,pymde,regseq,scanpy]"
]
tutorials = [
    "cell2location",
    "gdown",
    "jupyter",
    "leidenalg",
    "muon",
    "plotnine",
    "pooch",
    "pynndescent",
    "igraph",
    "scikit-misc",
    "scrublet",
    "scvi-tools[optional]",
    "squidpy",
]

all = ["scvi-tools[dev,docs,tutorials]"]

[tool.hatch.build.targets.wheel]
packages = ['src/scvi']

[tool.coverage.run]
source = ["scvi"]
omit = [
    "**/test_*.py",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
markers = [
    "internet: mark tests that requires internet access",
    "optional: mark optional tests",
    "private: mark tests that are private",
]

[tool.ruff]
src = ["src"]
line-length = 99
indent-width = 4
target-version = "py39"

# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]

[tool.ruff.lint]
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 = [
    # 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",
]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I", "BLE001"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
"src/scvi/__init__.py" = ["I"]

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

[tool.jupytext]
formats = "ipynb,md"