[build-system]

build-backend = "hatchling.build"

requires = ["hatchling"]

[project]

name = "nichecompass"

version = "0.2.3"

description = "End-to-end analysis of spatial multi-omics data"

readme = "README.md"

requires-python = ">=3.9"

license = {file = "LICENSE"}

authors = [

    {name = "Sebastian Birk"},

]

maintainers = [

    {name = "Sebastian Birk", email = "sebastian.birk@outlook.com"},

]

urls.Documentation = "https://nichecompass.readthedocs.io/"

urls.Source = "https://github.com/Lotfollahi-lab/nichecompass"

urls.Home-page = "https://github.com/Lotfollahi-lab/nichecompass"

classifiers = [

  "Development Status :: 3 - Alpha",

  "Intended Audience :: Science/Research",

  "Natural Language :: English",

  "Programming Language :: Python :: 3.9",

  "Operating System :: POSIX :: Linux",

  "Topic :: Scientific/Engineering :: Bio-Informatics",

]

dependencies = [

    "mlflow>=1.28.0",

    "pyreadr>=0.4.6",

    "scanpy>=1.9.3,<1.10.0",

    "torch-geometric>=2.2.0",

    "omnipath>=1.0.7",

    "decoupler>=1.4.0",

    "numpy<2",

]

optional-dependencies.dev = [

    "pre-commit",

    "twine>=4.0.2",

]

optional-dependencies.docs = [

    "docutils>=0.8,!=0.18.*,!=0.19.*",

    "sphinx>=4.1",

    "sphinx-book-theme>=1.0.0",

    "myst-nb",

    "myst-parser",

    "sphinxcontrib-bibtex>=1.0.0",

    "sphinx-autodoc-typehints",

    "sphinx_rtd_theme",

    "sphinxext-opengraph",

    "sphinx-copybutton",

    "sphinx-design",

    "sphinx-hoverxref",

    # For notebooks

    "ipykernel",

    "ipython",

    "pandas",

]

optional-dependencies.docsbuild = [

    "nichecompass[docs,benchmarking,multimodal]"

]  # docs build dependencies

optional-dependencies.tests = [

    "pytest",

    "coverage",

]

optional-dependencies.benchmarking = [

    "scib-metrics>=0.3.3",

    "pynndescent>=0.5.8",

    "scikit-misc>=0.3.0",

    "squidpy>=1.2.2",

    "jax==0.4.7",

    "jaxlib==0.4.7"

]

optional-dependencies.multimodal = [

    "scglue>=0.3.2",

]

optional-dependencies.tutorials = [

    "jupyter",

]

all = ["nichecompass[dev,docs,tests,benchmarking,multimodal,tutorials]"]

[tool.coverage.run]

source = ["nichecompass"]

omit = [

    "**/test_*.py",

]

[tool.pytest.ini_options]

testpaths = ["tests"]

xfail_strict = true

addopts = [

    "--import-mode=importlib",  # allow using test files with same name

]

[tool.ruff]

line-length = 120

src = ["src"]

extend-include = ["*.ipynb"]

[tool.ruff.format]

docstring-code-format = true

[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 = [

    # 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

    "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"]

"tests/*" = ["D"]

"*/__init__.py" = ["F401"]

[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",

]