[build-system]

build-backend = "hatchling.build"

requires = ["hatchling"]

[project]

name = "ehrapy"

version = "0.12.0"

description = "Electronic Health Record Analysis with Python."

readme = "README.md"

requires-python = ">=3.10,<3.14"

license = {file = "LICENSE"}

authors = [

    {name = "Lukas Heumos"},

    {name = "Philipp Ehmele"},

    {name = "Eljas Roellin"},

    {name = "Lilly May"},

    {name = "Tim Treis"},

    {name = "Altana Namsaraeva"},

    {name = "Vladimir Shitov"},

    {name = "Luke Zappia"},

    {name = "Xinyue Zhang"},

]

maintainers = [

    {name = "Lukas Heumos", email = "lukas.heumos@posteo.net"},

]

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

urls.Source = "https://github.com/theislab/ehrapy"

urls.Home-page = "https://github.com/theislab/ehrapy"

classifiers = [

    "License :: OSI Approved :: Apache Software License",

    "Development Status :: 4 - Beta",

    "Environment :: Console",

    "Framework :: Jupyter",

    "Intended Audience :: Developers",

    "Intended Audience :: Science/Research",

    "Natural Language :: English",

    "Operating System :: MacOS :: MacOS X",

    "Operating System :: POSIX :: Linux",

    "Programming Language :: Python :: 3",

    "Programming Language :: Python :: 3.10",

    "Programming Language :: Python :: 3.11",

    "Programming Language :: Python :: 3.12",

    "Programming Language :: Python :: 3.13",

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

    "Topic :: Scientific/Engineering :: Visualization",

]

dependencies = [

    "session-info2",

    "lamin_utils",

    "rich",

    "scanpy",

    "requests",

    "miceforest",

    "scikit-misc",  # required for seuratv3 highly variable features

    "lifelines>=0.30.0",

    "missingno",

    "thefuzz[speedup]",

    "dowhy",

    "fhiry",

    "pyampute",

    "tableone",

    "imbalanced-learn",

    "fknni>=1.2.0",

    "python-dateutil",

    "filelock",

    "numpy>=2.0.0",

    "numba>=0.60.0",

    "igraph"

]

[project.optional-dependencies]

medcat = [

    "medcat",

]

dask = [

    "anndata[dask]",

    "dask-ml>=2025.1.0",

]

dev = [

    "pre-commit",

]

docs = [

    "docutils",

    "sphinx",

    "furo",

    "myst-nb",

    "myst-parser",

    "sphinxcontrib-bibtex",

    "sphinx-gallery",

    "sphinx-autodoc-typehints",

    "sphinx-copybutton",

    "sphinx-remove-toctrees",

    "sphinx-design",

    "sphinx-last-updated-by-git",

    "sphinx-automodapi",

    "sphinxext-opengraph",

    "pygments",

    "nbsphinx",

    "nbsphinx-link",

    "ipykernel",

    "ipython",

    "ehrapy[dask]",

]

test = [

    "ehrapy[dask]",

    "pytest",

    "pytest-cov",

    "pytest-mock"

]

[tool.hatch.version]

source = "vcs"

[tool.coverage.run]

source_pkgs = ["ehrapy"]

omit = [

    "**/test_*.py",

    "ehrapy/data/_datasets.py",  # Difficult to test

]

[tool.pytest.ini_options]

testpaths = "tests"

xfail_strict = true

addopts = [

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

]

markers = [

    "conda: marks a subset of tests to be ran on the Bioconda CI.",

    "extra: marks tests that require extra dependencies."

]

filterwarnings = [

    "ignore::DeprecationWarning",

    "ignore::anndata.OldFormatWarning:",

    "ignore:X converted to numpy array with dtype object:UserWarning",

    "ignore:`flavor='seurat_v3'` expects raw count data, but non-integers were found:UserWarning",

    "ignore:All-NaN slice encountered:RuntimeWarning",

    "ignore:Observation names are not unique. To make them unique, call `.obs_names_make_unique`.:UserWarning",

    "ignore:Trying to modify attribute `.var` of view, initializing view as actual.:anndata.ImplicitModificationWarning",

    "ignore:Transforming to str index.:anndata.ImplicitModificationWarning:"

]

minversion = 6.0

norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__']

[tool.ruff]

line-length = 120

[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

    "TCH",  # Typing imports

    "NPY",  # Numpy specific rules

    "PTH"  # Use pathlib

]

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",

    # Imports unused

    "F401",

    # camcelcase imported as lowercase

    "N813",

    # module import not at top level of file

    "E402",

]

[tool.ruff.lint.pydocstyle]

convention = "google"

[tool.ruff.lint.per-file-ignores]

"docs/*" = ["I"]

"tests/*" = ["D"]

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

[tool.mypy]

strict = false

pretty = true

show_column_numbers = true

show_error_codes = true

show_error_context = true

ignore_missing_imports = true

no_strict_optional = true

[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"

]