--- a
+++ b/pyproject.toml
@@ -0,0 +1,231 @@
+[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"
+]