--- a
+++ b/pyproject.toml
@@ -0,0 +1,363 @@
+[build-system]
+requires = ["setuptools>=61", "setuptools-scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "moscot"
+dynamic = ["version"]
+description = "Multi-omic single-cell optimal transport tools"
+readme = "README.rst"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Typing :: Typed",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Mathematics"
+]
+keywords = [
+    "single-cell",
+    "bio-informatics",
+    "optimal transport"
+]
+authors = [
+    {name = "Dominik Klein"},
+    {name = "Giovanni Palla"},
+    {name = "Michal Klein"},
+    {name = "Zoe Piran"},
+    {name = "Marius Lange"},
+]
+maintainers = [
+    {name = "Dominik Klein", email = "dominik.klein@helmholtz-muenchen.de"},
+    {name = "Giovanni Palla", email = "giovanni.palla@helmholtz-muenchen.de"},
+    {name = "Michal Klein", email = "michal.klein@helmholtz-muenchen.de"}
+]
+
+
+dependencies = [
+    "numpy>=1.20.0",
+    "scipy>=1.7.0",
+    "pandas>=2.0.1",
+    "networkx>=3.2",
+    # https://github.com/scverse/scanpy/issues/2411
+    "matplotlib>=3.5.0",
+    "anndata>=0.9.1",
+    "scanpy>=1.9.3",
+    "wrapt>=1.13.2",
+    "docrep>=0.3.2",
+    "ott-jax>=0.5.0",
+    "cloudpickle>=2.2.0",
+    "rich>=13.5",
+    "docstring_inheritance>=2.0.0",
+    "mudata>=0.2.2"
+]
+
+[project.optional-dependencies]
+spatial = [
+    "squidpy>=1.2.3"
+]
+
+neural = [
+    "optax",
+    "flax",
+    "diffrax",
+    "ott-jax[neural]>=0.5.0",
+
+]
+dev = [
+    "pre-commit>=3.0.0",
+    "tox>=4",
+]
+test = [
+    "pytest>=7",
+    "pytest-xdist>=3",
+    "pytest-mock>=3.5.0",
+    "pytest-cov>=4",
+    "coverage[toml]>=7",
+    "moscot[neural]"
+]
+docs = [
+    "sphinx>=5.1.1",
+    "sphinx_copybutton>=0.5.0",
+    "sphinxcontrib-bibtex>=2.3.0",
+    "sphinxcontrib-spelling>=7.6.2",
+    "sphinx-autodoc-typehints",
+    "furo>=2022.09.29",
+    "sphinx-tippy>=0.4.1",
+    "myst-nb>=0.17.1",
+    "ipython>=7.20.0",
+    "sphinx_design>=0.3.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/theislab/moscot"
+Download = "https://moscot.readthedocs.io/en/latest/installation.html"
+"Bug Tracker" = "https://github.com/theislab/moscot/issues"
+Documentation = "https://moscot.readthedocs.io"
+"Source Code" = "https://github.com/theislab/moscot"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.setuptools_scm]
+
+[tool.ruff]
+exclude = [
+    ".git",
+    "__pycache__",
+    "build",
+    "docs/_build",
+    "dist"
+]
+ignore = [
+    # 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, i, j, k, l is reasonable indexing notation
+    "E741",
+    # Missing docstring in public package
+    "D104",
+    # Missing docstring in public module
+    "D100",
+    # Missing docstring in __init__
+    "D107",
+    # Missing docstring in magic method
+    "D105",
+    # Use `X | Y` for type annotations
+    "UP007",
+]
+line-length = 120
+select = [
+    "D", # flake8-docstrings
+    # TODO(michalk8): enable this in https://github.com/theislab/moscot/issues/483
+    # "I", # isort
+    "E", # pycodestyle
+    "F", # pyflakes
+    "W", # pycodestyle
+    "Q", # flake8-quotes
+    "SIM", # flake8-simplify
+    "NPY",  # NumPy-specific rules
+    "PT",  # flake8-pytest-style
+    "TID",  # flake8-tidy-imports
+    "B", # flake8-bugbear
+    "UP", # pyupgrade
+    "C4", # flake8-comprehensions
+    "BLE", # flake8-blind-except
+    "T20",  # flake8-print
+    "RET", # flake8-raise
+]
+unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
+target-version = "py38"
+[tool.ruff.per-file-ignores]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
+"docs/*" = ["D"]
+"src/moscot/constants.py" = ["D101"]
+"src/moscot/utils/subset_policy.py" = ["D101", "D102"]
+[tool.ruff.pydocstyle]
+convention = "numpy"
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
+[tool.ruff.flake8-quotes]
+inline-quotes = "double"
+
+[tool.black]
+line-length = 120
+target-version = ['py38']
+include = '\.pyi?$'
+
+[tool.isort]
+profile = "black"
+include_trailing_comma = true
+multi_line_output = 3
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "GENERIC", "NUMERIC", "PLOTTING", "BIO", "FIRSTPARTY", "LOCALFOLDER"]
+# also contains what we import in notebooks
+known_generic = ["wrapt", "joblib"]
+known_numeric = ["numpy", "scipy", "jax", "ott", "pandas", "sklearn", "networkx", "statsmodels"]
+known_bio = ["anndata", "scanpy", "squidpy"]
+known_plotting = ["IPython", "matplotlib", "mpl_toolkits", "seaborn"]
+
+[tool.pytest.ini_options]
+markers = ["fast: marks tests as fask"]
+xfail_strict = true
+filterwarnings = [
+    "ignore:No data for colormapping:UserWarning",
+    "ignore:The dtype argument will be deprecated in anndata:PendingDeprecationWarning"
+]
+
+[tool.coverage.run]
+branch = true
+parallel = true
+source = ["src/"]
+omit = [
+    "*/__init__.py",
+    "*/_version.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    '\#.*pragma:\s*no.?cover',
+    "^if __name__ == .__main__.:$",
+    '^\s*raise AssertionError\b',
+    '^\s*raise NotImplementedError\b',
+    '^\s*return NotImplemented\b',
+]
+precision = 2
+show_missing = true
+skip_empty = true
+sort = "Miss"
+
+[tool.rstcheck]
+ignore_directives = [
+    "toctree",
+    "currentmodule",
+    "autosummary",
+    "module",
+    "automodule",
+    "autoclass",
+    "bibliography",
+    "glossary",
+    "card",
+    "grid",
+]
+ignore_roles = [
+    "mod",
+]
+
+[tool.mypy]
+mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
+python_version = "3.10"
+plugins = "numpy.typing.mypy_plugin"
+
+ignore_errors = false
+
+warn_redundant_casts = true
+warn_unused_configs = true
+warn_unused_ignores = true
+
+disallow_untyped_calls = false
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+disallow_any_generics = true
+
+strict_optional = true
+strict_equality = true
+warn_return_any = false
+warn_unreachable = false
+check_untyped_defs = true
+no_implicit_optional = true
+no_implicit_reexport = true
+no_warn_no_return = true
+
+show_error_codes = true
+show_column_numbers = true
+error_summary = true
+ignore_missing_imports = true
+
+disable_error_code = ["assignment", "comparison-overlap", "no-untyped-def", "override"]
+
+[tool.doc8]
+max_line_length = 120
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+min_version = 4.0
+env_list = lint-code,py{3.10,3.11,3.12}
+skip_missing_interpreters = true
+
+[testenv]
+extras = test,neural
+commands =
+    python -m pytest {tty:--color=yes} {posargs: \
+        --cov={env_site_packages_dir}{/}moscot --cov-config={tox_root}{/}pyproject.toml \
+        --no-cov-on-fail --cov-report=xml --cov-report=term-missing:skip-covered}
+passenv = PYTEST_*,CI
+
+[testenv:lint-code]
+description = Lint the code.
+deps = pre-commit>=3.0.0
+skip_install = true
+commands =
+    pre-commit run --all-files --show-diff-on-failure
+
+[testenv:lint-docs]
+description = Lint the documentation.
+extras = docs,neural
+ignore_errors = true
+allowlist_externals = make
+pass_env = PYENCHANT_LIBRARY_PATH
+set_env = SPHINXOPTS = -W -q --keep-going
+changedir = {tox_root}{/}docs
+commands =
+    make linkcheck {posargs}
+    # TODO(michalk8): uncomment after https://github.com/theislab/moscot/issues/490
+    # make spelling {posargs}
+
+[testenv:examples-docs]
+allowlist_externals = bash
+description = Run the notebooks.
+use_develop = true
+deps =
+    ipykernel
+    jupytext
+    nbconvert
+    leidenalg
+extras = docs,neural
+changedir = {tox_root}{/}docs
+commands =
+    python -m ipykernel install --user --name=moscot
+    bash {tox_root}/.run_notebooks.sh {tox_root}{/}docs/notebooks
+
+[testenv:clean-docs]
+description = Remove the documentation.
+deps =
+skip_install = true
+changedir = {tox_root}{/}docs
+allowlist_externals = make
+commands =
+    make clean
+
+[testenv:build-docs]
+description = Build the documentation.
+deps =
+extras = docs,neural
+allowlist_externals = make
+changedir = {tox_root}{/}docs
+commands =
+    make html {posargs}
+commands_post =
+    python -c 'import pathlib; print("Documentation is under:", pathlib.Path("{tox_root}") / "docs" / "_build" / "html" / "index.html")'
+
+[testenv:build-package]
+description = Build the package.
+deps =
+    build
+    twine
+allowlist_externals = rm
+commands =
+    rm -rf {tox_root}{/}dist
+    python -m build --sdist --wheel --outdir {tox_root}{/}dist{/} {posargs:}
+    python -m twine check {tox_root}{/}dist{/}*
+commands_post =
+    python -c 'import pathlib; print(f"Package is under:", pathlib.Path("{tox_root}") / "dist")'
+
+[testenv:format-references]
+description = Format references.bib.
+deps =
+skip_install = true
+allowlist_externals = biber
+commands = biber --tool --output_file={tox_root}{/}docs{/}references.bib --nolog \
+    --output_align --output_indent=2 --output_fieldcase=lower \
+    --output_legacy_dates --output-field-replace=journaltitle:journal,thesis:phdthesis,institution:school \
+    {tox_root}{/}docs{/}references.bib
+"""