diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index afbbabcd..172fd236 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,16 +1,16 @@
 repos:
   # Hooks that are run everywhere
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.0.0-beta.5
+    rev: v2.5.0
     hooks:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.6.0
+    rev: v2.25.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.11
+    rev: v0.15.18
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/pyproject.toml b/pyproject.toml
index 13e8e696..6298610f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,8 +26,8 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
-
 dynamic = [ "version" ]
 dependencies = [
   "adjusttext",
@@ -46,7 +46,6 @@ dependencies = [
   "scipy<1.16",           # see https://github.com/statsmodels/statsmodels/issues/9584
   "session-info",
 ]
-
 optional-dependencies.dev = [
   "furo",
   "myst-nb",
@@ -67,7 +66,7 @@ optional-dependencies.docs = [
   "myst-nb>=1.1",
   "pandas",
   "scvi-tools>=1.3.1",
-  "setuptools",               # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+  "setuptools",                      # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
   "sphinx>=8",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
@@ -99,23 +98,19 @@ optional-dependencies.test = [
   "pytest-split",
   "pytest-xdist>=3",
 ]
-
 urls.Documentation = "https://cellflow.readthedocs.io/"
 urls.Home-page = "https://github.com/theislab/cellflow"
 urls.Source = "https://github.com/theislab/cellflow"
 
-[tool.hatch.build.targets.wheel]
-packages = [ 'src/cellflow' ]
-
-[tool.hatch.version]
-source = "vcs"
-fallback-version = "0.1.0"
+[tool.hatch]
+version.source = "vcs"
+version.fallback-version = "0.1.0"
+build.targets.wheel.packages = [ "src/cellflow" ]
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
 lint.select = [
   "B",      # flake8-bugbear
@@ -162,39 +157,62 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
-testpaths = [ "tests" ]
-xfail_strict = true
-addopts = [
+[tool.mypy]
+mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
+ignore_missing_imports = true
+python_version = "3.11"
+disallow_any_generics = true
+disallow_untyped_calls = false
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+strict_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_return_any = false
+warn_unreachable = false
+ignore_errors = false
+disable_error_code = [ "assignment", "comparison-overlap", "no-untyped-def", "override" ]
+strict_equality = true
+show_column_numbers = true
+error_summary = true
+plugins = "numpy.typing.mypy_plugin"
+warn_unused_configs = true
+no_implicit_optional = true
+no_implicit_reexport = true
+no_warn_no_return = true
+show_error_codes = true
+
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
-markers = [
-  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+ini_options.markers = [
   "internet: marks tests that require internet access (deselect with '-m \"not internet\"')",
+  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
 ]
+ini_options.xfail_strict = true
 
-[tool.coverage.run]
-branch = true
-source = [ "src/" ]
-concurrency = [ "multiprocessing" ]
-parallel = "true"
-
-[tool.coverage.report]
-exclude_lines = [
+[tool.coverage]
+run.branch = true
+run.concurrency = [ "multiprocessing" ]
+run.parallel = "true"
+run.source = [ "src/" ]
+report.exclude_lines = [
   '\#.*pragma:\s*no.?cover',
-  "^if __name__ == .__main__.:$",
   '^\s*raise AssertionError\b',
   '^\s*raise NotImplementedError\b',
   '^\s*return NotImplemented\b',
+  "^if __name__ == .__main__.:$",
 ]
-precision = 2
-show_missing = true
-skip_empty = true
-sort = "Miss"
+report.precision = 2
+report.show_missing = true
+report.skip_empty = true
+report.sort = "Miss"
 
 [tool.tox]
-legacy_tox_ini = """
-[tox]
+legacy_tox_ini = '''[tox]
 min_version = 4.0
 env_list = lint-code,py{3.11,3.12,3.13}
 skip_missing_interpreters = true
@@ -284,39 +302,7 @@ 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
-"""
-
-[tool.mypy]
-mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
-python_version = "3.11"
-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.cruft]
 skip = [