diff --git a/.cruft.json b/.cruft.json
index 36edd93..e2d3b27 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
   "context": {
     "cookiecutter": {
       "project_name": "infercnvpy",
@@ -12,7 +12,8 @@
       "project_repo": "https://github.com/icbi-lab/infercnvpy",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,
@@ -24,5 +25,5 @@
     }
   },
   "directory": null,
-  "checkout": "v0.3.0"
+  "checkout": "v0.4.0"
 }
diff --git a/.github/workflows/release.yaml.rej b/.github/workflows/release.yaml.rej
new file mode 100644
index 0000000..f65d3cd
--- /dev/null
+++ b/.github/workflows/release.yaml.rej
@@ -0,0 +1,10 @@
+diff a/.github/workflows/release.yaml b/.github/workflows/release.yaml	(rejected hunks)
+@@ -11,7 +11,7 @@ jobs:
+     runs-on: ubuntu-latest
+     environment:
+       name: pypi
+-      url: https://pypi.org/p/{{ cookiecutter.package_name }}
++      url: https://pypi.org/p/infercnvpy
+     permissions:
+       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+     steps:
diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej
new file mode 100644
index 0000000..e165fb8
--- /dev/null
+++ b/.github/workflows/test.yaml.rej
@@ -0,0 +1,16 @@
+diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml	(rejected hunks)
+@@ -24,11 +24,11 @@ jobs:
+       matrix:
+         include:
+           - os: ubuntu-latest
+-            python: "3.9"
++            python: "3.10"
+           - os: ubuntu-latest
+-            python: "3.11"
++            python: "3.12"
+           - os: ubuntu-latest
+-            python: "3.11"
++            python: "3.12"
+             pip-flags: "--pre"
+             name: PRE-RELEASE DEPENDENCIES
+ 
diff --git a/.gitignore b/.gitignore
index c50520b..7aab72c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/
diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej
new file mode 100644
index 0000000..5f9ac18
--- /dev/null
+++ b/.pre-commit-config.yaml.rej
@@ -0,0 +1,34 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -6,29 +6,18 @@ default_stages:
+   - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-  - repo: https://github.com/psf/black
+-    rev: "24.4.2"
+-    hooks:
+-      - id: black
+-  - repo: https://github.com/asottile/blacken-docs
+-    rev: 1.16.0
+-    hooks:
+-      - id: blacken-docs
+   - repo: https://github.com/pre-commit/mirrors-prettier
+     rev: v4.0.0-alpha.8
+     hooks:
+       - id: prettier
+-        # Newer versions of node don't work on systems that have an older version of GLIBC
+-        # (in particular Ubuntu 18.04 and Centos 7)
+-        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+-        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+-        # https://github.com/jupyterlab/jupyterlab/issues/12675
+-        language_version: "17.9.1"
+   - repo: https://github.com/astral-sh/ruff-pre-commit
+     rev: v0.4.4
+     hooks:
+       - id: ruff
++        types_or: [python, pyi, jupyter]
+         args: [--fix, --exit-non-zero-on-fix]
++      - id: ruff-format
++        types_or: [python, pyi, jupyter]
+   - repo: https://github.com/pre-commit/pre-commit-hooks
+     rev: v4.6.0
+     hooks:
diff --git a/README.md b/README.md
index 4ebb981..e34e4c1 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.9 or newer installed on your system. If you don't have
+You need to have Python 3.10 or newer installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 There are several alternative options to install infercnvpy:
diff --git a/docs/conf.py b/docs/conf.py
index 895af36..7c24ab8 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
diff --git a/docs/conf.py.rej b/docs/conf.py.rej
new file mode 100644
index 0000000..6a707c4
--- /dev/null
+++ b/docs/conf.py.rej
@@ -0,0 +1,16 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -36,10 +36,10 @@ needs_sphinx = "4.0"
+ 
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "grst",  # Username
+-    "github_repo": project_name,  # Repo name
+-    "github_version": "main",  # Version
+-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
++    "github_user": "grst",
++    "github_repo": "https://github.com/icbi-lab/infercnvpy",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+ 
+ # -- General configuration ---------------------------------------------------
diff --git a/docs/contributing.md b/docs/contributing.md
index 4794249..9bbacf1 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -51,7 +51,7 @@ and [prettier][prettier-editors].
 ## Writing tests
 
 ```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+Remember to first install the package with `pip install -e '.[dev,test]'`
 ```
 
 This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
@@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +157,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
diff --git a/pyproject.toml b/pyproject.toml
index afd54be..1c86a25 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -103,7 +103,7 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # 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",
@@ -117,7 +117,7 @@ ignore = [
     "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
+    # __magic__ methods are often self-explanatory, allow missing docstrings
     "D105",
     # first line should end with a period [Bug: doesn't work with single-line docstrings]
     "D400",
@@ -130,10 +130,10 @@ ignore = [
     "D213",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]
@@ -147,5 +147,5 @@ skip = [
     "docs/changelog.md",
     "docs/references.bib",
     "docs/references.md",
-    "docs/notebooks/example.ipynb"
+    "docs/notebooks/example.ipynb",
 ]
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..74b5700
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,53 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "infercnvpy"
+ version = "0.0.1"
+ description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. "
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Gregor Sturm"},
+@@ -21,19 +21,19 @@ urls.Home-page = "https://github.com/icbi-lab/infercnvpy"
+ dependencies = [
+     "anndata",
+     # for debug logging (referenced from the issue template)
+-    "session-info"
++    "session-info",
+ ]
+ 
+ [project.optional-dependencies]
+ dev = [
+     "pre-commit",
+-    "twine>=4.0.2"
++    "twine>=4.0.2",
+ ]
+ doc = [
+     "docutils>=0.8,!=0.18.*,!=0.19.*",
+     "sphinx>=4",
+     "sphinx-book-theme>=1.0.0",
+-    "myst-nb",
++    "myst-nb>=1.1.0",
+     "sphinxcontrib-bibtex>=1.0.0",
+     "sphinx-autodoc-typehints",
+     "sphinxext-opengraph",
+@@ -61,12 +61,15 @@ addopts = [
+     "--import-mode=importlib",  # allow using test files with same name
+ ]
+ 
+-[tool.black]
+-line-length = 120
+-
+ [tool.ruff]
+-src = ["src"]
+ 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