diff --git a/.cruft.json b/.cruft.json
index fe3fb17..7b48ddc 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "c6e5e5008a7b2915709b7def3cdcddcf6159c301",
-  "checkout": null,
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "pyLemur",
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index c5b152b..2bfe232 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -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 0dd3121..3800434 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,6 +55,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/
diff --git a/README.md.rej b/README.md.rej
new file mode 100644
index 0000000..a626528
--- /dev/null
+++ b/README.md.rej
@@ -0,0 +1,10 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -17,7 +17,7 @@ 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 pyLemur:
diff --git a/docs/conf.py b/docs/conf.py
index 4e0d94a..9fcda33 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
@@ -38,10 +38,10 @@
 
 html_context = {
     "display_github": True,  # Integrate GitHub
-    "github_user": "const-ae",  # 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": "const-ae",
+    "github_repo": "https://github.com/const-ae/pyLemur",
+    "github_version": "main",
+    "conf_py_path": "/docs/",
 }
 
 # -- General configuration ---------------------------------------------------
diff --git a/pyproject.toml b/pyproject.toml
index d80ce4c..f481ed3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,7 @@ 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",
@@ -108,7 +108,7 @@ 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",
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..914e89b
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,10 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "pyLemur"
+ version = "0.0.1"
+ description = "A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Your Name"},